diff options
| author |   Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
|---|---|---|
| committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
| commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
| tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-chemistry | |
| download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip | |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-chemistry')
814 files changed, 39094 insertions, 0 deletions
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild new file mode 100644 index 000000000000..ef7987d5d03e --- /dev/null +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +if [[ $PV = *9999* ]]; then + scm_eclass=git-2 + EGIT_REPO_URI=" + git://github.com/orbeckst/${PN}.git + https://github.com/orbeckst/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + scm_eclass=vcs-snapshot + SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +inherit eutils distutils-r1 ${scm_eclass} + +DESCRIPTION="Python framework for Gromacs" +HOMEPAGE="http://orbeckst.github.com/GromacsWrapper/" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="" + +DEPEND=" + >=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}] + >=dev-python/RecSQL-0.3[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + " +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/0001-Drop-chmod-hack.patch" +) diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild new file mode 100644 index 000000000000..6d95361ce0f4 --- /dev/null +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +if [[ $PV = *9999* ]]; then + scm_eclass=git-2 + EGIT_REPO_URI=" + git://github.com/orbeckst/${PN}.git + https://github.com/orbeckst/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + scm_eclass=vcs-snapshot + SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +inherit eutils distutils-r1 ${scm_eclass} + +DESCRIPTION="Python framework for Gromacs" +HOMEPAGE="http://orbeckst.github.com/GromacsWrapper/" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="" + +DEPEND=" + >=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}] + >=dev-python/RecSQL-0.3[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + " +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/0001-Drop-chmod-hack.patch" +) diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest new file mode 100644 index 000000000000..4c77ff3c1ead --- /dev/null +++ b/sci-chemistry/GromacsWrapper/Manifest @@ -0,0 +1,2 @@ +DIST GromacsWrapper-0.3.1.tar.gz 1575486 SHA256 ddd2668060668528878370961a9a33257cf3643fd0d9e9191b1d26d4f78e803b SHA512 655dae431bf575963af58a5f75abe6703fe1ecdddba5839b671d9237ddee0e33ab19b528e89bcba4db9063fe30622d44e8f47c7b6452b4d1eed8c7400873a012 WHIRLPOOL 3b848aff931190eabd49426d61186a3c1eef9779a9fabf95b4d21d47793e5543adbcba5ac2b39c8a9af7c2479930a8ea65bb336e2155dfca98378df56ba4cb3e +DIST GromacsWrapper-0.3.2.tar.gz 1592147 SHA256 2fe0173275ca125a4260aa05f82746338f237766fe8aa998e85a5b40cf83e42c SHA512 a9e0abb5e7ad0c6831e23b6a8c09c6e4cc74b33d66cd17df8e00b876dc275dda11c3d3723565d8d58c45bdf6b2b00323bf85e24e2d5324a8d8b597cc3e5d78a4 WHIRLPOOL 852d73d01e1060369521ec5ff5197c86daa30ae98f285fe5e3d392a315cff10c68e2ba54ec9a2659260cf6830cf17cb1e094eecbd63652e9c3f13fff8707a824 diff --git a/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch b/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch new file mode 100644 index 000000000000..8645df77b86e --- /dev/null +++ b/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch @@ -0,0 +1,28 @@ +From 49b8d9662365e0e9b0725682b8a8479de402b272 Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov <alexxy@gentoo.org> +Date: Sat, 23 Mar 2013 16:40:04 +0400 +Subject: [PATCH] Drop chmod hack. + +It doesnt work if wrapper installed system-wide + +Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> +--- + gromacs/config.py | 2 -- + 1 file changed, 2 deletions(-) + +diff --git a/gromacs/config.py b/gromacs/config.py +index cece6fc..2e686e7 100644 +--- a/gromacs/config.py ++++ b/gromacs/config.py +@@ -619,8 +619,6 @@ del g + # Must extract because it is part of a zipped python egg; + # see http://peak.telecommunity.com/DevCenter/PythonEggs#accessing-package-resources + GridMAT_MD = resource_filename(__name__,'external/GridMAT-MD_v1.0.2/GridMAT-MD.pl') +-os.chmod(GridMAT_MD, 0755) +- + + #: 3rd party bundled analysis scripts and tools; this is a list of triplets of + #: +-- +1.8.1.5 + diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml new file mode 100644 index 000000000000..43390c98619e --- /dev/null +++ b/sci-chemistry/GromacsWrapper/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <upstream> + <remote-id type="github">orbeckst/GromacsWrapper</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/PyMca/Manifest b/sci-chemistry/PyMca/Manifest new file mode 100644 index 000000000000..c6899e234b21 --- /dev/null +++ b/sci-chemistry/PyMca/Manifest @@ -0,0 +1 @@ +DIST pymca4.6.2-src.tgz 15979581 SHA256 c50d3a54cad633bac3ec361d1b3b63a78292f1ad4ed976e5206665edd76bc32d SHA512 e33188b446c399e50cf65ebca4bfeef34e1b7d99c331f670dc41ca204284fbba996a1c83bd12a2410a9972927aa9c92b42b5374c58c924b3a8583d4f37be6528 WHIRLPOOL 47f0491aa0e470661bea1aa247d1db730f1db7266f1d2be2272d08f203faa2a084bcb40d579861365ace26d2f94abe03485183eed03139ad7b697cf57bfa5324 diff --git a/sci-chemistry/PyMca/PyMca-4.6.2-r1.ebuild b/sci-chemistry/PyMca/PyMca-4.6.2-r1.ebuild new file mode 100644 index 000000000000..449f9b5ab220 --- /dev/null +++ b/sci-chemistry/PyMca/PyMca-4.6.2-r1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +MY_PV="${PV/_}" + +DESCRIPTION="X-ray Fluorescence Toolkit" +HOMEPAGE="http://pymca.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/pymca/pymca/${PN}${PV/_p1}/pymca${MY_PV}-src.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="X hdf5 matplotlib" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + virtual/opengl + X? ( + dev-python/PyQt4[${PYTHON_USEDEP}] + dev-python/pyqwt[${PYTHON_USEDEP}] + ) + hdf5? ( dev-python/h5py[${PYTHON_USEDEP}] ) + matplotlib? ( dev-python/matplotlib[${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +#S="${WORKDIR}/${PN}${MY_PV}" + +python_prepare_all() { + local PATCHES=( "${FILESDIR}"/${P}-gentoo.patch ) + export SPECFILE_USE_GNU_SOURCE=1 + distutils-r1_python_prepare_all +} diff --git a/sci-chemistry/PyMca/PyMca-4.6.2.ebuild b/sci-chemistry/PyMca/PyMca-4.6.2.ebuild new file mode 100644 index 000000000000..b1e6d2f50524 --- /dev/null +++ b/sci-chemistry/PyMca/PyMca-4.6.2.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_DEPEND="2" +SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.* *-pypy-*" + +inherit distutils eutils + +MY_PV="${PV/_}" + +DESCRIPTION="X-ray Fluorescence Toolkit" +HOMEPAGE="http://pymca.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/pymca/pymca/${PN}${PV/_p1}/pymca${MY_PV}-src.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="X hdf5 matplotlib" + +DEPEND=" + dev-python/numpy + dev-python/sip + virtual/opengl + dev-python/pyopengl + X? ( + dev-python/PyQt4 + dev-python/pyqwt + ) + hdf5? ( dev-python/h5py ) + matplotlib? ( dev-python/matplotlib )" +RDEPEND="${DEPEND}" + +#S="${WORKDIR}/${PN}${MY_PV}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gentoo.patch + export SPECFILE_USE_GNU_SOURCE=1 + distutils_src_prepare +} diff --git a/sci-chemistry/PyMca/files/4.4.1_p1-gentoo.patch b/sci-chemistry/PyMca/files/4.4.1_p1-gentoo.patch new file mode 100644 index 000000000000..487a45963d21 --- /dev/null +++ b/sci-chemistry/PyMca/files/4.4.1_p1-gentoo.patch @@ -0,0 +1,40 @@ +diff --git a/setup.py b/setup.py +index 0b0fa58..a4fdab6 100755 +--- a/setup.py ++++ b/setup.py +@@ -41,34 +41,8 @@ for line in file(os.path.join('PyMca', 'PyMcaMain.py')).readlines(): + print "PyMca X-Ray Fluorescence Toolkit %s" % __version__ + print + +-print "Type 'L' to view the license." +-print "Type 'yes' to accept the terms of the license." +-print "Type 'no' to decline the terms of the license." +-print +- +-while 1: +- try: +- resp = raw_input("Do you accept the terms of the license? ") +- except KeyboardInterrupt: +- raise SystemExit +- except: +- resp = "" +- +- resp = string.lower(string.strip(resp)) +- +- if resp == "yes": +- break +- +- if resp == "no": +- sys.exit(1) +- +- if resp == "l": +- os.system("more LICENSE.GPL") +- +- + # Specify all the required PyMca data +-data_files = [('PyMca', ['LICENSE.GPL', +- 'PyMca/Scofield1973.dict', ++data_files = [('PyMca', ['PyMca/Scofield1973.dict', + 'PyMca/changelog.txt', + 'PyMca/McaTheory.cfg', + 'PyMca/PyMcaSplashImage.png', diff --git a/sci-chemistry/PyMca/files/4.4.1_p1-impl-dec.patch b/sci-chemistry/PyMca/files/4.4.1_p1-impl-dec.patch new file mode 100644 index 000000000000..ea37348066d2 --- /dev/null +++ b/sci-chemistry/PyMca/files/4.4.1_p1-impl-dec.patch @@ -0,0 +1,12 @@ +diff --git a/PyMca/specfile/src/sfwrite.c b/PyMca/specfile/src/sfwrite.c +index 24df907..93c18e9 100755 +--- a/PyMca/specfile/src/sfwrite.c ++++ b/PyMca/specfile/src/sfwrite.c +@@ -55,6 +55,7 @@ + */ + #include <SpecFile.h> + #include <SpecFileP.h> ++#include <unistd.h> + + /* + * Declarations diff --git a/sci-chemistry/PyMca/files/PyMca-4.6.2-gentoo.patch b/sci-chemistry/PyMca/files/PyMca-4.6.2-gentoo.patch new file mode 100644 index 000000000000..81dfaf038fa6 --- /dev/null +++ b/sci-chemistry/PyMca/files/PyMca-4.6.2-gentoo.patch @@ -0,0 +1,16 @@ + setup.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/setup.py b/setup.py +index 0a77cdf..e7ba643 100644 +--- a/setup.py ++++ b/setup.py +@@ -55,7 +55,7 @@ packages = ['PyMca','PyMca.PyMcaPlugins', 'PyMca.tests'] + py_modules = [] + + # Specify all the required PyMca data +-data_files = [(PYMCA_DATA_DIR, ['LICENSE.GPL', ++data_files = [(PYMCA_DATA_DIR, [ + 'PyMca/PyMcaData/Scofield1973.dict', + 'changelog.txt', + 'PyMca/PyMcaData/McaTheory.cfg', diff --git a/sci-chemistry/PyMca/metadata.xml b/sci-chemistry/PyMca/metadata.xml new file mode 100644 index 000000000000..91146f1d585b --- /dev/null +++ b/sci-chemistry/PyMca/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +The PyMca Toolkit is a collection of Python tools for visualization and +analysis of energy-dispersive X-ray fluorescence data. It builds its graphic +interface and plotting routines on top of the C++ libraries Qt and Qwt +through their respective Python bindings PyQt and PyQwt. Nevertheless, +the data analysis routines can be used independently of any graphical +interface. +</longdescription> + <use> + <flag name="matplotlib">Support for plotting through matplotlib</flag> + </use> + <upstream> + <remote-id type="sourceforge">pymca</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/acpype/Manifest b/sci-chemistry/acpype/Manifest new file mode 100644 index 000000000000..e1cd9723b479 --- /dev/null +++ b/sci-chemistry/acpype/Manifest @@ -0,0 +1,3 @@ +DIST acpype-366.tar.xz 539408 SHA256 f0c77abea0a5680ecbbecadc1a95c8f851159b7c84d079f6f527336d447e1e9d +DIST acpype-374.tar.xz 521076 SHA256 60a15d1c29ba3254a17c0792ae859444641e7a9375bd24cdd8baccc27920fde3 SHA512 99915299b32878e2139f67503260b491e05f8a592c37c5668e5aea3414822965827a91e09578264cfb48684decbadfb60c833706b756ff277ffde8b15159391e WHIRLPOOL b4e59eec36438eb2ee6d05183a6f08200213923ff50fbff1377cd976c8e39cc24429eb727d890028af2b5b5ad90428c70a10821ae20b50f7fc494ff9163322a8 +DIST acpype-389.tar.xz 524460 SHA256 4fd4036308cd81a480beaa56ae65b43a8c5ee3bbfc64b07b4d0b6649602f529a SHA512 0fbcb83ae8306d6bcc1cfd921d70c67a15e14c443453ab8c4cfd7082c15b95599801abbe31a46313674aa4841c5cd5499b69cc080221acc2793dc808df247987 WHIRLPOOL 21c8ee51c651c7a519716c818b0febd5fd62384aeeb6a5ce0f8dcf877181edba75fdd15be0d5a158b5a22d051765fb231c7c10038b8da1bcd98bede848057e95 diff --git a/sci-chemistry/acpype/acpype-366.ebuild b/sci-chemistry/acpype/acpype-366.ebuild new file mode 100644 index 000000000000..01a804da9cba --- /dev/null +++ b/sci-chemistry/acpype/acpype-366.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +inherit eutils python +PYTHON_DEPEND="2:2.5" + +DESCRIPTION="AnteChamber PYthon Parser interfacE" +HOMEPAGE="http://code.google.com/p/acpype/" +SRC_URI="mirror://gentoo/${P}.tar.xz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="" + +DEPEND="sci-chemistry/ambertools" +RDEPEND="${DEPEND}" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + epatch "${FILESDIR}/${PN}.patch" + python_convert_shebangs -r 2 . +} + +src_install() { + newbin ${PN}.py ${PN} + newbin CcpnToAcpype.py CcpnToAcpype + dodoc NOTE.txt README.txt + insinto /usr/share/${PN} + doins -r ffamber_additions test +} diff --git a/sci-chemistry/acpype/acpype-374.ebuild b/sci-chemistry/acpype/acpype-374.ebuild new file mode 100644 index 000000000000..56036152102c --- /dev/null +++ b/sci-chemistry/acpype/acpype-374.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +PYTHON_DEPEND="2:2.5" + +inherit python + +DESCRIPTION="AnteChamber PYthon Parser interfacE" +HOMEPAGE="http://code.google.com/p/acpype/" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="" + +DEPEND="sci-chemistry/ambertools" +RDEPEND="${DEPEND}" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + python_convert_shebangs -r 2 . +} + +src_install() { + newbin ${PN}.py ${PN} + newbin CcpnToAcpype.py CcpnToAcpype + dodoc NOTE.txt README.txt + insinto /usr/share/${PN} + doins -r ffamber_additions test +} diff --git a/sci-chemistry/acpype/acpype-389.ebuild b/sci-chemistry/acpype/acpype-389.ebuild new file mode 100644 index 000000000000..6ff35e1fcc47 --- /dev/null +++ b/sci-chemistry/acpype/acpype-389.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +DESCRIPTION="AnteChamber PYthon Parser interfacE" +HOMEPAGE="http://code.google.com/p/acpype/" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND=" + ${PYTHON_DEPS} + sci-chemistry/ambertools" +RDEPEND="${DEPEND}" + +src_prepare() { + sed \ + -e '1s:^:#!/usr/bin/python\n\n:g' \ + -i CcpnToAcpype.py || die +} + +src_install() { + python_parallel_foreach_impl python_newscript ${PN}.py ${PN} + python_parallel_foreach_impl python_newscript CcpnToAcpype.py CcpnToAcpype + dodoc NOTE.txt README.txt + insinto /usr/share/${PN} + doins -r ffamber_additions test +} diff --git a/sci-chemistry/acpype/files/acpype.patch b/sci-chemistry/acpype/files/acpype.patch new file mode 100644 index 000000000000..9354527cc8a9 --- /dev/null +++ b/sci-chemistry/acpype/files/acpype.patch @@ -0,0 +1,37 @@ +Index: acpype.py +=================================================================== +--- acpype.py (revision 366) ++++ acpype.py (working copy) +@@ -3020,32 +3020,6 @@ + acMol2FileName = '%s_%s_%s.mol2' % (base, chargeType, atomType) + self.acMol2FileName = acMol2FileName + self.charmmBase = '%s_CHARMM' % base +- # check for which version of antechamber +- if 'amber10' in self.acExe: +- if qprog == 'sqm': +- self.printWarn("SQM is not implemented in AmberTools 1.2") +- self.printWarn("Setting mopac for antechamber") +- qprog = 'mopac' +- elif qprog == 'divcon': +- if not os.path.exists(os.path.join(os.path.dirname(self.acExe), qprog)): +- self.printWarn("DIVCON is not installed") +- self.printWarn("Setting mopac for antechamber") +- qprog = 'mopac' +- elif 'amber11' in self.acExe: +- if qprog == 'divcon': +- self.printWarn("DIVCON is not implemented in AmberTools 1.3 anymore") +- self.printWarn("Setting sqm for antechamber") +- qprog = 'sqm' +- elif qprog == 'mopac': +- if not os.path.exists(os.path.join(os.path.dirname(self.acExe), qprog)): +- self.printWarn("MOPAC is not installed") +- self.printWarn("Setting sqm for antechamber") +- return None +- qprog = 'sqm' +- else: +- self.printWarn("Old version of antechamber. Strongly consider upgrading to AmberTools") +- self.printWarn("Setting mopac for antechamber") +- qprog = 'mopac' + self.qFlag = qDict[qprog] + self.outTopols = [outTopol] + if outTopol == 'all': diff --git a/sci-chemistry/acpype/metadata.xml b/sci-chemistry/acpype/metadata.xml new file mode 100644 index 000000000000..13ef0bf5a17c --- /dev/null +++ b/sci-chemistry/acpype/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest new file mode 100644 index 000000000000..747dbffa95d4 --- /dev/null +++ b/sci-chemistry/ambertools/Manifest @@ -0,0 +1,2 @@ +DIST AmberTools-1.5.tar.bz2 121062582 SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c +DIST ambertools-1.5-bugfix_1-10.patch.xz 31708 SHA256 5773aaa8a2478ad478f0f3afafaa39669002c31ebe755c0d12ff277ce9ab8352 diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild new file mode 100644 index 000000000000..47adf6201db7 --- /dev/null +++ b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild @@ -0,0 +1,144 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 multilib toolchain-funcs + +DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" +HOMEPAGE="http://ambermd.org/#AmberTools" +SRC_URI=" + AmberTools-${PV}.tar.bz2 + mirror://gentoo/${P}-bugfix_1-10.patch.xz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="mpi openmp static-libs X" + +RESTRICT="fetch" + +RDEPEND=" + virtual/cblas + virtual/lapack + sci-libs/clapack + sci-libs/arpack + sci-libs/cifparse-obj + sci-chemistry/mopac7 + sci-libs/netcdf + sci-libs/fftw:2.1 + sci-chemistry/reduce" +DEPEND="${RDEPEND} + dev-util/byacc + dev-libs/libf2c + sys-devel/ucpp + virtual/pkgconfig" +S="${WORKDIR}/amber11" + +pkg_nofetch() { + einfo "Go to ${HOMEPAGE} and get ${A}" + einfo "Place it in ${DISTDIR}" +} + +pkg_setup() { + fortran-2_pkg_setup + if use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" + fi + AMBERHOME="${S}" +} + +src_prepare() { + epatch \ + "${WORKDIR}/${P}-bugfix_1-10.patch" \ + "${FILESDIR}/${P}-gentoo.patch" + cd AmberTools/src + rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die +} + +src_configure() { + cd AmberTools/src + sed \ + -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ + -e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) --libs lapack) -lclapack:g" \ + -e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) --libs blas cblas):g" \ + -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ + -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ + -e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \ + -e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \ + -e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \ + -e "s:fc=g77:fc=$(tc-getFC):g" \ + -e "s:\$netcdflib:$($(tc-getPKG_CONFIG) --libs netcdf):g" \ + -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ + -e "s:-O3::g" \ + -i configure || die + sed -e "s:arsecond_:arscnd_:g" \ + -i sff/time.c \ + -i sff/sff.h \ + -i sff/sff.c || die + sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ + -i nss/Makefile || die + + local myconf + + use X || myconf="${myconf} -noX11" + + for x in mpi openmp; do + use ${x} && myconf="${myconf} -${x}" + done + + ./configure \ + ${myconf} \ + -nobintraj \ + -nomdgx \ + -nopython \ + -nomtkpp \ + gnu +# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)') +} + +src_compile() { + cd AmberTools/src + emake +} + +src_install() { + rm -r bin/chemistry bin/MMPBSA_mods + rm bin/ante-MMPBSA.py bin/extractFrcmod.py + for x in bin/* + do dobin ${x} || die + done + rm "${ED}/usr/bin/yacc" + dobin AmberTools/src/antechamber/mopac.sh + sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ + -i "${ED}/usr/bin/mopac.sh" || die + # Make symlinks untill binpath for amber will be fixed + dodir /usr/share/${PN}/bin + cd "${ED}/usr/bin" + for x in *; do + dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} + done + cd "${S}" +# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \ +# -i "${ED}/usr/bin/xleap" \ +# -i "${ED}/usr/bin/tleap" || die + dodoc doc/AmberTools.pdf doc/leap_pg.pdf + + use static-libs && dolib.a lib/* + + insinto /usr/include/${PN} + doins include/* + + insinto /usr/share/${PN} + doins -r dat + + cd AmberTools + doins -r benchmarks examples test + + cat >> "${T}"/99ambertools <<- EOF + AMBERHOME="${EPREFIX}/usr/share/ambertools" + EOF + doenvd "${T}"/99ambertools +} diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch new file mode 100644 index 000000000000..0e41d26d6f9c --- /dev/null +++ b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch @@ -0,0 +1,386 @@ +diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure +--- amber11.orig/AmberTools/src/configure 2011-04-14 15:30:55.000000000 +0300 ++++ amber11/AmberTools/src/configure 2011-06-04 12:26:45.000000000 +0300 +@@ -293,7 +293,8 @@ + echo "Your AMBERHOME environment variable is not set! It should be set to" + echo "$ambhome NOT doing so may cause errors when you compile. Continue" + echo "anyway? (yes or no)" +- read answer ++ #read answer ++ answer='yes' + if [ "$answer" = 'yes' -o "$answer" = 'Yes' -o "$answer" = 'YES' -o "$answer" = 'y' -o "$answer" = 'Y' ]; then + echo "" + echo "Continuing anyway... Setting AMBERHOME to $ambhome temporarily" +@@ -356,11 +357,11 @@ + mpi_flag= + lex=flex + flibs_mkl= +-lapack=install +-blas=install ++lapack=skip ++blas=skip + f2c=skip +-ucpp=install +-cpp="\$(BINDIR)/ucpp -l" ++ucpp=skip ++cpp="\$(EPREFIX)/usr/bin/ucpp -l" + + #----------------------------------- + # skip building of sleap? +@@ -1655,24 +1656,24 @@ + #-------------------------------------------------------------------------- + # Configure fftw-3.2.2: + #-------------------------------------------------------------------------- +- if [ "$mdgx" = 'yes' ]; then +- mdgxflag="--prefix=$AMBERHOME --disable-fortran" +- echo +- echo "Configuring fftw-3.2.2 (may be time-consuming)..." +- echo +- cd fftw-3.2.2 && \ +- env CC="$cc" CFLAGS="$cflags $cnooptflags" \ +- ./configure $mdgxflag > ../fftw3_config.log 2>&1 +- ncerror=$? +- if [ $ncerror -gt 0 ]; then +- echo " Error: FFTW configure returned $ncerror" +- echo " FFTW configure failed! Check the fftw3_config.log file." +- exit 1 +- else +- echo " fftw-3.2.2 configure succeeded." +- fi +- cd .. +- fi ++ #if [ "$mdgx" = 'yes' ]; then ++ # mdgxflag="--prefix=$AMBERHOME --disable-fortran" ++ # echo ++ # echo "Configuring fftw-3.2.2 (may be time-consuming)..." ++ # echo ++ # cd fftw-3.2.2 && \ ++ # env CC="$cc" CFLAGS="$cflags $cnooptflags" \ ++ # ./configure $mdgxflag > ../fftw3_config.log 2>&1 ++ # ncerror=$? ++ # if [ $ncerror -gt 0 ]; then ++ # echo " Error: FFTW configure returned $ncerror" ++ # echo " FFTW configure failed! Check the fftw3_config.log file." ++ # exit 1 ++ # else ++ # echo " fftw-3.2.2 configure succeeded." ++ # fi ++ # cd .. ++ #fi + + #-------------------------------------------------------------------------- + # Configure python +@@ -1792,27 +1793,27 @@ + echo + echo "Configuring fftw-2.1.5 (may be time-consuming)..." + echo +- cd fftw-2.1.5 +- if [ "$mpi" = 'yes' ]; then +- ./configure $rismflag --enable-mpi \ +- CC="$cc" CFLAGS="$cflags $coptflags" \ +- F77="$fc" FFLAGS="$fflags $foptflags" \ +- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 +- else +- ./configure $rismflag \ +- CC="$cc" CFLAGS="$cflags $coptflags" \ +- F77="$fc" FFLAGS="$fflags $foptflags" \ +- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 +- fi +- ncerror=$? +- if [ $ncerror -gt 0 ]; then +- echo " Error: fftw configure returned $ncerror" +- echo " fftw configure failed! Check the fftw2_config.log file." +- exit 1 +- else +- echo " fftw-2.1.5 configure succeeded." +- fi +- cd .. ++ # cd fftw-2.1.5 ++ # if [ "$mpi" = 'yes' ]; then ++ # ./configure $rismflag --enable-mpi \ ++ # CC="$cc" CFLAGS="$cflags $coptflags" \ ++ # F77="$fc" FFLAGS="$fflags $foptflags" \ ++ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 ++ # else ++ # ./configure $rismflag \ ++ # CC="$cc" CFLAGS="$cflags $coptflags" \ ++ # F77="$fc" FFLAGS="$fflags $foptflags" \ ++ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 ++ # fi ++ # ncerror=$? ++ # if [ $ncerror -gt 0 ]; then ++ # echo " Error: fftw configure returned $ncerror" ++ # echo " fftw configure failed! Check the fftw2_config.log file." ++ # exit 1 ++ # else ++ # echo " fftw-2.1.5 configure succeeded." ++ # fi ++ # cd .. + flibs_fftw2="-ldrfftw -ldfftw" + if [ "$mpi" = 'yes' ]; then + flibs_fftw2="-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2" +diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at +--- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at 2011-04-14 15:30:16.000000000 +0300 ++++ amber11/AmberTools/src/cpptraj/src/Makefile_at 2011-05-20 00:45:48.000000000 +0300 +@@ -65,8 +65,8 @@ + -/bin/rm FindDepend.o + -/bin/rm findDepend + +-cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS) +- $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) ++cpptraj$(SFX): $(OBJECTS) ++ $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp + + $(NETCDFLIB): ../../netcdf_config.log + cd ../../netcdf/src && $(MAKE) install +diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile +--- amber11.orig/AmberTools/src/Makefile 2011-04-14 15:30:12.000000000 +0300 ++++ amber11/AmberTools/src/Makefile 2011-05-19 23:36:36.000000000 +0300 +@@ -8,15 +8,15 @@ + + install: $(INSTALLTYPE) + +-serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP) ++serial: configured_serial + @echo "Starting installation of ${AMBERTOOLS} serial at `date`". + # utility routines and libraries: +- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) ++# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) + (cd byacc && $(MAKE) install ) +- (cd arpack && $(MAKE) install ); +- (cd lapack && $(MAKE) $(LAPACK) ) +- (cd blas && $(MAKE) $(BLAS) ) +- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) ++# (cd arpack && $(MAKE) install ); ++# (cd lapack && $(MAKE) $(LAPACK) ) ++# (cd blas && $(MAKE) $(BLAS) ) ++# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) + (cd etc && $(MAKE) install ) + (cd chamber && $(MAKE) install ) + (cd pbsa && $(MAKE) install ) +@@ -32,7 +32,7 @@ + (cd cpptraj && $(MAKE) $(CPPTRAJ)) + + # miscellaneous: +- (cd reduce && $(MAKE) install ) ++# (cd reduce && $(MAKE) install ) + + # leap and gleap: + (cd leap && $(MAKE) install ) +@@ -42,7 +42,7 @@ + (cd rism && $(MAKE) install ) + + # nab: +- (cd cifparse && $(MAKE) install ) ++# (cd cifparse && $(MAKE) install ) + (cd sff && $(MAKE) install ) + (cd pbsa && $(MAKE) libinstall ) + (cd nab && $(MAKE) install ) +@@ -63,19 +63,19 @@ + @echo "Installation of ${AMBERTOOLS} serial is complete at `date`." + @echo "" + +-nabonly: $(NETCDFLIB) ++nabonly: + # utility routines and libraries: +- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) ++# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) + (cd byacc && $(MAKE) install ) +- (cd arpack && $(MAKE) install ); +- (cd lapack && $(MAKE) $(LAPACK) ) +- (cd blas && $(MAKE) $(BLAS) ) +- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) ++# (cd arpack && $(MAKE) install ); ++# (cd lapack && $(MAKE) $(LAPACK) ) ++# (cd blas && $(MAKE) $(BLAS) ) ++# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) + (cd pbsa && $(MAKE) libinstall ) + (cd rism && $(MAKE) install ) + + # nab: +- (cd cifparse && $(MAKE) install ) ++# (cd cifparse && $(MAKE) install ) + (cd sff && $(MAKE) install ) + (cd nab && $(MAKE) install ) + (cd nss && $(MAKE) install ) +diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/src/mdgx/Makefile +--- amber11.orig/AmberTools/src/mdgx/Makefile 2011-04-14 15:30:17.000000000 +0300 ++++ amber11/AmberTools/src/mdgx/Makefile 2011-05-20 12:44:38.000000000 +0300 +@@ -109,7 +109,7 @@ + + FFTW_LIBS = $(LIBDIR)/libfftw3.a + +-mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) ++mdgx$(SFX) : $(MDGX_OBJS) + $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \ + -o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM) + +diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile +--- amber11.orig/AmberTools/src/pbsa/Makefile 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/pbsa/Makefile 2011-05-19 22:27:40.000000000 +0300 +@@ -148,7 +148,7 @@ + ) + + #--------------------------------------------------------------------------- +-pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial ++pbsa$(SFX): $(OBJ) syslib configured_serial + $(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \ + ../lib/nxtsec.o ../lib/random.o \ + $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) +@@ -158,7 +158,7 @@ + ../lib/nxtsec.o ../lib/random.o \ + $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) + +-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex ++simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib + $(FC) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \ + libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) +@@ -194,15 +194,15 @@ + sfflib: + cd ../sff && $(MAKE) install + +-netlib: +- cd ../lapack && $(MAKE) $(LAPACK) +- cd ../blas && $(MAKE) $(BLAS) +- cd ../arpack && $(MAKE) install +- +-c9x-complex: +- @if test $(C9XCOMPLEX) != "skip"; then \ +- cd ../c9x-complex && $(MAKE) libmc.a; \ +- fi ++#netlib: ++# cd ../lapack && $(MAKE) $(LAPACK) ++# cd ../blas && $(MAKE) $(BLAS) ++# cd ../arpack && $(MAKE) install ++ ++#c9x-complex: ++# @if test $(C9XCOMPLEX) != "skip"; then \ ++# cd ../c9x-complex && $(MAKE) libmc.a; \ ++# fi + + %.LIBPBSA.o: %.f + $(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$< +diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile +--- amber11.orig/AmberTools/src/ptraj/Makefile 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/ptraj/Makefile 2011-05-19 23:38:36.000000000 +0300 +@@ -57,25 +57,25 @@ + pubfft.o: pubfft.f + $(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $< + +-rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS) ++rdparm$(SFX): libs $(OBJECTS) + $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ + -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) + +-ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS) ++ptraj$(SFX): libs $(OBJECTS) + $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ + -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) + +-ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS) ++ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS) + $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ + -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM) + + libs: + cd pdb && $(MAKE) +- cd ../arpack && $(MAKE) ++# cd ../arpack && $(MAKE) + +-netlib: +- cd ../lapack && $(MAKE) $(LAPACK) +- cd ../blas && $(MAKE) $(BLAS) ++#netlib: ++# cd ../lapack && $(MAKE) $(LAPACK) ++# cd ../blas && $(MAKE) $(BLAS) + + clean: + cd pdb && $(MAKE) clean +diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h +--- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-05-19 22:30:43.000000000 +0300 +@@ -4,7 +4,7 @@ + # include "../../include/pnetcdf.h" + # define nc_strerror ncmpi_strerror + # else +-# include "../../include/netcdf.h" ++# include <netcdf.h> + # endif + #endif + +diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h +--- amber11.orig/AmberTools/src/ptraj/ptraj.h 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/ptraj/ptraj.h 2011-06-04 13:25:01.000000000 +0300 +@@ -94,7 +94,7 @@ + #define nc_strerror ncmpi_strerror + #include "../../include/pnetcdf.h" + #else +-#include "../../include/netcdf.h" ++#include <netcdf.h> + #endif + #endif + +diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/src/rism/Makefile +--- amber11.orig/AmberTools/src/rism/Makefile 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/rism/Makefile 2011-05-20 01:07:26.000000000 +0300 +@@ -49,7 +49,7 @@ + mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \ + fce_c.o erfcfun.o safemem.o blend.o timer_c.o + +-librism: $(LIBOBJ) $(FLIBS_FFTW2) ++librism: $(LIBOBJ) + $(AR) $(LIBDIR)/$@.a $(LIBOBJ) + $(RANLIB) $(LIBDIR)/$@.a + +diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberTools/src/sff/AmberNetcdf.c +--- amber11.orig/AmberTools/src/sff/AmberNetcdf.c 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/sff/AmberNetcdf.c 2011-05-20 10:49:06.000000000 +0300 +@@ -27,7 +27,7 @@ + #endif + + #ifdef BINTRAJ +-#include "../../include/netcdf.h" ++#include <netcdf.h> + + #define NCFRAME "frame" + #define NCSPATIAL "spatial" +diff -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/src/sff/Makefile +--- amber11.orig/AmberTools/src/sff/Makefile 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/sff/Makefile 2011-05-20 09:53:27.000000000 +0300 +@@ -1,7 +1,7 @@ + include ../config.h + + .c.o: +- $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $< ++ $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $< + + OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \ + prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \ +diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile +--- amber11.orig/AmberTools/src/sqm/Makefile 2011-04-14 15:30:20.000000000 +0300 ++++ amber11/AmberTools/src/sqm/Makefile 2011-05-19 22:31:49.000000000 +0300 +@@ -77,7 +77,7 @@ + install: sqm$(SFX) + mv sqm$(SFX) $(BINDIR) + +-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys ++sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys + $(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \ + $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS) + +@@ -94,10 +94,10 @@ + sys: + cd ../lib; $(MAKE) sys.a + +-netlib: +- cd ../lapack; $(MAKE) $(LAPACK) +- cd ../blas; $(MAKE) $(BLAS) +- cd ../arpack && $(MAKE) install ++#netlib: ++# cd ../lapack; $(MAKE) $(LAPACK) ++# cd ../blas; $(MAKE) $(BLAS) ++# cd ../arpack && $(MAKE) install + + clean: + /bin/rm -f *.o _*.f *.mod *.d sqm$(SFX) diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml new file mode 100644 index 000000000000..13ef0bf5a17c --- /dev/null +++ b/sci-chemistry/ambertools/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest new file mode 100644 index 000000000000..fef1437b89f5 --- /dev/null +++ b/sci-chemistry/apbs/Manifest @@ -0,0 +1 @@ +DIST apbs-1.4.1.zip 37999283 SHA256 1156c44fb65bb7c884801f3111ca1cdb1dfba6f5308226587db112aac4969027 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a WHIRLPOOL 6729571f13c953ec0bcf90da73ef0c39cf769f1498a767d3280de3ffbeea18eda718373efca0468436c4b18357fe450865f661daba79eeb66778c572c43ff39a diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild new file mode 100644 index 000000000000..cabbd1e45e92 --- /dev/null +++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild @@ -0,0 +1,128 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +DISTUTILS_SINGLE_IMPL=true + +inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs + +GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65" + +DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems" +HOMEPAGE="http://www.poissonboltzmann.org/apbs/" +#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz" +SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="debug doc examples fast +fetk iapbs mpi openmp python tools" + +REQUIRED_USE=" + iapbs? ( fetk ) + mpi? ( !python ) + python? ( tools fetk iapbs ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/maloc[mpi=] + virtual/blas + sys-libs/readline + fetk? ( + sci-libs/fetk + sci-libs/amd + sci-libs/umfpack + sci-libs/superlu + ) + mpi? ( virtual/mpi ) + python? ( ${PYTHON_DEPS} ) +" +DEPEND="${DEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen ) +" + +S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN} + +PATCHES=( + "${FILESDIR}"/${P}-multilib.patch + "${FILESDIR}"/${P}-manip.patch + "${FILESDIR}"/${P}-python.patch +) + +src_prepare() { + cmake-utils_src_prepare + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + + sed \ + -e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \ + -e "/TOOLS_PATH/d" \ + -i CMakeLists.txt || die + use doc && MAKEOPTS+=" -j1" + if use python; then + unset PATCHES || die + cd tools/python && distutils-r1_src_prepare + fi +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_SKIP_RPATH=ON + -DTOOLS_PATH="${ED}"/usr + -DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir) + -DLIBRARY_INSTALL_PATH=$(get_libdir) + -DFETK_PATH="${EPREFIX}"/usr/ + -DBUILD_SHARED_LIBS=ON + -DENABLE_QUIT=OFF + $(cmake-utils_use_build doc DOC) + $(cmake-utils_use_build tools TOOLS) + -DENABLE_BEM=OFF +# ENABLE_BEM: Boundary element method using TABIPB + $(cmake-utils_use_enable debug DEBUG) + $(cmake-utils_use_enable debug VERBOSE_DEBUG) + $(cmake-utils_use_enable fast FAST) + $(cmake-utils_use_enable fetk FETK) + $(cmake-utils_use_enable mpi MPI) + $(cmake-utils_use_enable python PYTHON) +# ENABLE_TINKER: Enable TINKER support + $(cmake-utils_use_enable iapbs iAPBS) +# MAX_MEMORY: Set the maximum memory (in MB) to be used for a job + ) + cmake-utils_src_configure + if use python; then + cd tools/python && distutils-r1_src_configure + fi +} + +src_compile(){ + cmake-utils_src_compile + if use python; then + append-ldflags -L"${S}"/lib + cd tools/python && distutils-r1_src_compile + fi +} + +src_test() { + python_export_best + cd tests || die + LD_LIBRARY_PATH="${S}"/lib "${PYTHON}" apbs_tester.py -l log || die + grep -q 'FAILED' log && die "Tests failed" +} + +src_install() { + dodir /usr/bin + cmake-utils_src_install + local i + for i in "${ED}"/usr/bin/*; do + if [[ ! "${i}" =~ .*apbs$ ]]; then + mv "${i}" "${i}-apbs" || die + fi + done + if use python; then + cd tools/python && distutils-r1_src_install + rm -rf "${ED}"/usr/share/apbs/tools/python || die + fi +} diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch new file mode 100644 index 000000000000..378223397594 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch @@ -0,0 +1,50 @@ + apbs/CMakeLists.txt | 2 +- + apbs/tools/CMakeLists.txt | 4 ---- + apbs/tools/mesh/CMakeLists.txt | 4 ++-- + 4 files changed, 5 insertions(+), 9 deletions(-) + +diff --git a/apbs/CMakeLists.txt b/apbs/CMakeLists.txt +index 8917fc4..5152008 100644 +--- a/apbs/CMakeLists.txt ++++ b/apbs/CMakeLists.txt +@@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF) + + if(ENABLE_FETK) + message(STATUS "Checking for fetk components") +- set(FETK_ENALBED 1) ++ set(FETK_ENABLED 1) + + list(APPEND APBS_LIBS "-lstdc++") + list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") +diff --git a/apbs/tools/manip/CMakeLists.txt b/apbs/tools/manip/CMakeLists.txt +index 937dac7..5768cc5 100644 +--- a/apbs/tools/manip/CMakeLists.txt ++++ b/apbs/tools/manip/CMakeLists.txt +@@ -4,9 +4,9 @@ set(LIBS "") + list(APPEND LIBS "apbs_generic") + list(APPEND LIBS "apbs_mg") + list(APPEND LIBS "apbs_pmgc") +-if(FETK_ENALBED) ++if(FETK_ENABLED) + list(APPEND LIBS "apbs_fem") +-endif(FETK_ENALBED) ++endif(FETK_ENABLED) + + message(STATUS "libraries: ${LIBS}") + +diff --git a/apbs/tools/mesh/CMakeLists.txt b/apbs/tools/mesh/CMakeLists.txt +index 1406377..6e6dfb9 100644 +--- a/apbs/tools/mesh/CMakeLists.txt ++++ b/apbs/tools/mesh/CMakeLists.txt +@@ -4,9 +4,9 @@ set(LIBS "") + list(APPEND LIBS "apbs_generic") + list(APPEND LIBS "apbs_mg") + list(APPEND LIBS "apbs_pmgc") +-if(FETK_ENALBED) ++if(FETK_ENABLED) + list(APPEND LIBS "apbs_fem") +-endif(FETK_ENALBED) ++endif(FETK_ENABLED) + + message(STATUS "libraries: ${LIBS}") + diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch new file mode 100644 index 000000000000..a4e2d1761cf4 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch @@ -0,0 +1,92 @@ + CMakeLists.txt | 18 +++++++++--------- + src/CMakeLists.txt | 1 - + src/fem/CMakeLists.txt | 2 +- + src/pmgc/CMakeLists.txt | 2 +- + 4 files changed, 11 insertions(+), 12 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 75ddbdd..c46f5e7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -61,7 +61,7 @@ set(LIBRARY_OUTPUT_PATH ${APBS_ROOT}/lib) + set(TOOLS_PATH ${APBS_ROOT}/tools) + set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) + +-set(LIBRARY_INSTALL_PATH lib) ++set(LIBRARY_INSTALL_PATH ${CMAKE_INSTALL_LIBDIR}) + set(HEADER_INSTALL_PATH include/apbs) + set(EXECUTABLE_INSTALL_PATH bin) + set(SHARE_INSTALL_PATH share/apbs) +@@ -93,8 +93,6 @@ set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") + list(APPEND CMAKE_INCLUDE_PATH /usr/include) + list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) + +-set(APBS_LIBS "-L${APBS_ROOT}/lib -lapbs_geoflow") +- + ################################################################################ + # Enable ansi pedantic compiling # + ################################################################################ +@@ -193,9 +191,11 @@ if(ENABLE_BEM) + else() + set(TABI_LIBRARY_BASENAME ${CMAKE_STATIC_LIBRARY_PREFIX}${TABI}${CMAKE_STATIC_LIBRARY_SUFFIX}) + endif() +- ++ ++ file(GLOB MODS ${LIBRARY_OUTPUT_PATH}/*.mod) ++ + install( +- FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${LIBRARY_OUTPUT_PATH}/*.mod ++ FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${MODS} + DESTINATION ${LIBRARY_INSTALL_PATH} + ) + set(TABI_LIBRARY ${APBS_ROOT}/${LIBRARY_INSTALL_PATH}/${TABI_LIBRARY_BASENAME}) +@@ -210,7 +210,7 @@ if(ENABLE_BEM) + endif() + get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH) + find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH}) +- list(APPEND APBS_LIBS "-L${APBS_ROOT}/${LIBRARY_INSTALL_PATH} -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" ) ++ list(APPEND APBS_LIBS "-L${APBS_ROOT}/lib -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" ) + endif() # ENABLE_BEM + + find_file( # this should be find path... +@@ -228,7 +228,7 @@ endif() + + + find_library(MALOC_LIBRARY "maloc" +- PATHS ${FETK_PATH}/lib ${CONTRIB_PATH} ++ PATHS ${FETK_PATH}/${CMAKE_INSTALL_LIBDIR} ${CONTRIB_PATH} + DOC "The fetk/maloc library" + ) + if(MALOC_LIBRARY) +@@ -296,9 +296,9 @@ if(ENABLE_FETK) + set(FETK_ENALBED 1) + + list(APPEND APBS_LIBS "-lstdc++") +- list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") ++ list(APPEND APBS_LIBS "-L${FETK_PATH}/${CMAKE_INSTALL_LIBDIR}") + list(APPEND APBS_LIBS -lamd -lpunc -lmc -lgamer -lsuperlu -lumfpack +--lblas -lvf2c -ltetgen -ltriangle -lg2c -lreadline ) ++-lblas -lvf2c -ltetgen -ltriangle -lreadline ) + + SET(HAVE_MC_H YES) + endif() +diff --git a/src/fem/CMakeLists.txt b/src/fem/CMakeLists.txt +index 5a950c2..dc37f48 100644 +--- a/src/fem/CMakeLists.txt ++++ b/src/fem/CMakeLists.txt +@@ -12,4 +12,4 @@ add_items( + vpee.h + ) + +-add_sublibrary(fem) ++add_sublibrary(fem apbs_geoflow) +diff --git a/src/pmgc/CMakeLists.txt b/src/pmgc/CMakeLists.txt +index 85b0c1e..97c95f0 100644 +--- a/src/pmgc/CMakeLists.txt ++++ b/src/pmgc/CMakeLists.txt +@@ -42,4 +42,4 @@ add_items( + mgfasd.h + ) + +-add_sublibrary(pmgc) ++add_sublibrary(pmgc apbs_geoflow) diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch new file mode 100644 index 000000000000..db9f86ba120a --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch @@ -0,0 +1,122 @@ + apbs/contrib/iapbs/src/apbs_driver.c | 6 +++--- + apbs/src/CMakeLists.txt | 1 + + apbs/tools/CMakeLists.txt | 2 +- + apbs/tools/python/CMakeLists.txt | 1 + + apbs/tools/python/apbslib.c | 4 ++-- + apbs/tools/python/apbslib.i | 4 ++-- + apbs/tools/python/setup.py | 16 ++++++++++++++++ + 7 files changed, 26 insertions(+), 8 deletions(-) + +diff --git a/apbs/contrib/iapbs/src/apbs_driver.c b/apbs/contrib/iapbs/src/apbs_driver.c +index c9e443b..e1ad67f 100644 +--- a/apbs/contrib/iapbs/src/apbs_driver.c ++++ b/apbs/contrib/iapbs/src/apbs_driver.c +@@ -595,7 +595,7 @@ int apbsdrv_( + printPBEPARM(pbeparm); + + /* Refine mesh */ +- if (!preRefineFE(i, nosh, feparm, fetk)) { ++ if (!preRefineFE(i, feparm, fetk)) { + Vnm_tprint( 2, "Error pre-refining mesh!\n"); + VJMPERR1(0); + } +@@ -609,7 +609,7 @@ int apbsdrv_( + Vnm_tprint(1, " Beginning solve-estimate-refine cycle:\n"); + for (isolve=0; isolve<feparm->maxsolve; isolve++) { + Vnm_tprint(1, " Solve #%d...\n", isolve); +- if (!solveFE(i, nosh, pbeparm, feparm, fetk)) { ++ if (!solveFE(i, pbeparm, feparm, fetk)) { + Vnm_tprint(2, "ERROR SOLVING EQUATION!\n"); + VJMPERR1(0); + } +@@ -622,7 +622,7 @@ int apbsdrv_( + /* We're not going to refine if we've hit the max number + * of solves */ + if (isolve < (feparm->maxsolve)-1) { +- if (!postRefineFE(i, nosh, feparm, fetk)) break; ++ if (!postRefineFE(i, feparm, fetk)) break; + } + bytesTotal = Vmem_bytesTotal(); + highWater = Vmem_highWaterTotal(); +diff --git a/apbs/src/CMakeLists.txt b/apbs/src/CMakeLists.txt +index 44d20fa..2577343 100644 +--- a/apbs/src/CMakeLists.txt ++++ b/apbs/src/CMakeLists.txt +@@ -68,6 +68,7 @@ configure_file( + + if(ENABLE_iAPBS) + ADD_LIBRARY(apbs_routines routines.c routines.h) ++ target_link_libraries(apbs_routines apbs_mg apbs_fem) + INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH}) + INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH}) + endif() +diff --git a/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt +index 1982a3c..4acbe68 100644 +--- a/apbs/tools/CMakeLists.txt ++++ b/apbs/tools/CMakeLists.txt +@@ -4,5 +4,5 @@ add_subdirectory(mesh) + add_subdirectory(manip) + + if(ENABLE_PYTHON) +- add_subdirectory(manip) ++ add_subdirectory(python) + endif(ENABLE_PYTHON) +diff --git a/apbs/tools/python/CMakeLists.txt b/apbs/tools/python/CMakeLists.txt +new file mode 100644 +index 0000000..8b13789 +--- /dev/null ++++ b/apbs/tools/python/CMakeLists.txt +@@ -0,0 +1 @@ ++ +diff --git a/apbs/tools/python/apbslib.c b/apbs/tools/python/apbslib.c +index fef5cc8..feaaa2c 100644 +--- a/apbs/tools/python/apbslib.c ++++ b/apbs/tools/python/apbslib.c +@@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0}; + #include "maloc/maloc.h" + #include "apbscfg.h" + #include "routines.h" +-#include "apbs/valist.h" +-#include "apbs/vatom.h" ++#include "generic/valist.h" ++#include "generic/vatom.h" + + + #include <limits.h> +diff --git a/apbs/tools/python/apbslib.i b/apbs/tools/python/apbslib.i +index 17fe521..44d05ea 100644 +--- a/apbs/tools/python/apbslib.i ++++ b/apbs/tools/python/apbslib.i +@@ -15,8 +15,8 @@ Header files: + #include "maloc/maloc.h" + #include "apbscfg.h" + #include "routines.h" +-#include "apbs/valist.h" +-#include "apbs/vatom.h" ++#include "generic/valist.h" ++#include "generic/vatom.h" + %} + + /* +diff --git a/apbs/tools/python/setup.py b/apbs/tools/python/setup.py +new file mode 100644 +index 0000000..4a20198 +--- /dev/null ++++ b/apbs/tools/python/setup.py +@@ -0,0 +1,16 @@ ++from distutils.core import setup, Extension ++setup(name='apbs', ++ version='1.4.1', ++ package_dir={'apbs': '', 'vgrid': 'vgrid'}, ++ packages=['apbs', 'vgrid'], ++ py_modules=['apbslib', 'main', 'noinput'], ++ ext_modules=[ ++ Extension( ++ '_apbslib', ++ ['apbslib.i'], ++ swig_opts=['-module', 'apbslib', '-I../include'], ++ include_dirs=["../../src"], ++ libraries=["apbs_generic", "apbs_routines"] ++ ) ++ ], ++ ) diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml new file mode 100644 index 000000000000..f1b8467dd96e --- /dev/null +++ b/sci-chemistry/apbs/metadata.xml @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher</name> + <description>Ebuild Crasher</description> + </maintainer> + <use> + <flag name="fetk">Include support for FeTK</flag> + <flag name="fast">APBS fast mode (experimental)</flag> + <flag name="iapbs">C/C++/Fortran interface</flag> + <flag name="tools">Install optional tools</flag> + </use> + <longdescription> +APBS is a software package for modeling biomolecular solvation through solution +of the Poisson-Boltzmann equation (PBE), one of the most popular continuum +models for describing electrostatic interactions between molecular solutes in +salty, aqueous media. Continuum electrostatics plays an important role in +several areas of biomolecular simulation +</longdescription> + <upstream> + <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest new file mode 100644 index 000000000000..7f6594d70fe4 --- /dev/null +++ b/sci-chemistry/aqua/Manifest @@ -0,0 +1,2 @@ +DIST aqua-3.2-nmr_manual.tar.gz 632031 SHA256 89bbc2501831e547fec2fe755bbc0081f672e5e2c7adb83618699e6825f73996 +DIST aqua3.2.tar.gz 688408 SHA256 895291b1771f4db5b4a010ce797400a8c4d84095bf34d660dd3405223419242f diff --git a/sci-chemistry/aqua/aqua-3.2-r2.ebuild b/sci-chemistry/aqua/aqua-3.2-r2.ebuild new file mode 100644 index 000000000000..74fccddc5dd2 --- /dev/null +++ b/sci-chemistry/aqua/aqua-3.2-r2.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="Program suite in this distribution calculates restraint violations" +HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html" +SRC_URI=" + ${PN}${PV}.tar.gz + doc? ( ${P}-nmr_manual.tar.gz )" + +SLOT="0" +LICENSE="procheck" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples" + +RDEPEND="sci-chemistry/procheck" +DEPEND="" + +RESTRICT="fetch" + +S="${WORKDIR}"/${PN}${PV} + +pkg_nofetch() { + elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html" + elog "And follow the instruction for downloading ${PN}${PV}.tar.gz -> ${DISTDIR}/${PN}${PV}.tar.gz." + if use doc; then + elog "nmr_manual.tar.gz -> ${DISTDIR}/${P}-nmr_manual.tar.gz" + fi +} + +src_prepare() { + sed \ + -e 's:nawk:gawk:g' \ + -e "s:/bin/gawk:${EPREFIX}/usr/bin/gawk:g" \ + -e "s:/usr/local/bin/perl:${EPREFIX}/usr/bin/perl:g" \ + -i $(find . -type f) || die + epatch "${FILESDIR}"/${PV}-flags.patch +} + +src_compile() { + pushd src > /dev/null + emake \ + MYROOT="${WORKDIR}" \ + CC="$(tc-getCC)" \ + FC="$(tc-getFC)" \ + CFLAGS="${CFLAGS} -I../sub/lib" \ + FFLAGS="${FFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + exth + emake \ + MYROOT="${WORKDIR}" \ + CC="$(tc-getCC)" \ + FC="$(tc-getFC)" \ + CFLAGS="${CFLAGS} -I../sub/lib" \ + FFLAGS="${FFLAGS}" \ + LDFLAGS="${LDFLAGS}" + popd +} + +src_install() { + rm -f scripts/conv* || die + dobin bin/* scripts/* + dosym AquaWhat /usr/bin/qwhat + dosym AquaHow /usr/bin/qhow + dosym AquaPseudo /usr/bin/qpseudo + dosym AquaDist /usr/bin/qdist + dosym AquaCalc /usr/bin/qcalc + dosym AquaAssign /usr/bin/qassign + dosym AquaRedun /usr/bin/qredun + dosym AquaCompl /usr/bin/qcompl + + dodoc HISTORY HOW_TO_USE NEW README doc/* + dohtml html/* + + insinto /usr/share/${PN} + doins data/* + if use examples; then + doins -r exmpls + fi + + if use doc; then + dohtml -r manual + fi + + cat >> "${T}"/34aqua <<- EOF + AQUADATADIR="${EPREFIX}/usr/share/${PN}" + EOF + doenvd "${T}"/34aqua +} diff --git a/sci-chemistry/aqua/files/3.2-flags.patch b/sci-chemistry/aqua/files/3.2-flags.patch new file mode 100644 index 000000000000..cd12fbb9a324 --- /dev/null +++ b/sci-chemistry/aqua/files/3.2-flags.patch @@ -0,0 +1,84 @@ +diff --git a/src/makefile b/src/makefile +index 3113471..dd7a320 100644 +--- a/src/makefile ++++ b/src/makefile +@@ -176,47 +176,46 @@ nrutil.h: + # Executable files + + $(BIN)/AquaWhat: AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) + + $(BIN)/AquaHow: AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) + + $(BIN)/AquaPseudo: AquaPseudo.o $(OBJECTS) $(R_OBJECTS) +- $(CC) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) + + $(BIN)/AquaDist: AquaDist.o $(OBJECTS) +- $(CC) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) $(LDFLAGS) -lm ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) -lm + + $(BIN)/AquaCalc: AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) -lm ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) -lm + + $(BIN)/AquaAssign: AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) + + $(BIN)/AquaCompl: AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -lm ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -lm + + $(BIN)/AquaRedun: AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) + + $(BIN)/testnew: testnew.o $(OBJECTS) +- $(CC) -o $(BIN)/testnew testnew.o $(OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/testnew testnew.o $(OBJECTS) + + $(BIN)/getproj: getproj.c +- $(CC) -o $(BIN)/getproj -O getproj.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(BIN)/getproj getproj.c + + $(BIN)/AquaPlot: AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o +- $(CC) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o + + $(BIN)/Qext: Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o +- $(CC) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o + + $(BIN)/StarTest: StarTest.o +- $(CC) -o $(BIN)/StarTest StarTest.o $(LDFLAGS) $(STARFLAGS) $(STARLIBS) ++ $(CC) $(LDFLAGS) -o $(BIN)/StarTest StarTest.o $(STARFLAGS) $(STARLIBS) + + exth: exth.f +- f77 -o exth -O2 exth.f +- strip exth ++ $(FC) $(FFLAGS) -o exth -O2 exth.f + + + # Object files +@@ -269,7 +268,7 @@ AquaCommon.o: AquaCommon.c AquaCommon.h nrutil.h \ + $(CC) -c AquaCommon.c $(CFLAGS) + + nrutil.o: nrutil.c nrutil.h +- $(CC) -c nrutil.c -DANSI ++ $(CC) $(CFLAGS) -c nrutil.c -DANSI + + AquaFuncts.o: AquaFuncts.c AquaFuncts.h AquaFuncts_cv.h AquaFuncts_io.h\ + AquaStrucset.h AquaFiles.h\ +@@ -319,7 +318,7 @@ $(LIB)/MenuFuncts.o: $(LIB)/MenuFuncts.c $(LIB)/MenuTypes.h $(LIB)/MenuFuncts.h\ + cd $(LIB); $(CC) -c MenuFuncts.c $(CFLAGS) + + cv_subs.o: cv_subs.f +- f77 -c cv_subs.f $(FFLAGS) ++ $(FC) -c cv_subs.f $(FFLAGS) + + Qext.o: Qext.c Qext.h\ + $(LIB)/MenuFuncts.h $(LIB)/Functs.h $(G_HEADERS) diff --git a/sci-chemistry/aqua/metadata.xml b/sci-chemistry/aqua/metadata.xml new file mode 100644 index 000000000000..1837bbc07a6e --- /dev/null +++ b/sci-chemistry/aqua/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/aria/Manifest b/sci-chemistry/aria/Manifest new file mode 100644 index 000000000000..28b40aa5c0c8 --- /dev/null +++ b/sci-chemistry/aria/Manifest @@ -0,0 +1 @@ +DIST aria2.3.2_08.26.2013.tar.gz 1878602 SHA256 b9b892de2070a77812733faf4b6a1dbec4bba6dec80e5630088cab8b11cbfaf0 SHA512 a6d8c45218f5d494174587a5f8f1feec940ac8cc4cd7b707dac65b2378219ecf27967e70807e6cb7ae22a7d4aec7239af763f077ad7183c078b1991cac71bc3e WHIRLPOOL 59c0b79fab40201d903c484bf63e8339c235207306efc848965d260c02b00c9a408297df0f211cf45f30d13ec35175bf7d566bb5c6d59b944eb22d9aacf0384d diff --git a/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild b/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild new file mode 100644 index 000000000000..7c4026fb1070 --- /dev/null +++ b/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild @@ -0,0 +1,89 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit eutils python-single-r1 versionator + +MY_P="${PN}$(get_version_component_range 1-2 ${PV})" +DATE="08.26.2013" + +DESCRIPTION="Automated NOE assignment and NMR structure calculation" +HOMEPAGE="http://aria.pasteur.fr/" +SRC_URI="http://aria.pasteur.fr/archives/${MY_P}.2_${DATE}.tar.gz" + +SLOT="0" +LICENSE="cns" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-tcltk/tix + dev-lang/tk + >=dev-python/numpy-1.1[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP},tk] + >=sci-chemistry/cns-1.2.1-r7[aria,openmp] + >=sci-chemistry/ccpn-2.2[${PYTHON_USEDEP}] + sci-chemistry/clashlist + sci-chemistry/procheck + sci-libs/clashscore-db" +DEPEND="${RDEPEND}" + +RESTRICT="fetch" + +S="${WORKDIR}/${MY_P}" + +pkg_nofetch(){ + einfo "Go to http://aria.pasteur.fr/archives/aria2.3.2.tar.gz/view, download ${A}" + einfo "and place it in ${DISTDIR}" +} + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_test(){ + export CCPNMR_TOP_DIR=$(python_get_sitedir) + export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python + ${PYTHON} check.py || die +} + +src_install(){ + python_moduleinto ${PN} + python_domodule src aria2.py + python_moduleinto ${PN}/cns + python_domodule cns/{protocols,toppar,src/helplib} + + if use examples; then + insinto /usr/share/${P}/ + doins -r examples + fi + + # ENV + cat >> "${T}"/20aria <<- EOF + ARIA2="$(python_get_sitedir)/${PN}" + EOF + + doenvd "${T}"/20aria + + # Launch Wrapper + cat >> "${T}"/aria <<- EOF + #!/bin/sh + export CCPNMR_TOP_DIR="$(python_get_sitedir)" + export PYTHONPATH="$(python_get_sitedir)/ccpn/python" + exec "${PYTHON}" -O "\${ARIA2}"/aria2.py \$@ + EOF + + dobin "${T}"/aria + dosym aria /usr/bin/aria2 + + dodoc README + python_optimize "${D}/$(python_get_sitedir)" +} diff --git a/sci-chemistry/aria/files/aria-2.3.2-python.patch b/sci-chemistry/aria/files/aria-2.3.2-python.patch new file mode 100644 index 000000000000..1f9ae1fcc5f6 --- /dev/null +++ b/sci-chemistry/aria/files/aria-2.3.2-python.patch @@ -0,0 +1,30 @@ + src/py/aria/legacy/QualityChecks/Descriptive.py | 5 +++-- + 1 files changed, 3 insertions(+), 2 deletions(-) + +diff --git a/src/py/aria/legacy/QualityChecks/Descriptive.py b/src/py/aria/legacy/QualityChecks/Descriptive.py +index ae5913c..550d20c 100644 +--- a/src/py/aria/legacy/QualityChecks/Descriptive.py ++++ b/src/py/aria/legacy/QualityChecks/Descriptive.py +@@ -1,3 +1,6 @@ ++from math import * ++from numpy import * ++ + class Descriptive: + """ + some basic statistics +@@ -55,7 +58,6 @@ class Descriptive: + + def getStdDev(self): + if( len(self.myData) == 0): return None +- from math import * + if( (self.count - 1) > 0 ): + return sqrt( self.pseudoVariance/ (self.count - 1)) + else: +@@ -89,7 +91,6 @@ class Descriptive: + def getMedian(self): + if( len(self.myData) == 0): return None + if( self.median == None ): +- from numpy import * + sort(self.myData) + if( self.count%2 == 1): + self.median = self.myData[(self.count-1)/2] diff --git a/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch b/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch new file mode 100644 index 000000000000..6a363d098632 --- /dev/null +++ b/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch @@ -0,0 +1,139 @@ + src/py/aria/exportToCcpn.py | 24 +++++++++++------------- + src/py/aria/importFromCcpn.py | 32 ++++++++++++-------------------- + 2 files changed, 23 insertions(+), 33 deletions(-) + +diff --git a/src/py/aria/exportToCcpn.py b/src/py/aria/exportToCcpn.py +index c742a88..aae7b7d 100644 +--- a/src/py/aria/exportToCcpn.py ++++ b/src/py/aria/exportToCcpn.py +@@ -1,5 +1,5 @@ + from ccpnmr.analysis.core.ConstraintBasic import makeNmrConstraintStore, makeStructureGeneration, getFixedResonance +-from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims ++from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims, getThroughSpaceDataDims + from ccpnmr.analysis.core.AssignmentBasic import assignAtomsToRes, assignResToDim + from ccpnmr.analysis.core.PeakBasic import pickPeak, setManualPeakIntensity + from ccpnmr.analysis.core.MoleculeBasic import DEFAULT_ISOTOPES +@@ -791,12 +791,13 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None, + ariaDims = ariaDimDict.get(spectrum) + if not ariaDims: + ariaDims = [] #[0,1,2] ++ throughSpaceDataDims = getThroughSpaceDataDims(spectrum) + + dataDims = spectrum.sortedDataDims() + if len(dataDims) == 3: + for dataDim in dataDims: + expDimRef = dataDim.findFirstDataDimRef().expDimRef +- if '1H' in expDimRef.isotopeCodes: # 0 or 2 ++ if dataDim in throughSpaceDataDims: # 0 or 2 + if onebondDims.get(dataDim.dim): + if ppmX1 is None: + ariaDims.append(2) +@@ -816,21 +817,18 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None, + ariaDims.append(1) + + else: +- transfer = spectrum.experiment.findFirstExpTransfer(transferType='through-space') or \ +- spectrum.experiment.findFirstExpTransfer(transferType='NOESY') + ++ i = 0 + for dataDim in dataDims: +- expDimRefs = [dataDimRef.expDimRef for dataDimRef in dataDim.dataDimRefs] +- i = 0 +- for expDimRef in transfer.sortedExpDimRefs(): +- if expDimRef in expDimRefs: +- ariaDims.append(i) +- boundDim = onebondDims.get(dataDim.dim) +- if boundDim: +- ariaDims.append(i+1) +- ++ if dataDim in throughSpaceDataDims: ++ ariaDims.append(i) ++ boundDim = onebondDims.get(dataDim.dim) ++ if boundDim: ++ ariaDims.append(i+1) ++ + i += 2 + ++ + ariaDimDict[spectrum] = ariaDims + + if namesDict: +diff --git a/src/py/aria/importFromCcpn.py b/src/py/aria/importFromCcpn.py +index a65ae3e..f63ba16 100644 +--- a/src/py/aria/importFromCcpn.py ++++ b/src/py/aria/importFromCcpn.py +@@ -165,7 +165,7 @@ def getStructureEnsembles(project, ccpChains): + + return ensembles + +-def getNoesyPeakLists(project, molSystem=None): ++def getNoesyPeakLists(project, molSystem=None, excludeSimulated=True): + """Descrn: Get the NOE peak lists from a CCPN project. Can filter if appropriate to a given + molecular system if passed in. + Inputs: Implementation.Project, ccp.molecule.MolSystem.MolSystem +@@ -196,19 +196,10 @@ def getNoesyPeakLists(project, molSystem=None): + + for spectrum in experiment.dataSources: + if (spectrum.dataType == 'processed') and (spectrum.numDim > 1): +- +- isotopes = [] +- for dataDim in spectrum.dataDims: +- for expDimRef in dataDim.expDim.expDimRefs: +- if expDimRef.measurementType in ('shift','Shift'): +- isotope = ','.join(expDimRef.isotopeCodes) +- isotopes.append(isotope) +- break +- +- if isotopes.count('1H') > 1: +- for peakList in spectrum.peakLists: +- if peakList.findFirstPeak(): +- peakLists.append(peakList) ++ for peakList in spectrum.sortedPeakLists(): ++ if excludeSimulated and peakList.isSimulated: ++ continue ++ peakLists.append(peakList) + + + return peakLists +@@ -490,7 +481,10 @@ def makeAriaChain(ccpChain): + # Does below work for DNA/RNA? + + aria_settings = ChainSettings() +- aria_settings['type'] = chainTypeMapping[ccpChain.molecule.molType] ++ # wb104: below changed 31 Oct 2011 to try and get around case when molType is None ++ #aria_settings['type'] = chainTypeMapping[ccpChain.molecule.molType] ++ molType = ccpChain.molecule.molType or 'protein' ++ aria_settings['type'] = chainTypeMapping[molType] + + aria_chain = Chain(settings=aria_settings, segid=string_to_segid(ccpChain.code)) + +@@ -952,8 +946,6 @@ def makeAriaSpectrum(peakList, ariaMolecule, filterRejected=True): + expDimRefDict = {} + + for expDimRef in transfer.sortedExpDimRefs(): +- if expDimRef.isotopeCodes != ('1H',): +- raise Exception('Not an H-H experiment') + + onebondTransfer = expDimRef.findFirstExpTransfer(transferType='onebond') + +@@ -1095,7 +1087,7 @@ def getAriaAtomsFromResonance(resonance, ariaMolecule, cache={}): + + # TJS modify to return just a list of atoms, rather than a list of list + ariaAtoms = [] +- for atom in atomSet.sortedAtoms(): ++ for atom in atomSet.atoms: + ariaAtom = ariaResidue.atoms.get(atom.name) + if not ariaAtom: + messager.warning('Could not find ARIA Atom for CCPN atom %d%s %s' % (residue.seqCode,residue.ccpCode, atom.name)) +@@ -1256,9 +1248,9 @@ def getAriaDistanceRestraintsList(constraint_list, constraint_type, aria_mol): + restraint.setWeight(weight) + + +- for constrItem in distConstr.sortedItems(): ++ for constrItem in distConstr.items: + +- reso1, reso2 = constrItem.sortedResonances() ++ reso1, reso2 = constrItem.resonances + + # TJS fix for mapping prochirals + # always use real resonnances where possible diff --git a/sci-chemistry/aria/files/aria-2.3.2-through-space.patch b/sci-chemistry/aria/files/aria-2.3.2-through-space.patch new file mode 100644 index 000000000000..bda76aa11c80 --- /dev/null +++ b/sci-chemistry/aria/files/aria-2.3.2-through-space.patch @@ -0,0 +1,118 @@ + src/py/aria/exportToCcpn.py | 24 +++++++++++------------- + src/py/aria/importFromCcpn.py | 25 +++++++------------------ + 2 files changed, 18 insertions(+), 31 deletions(-) + +diff --git a/src/py/aria/exportToCcpn.py b/src/py/aria/exportToCcpn.py +index c742a88..aae7b7d 100644 +--- a/src/py/aria/exportToCcpn.py ++++ b/src/py/aria/exportToCcpn.py +@@ -1,5 +1,5 @@ + from ccpnmr.analysis.core.ConstraintBasic import makeNmrConstraintStore, makeStructureGeneration, getFixedResonance +-from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims ++from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims, getThroughSpaceDataDims + from ccpnmr.analysis.core.AssignmentBasic import assignAtomsToRes, assignResToDim + from ccpnmr.analysis.core.PeakBasic import pickPeak, setManualPeakIntensity + from ccpnmr.analysis.core.MoleculeBasic import DEFAULT_ISOTOPES +@@ -791,12 +791,13 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None, + ariaDims = ariaDimDict.get(spectrum) + if not ariaDims: + ariaDims = [] #[0,1,2] ++ throughSpaceDataDims = getThroughSpaceDataDims(spectrum) + + dataDims = spectrum.sortedDataDims() + if len(dataDims) == 3: + for dataDim in dataDims: + expDimRef = dataDim.findFirstDataDimRef().expDimRef +- if '1H' in expDimRef.isotopeCodes: # 0 or 2 ++ if dataDim in throughSpaceDataDims: # 0 or 2 + if onebondDims.get(dataDim.dim): + if ppmX1 is None: + ariaDims.append(2) +@@ -816,21 +817,18 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None, + ariaDims.append(1) + + else: +- transfer = spectrum.experiment.findFirstExpTransfer(transferType='through-space') or \ +- spectrum.experiment.findFirstExpTransfer(transferType='NOESY') + ++ i = 0 + for dataDim in dataDims: +- expDimRefs = [dataDimRef.expDimRef for dataDimRef in dataDim.dataDimRefs] +- i = 0 +- for expDimRef in transfer.sortedExpDimRefs(): +- if expDimRef in expDimRefs: +- ariaDims.append(i) +- boundDim = onebondDims.get(dataDim.dim) +- if boundDim: +- ariaDims.append(i+1) +- ++ if dataDim in throughSpaceDataDims: ++ ariaDims.append(i) ++ boundDim = onebondDims.get(dataDim.dim) ++ if boundDim: ++ ariaDims.append(i+1) ++ + i += 2 + ++ + ariaDimDict[spectrum] = ariaDims + + if namesDict: +diff --git a/src/py/aria/importFromCcpn.py b/src/py/aria/importFromCcpn.py +index a65ae3e..91ad123 100644 +--- a/src/py/aria/importFromCcpn.py ++++ b/src/py/aria/importFromCcpn.py +@@ -196,19 +196,10 @@ def getNoesyPeakLists(project, molSystem=None): + + for spectrum in experiment.dataSources: + if (spectrum.dataType == 'processed') and (spectrum.numDim > 1): +- +- isotopes = [] +- for dataDim in spectrum.dataDims: +- for expDimRef in dataDim.expDim.expDimRefs: +- if expDimRef.measurementType in ('shift','Shift'): +- isotope = ','.join(expDimRef.isotopeCodes) +- isotopes.append(isotope) +- break +- +- if isotopes.count('1H') > 1: +- for peakList in spectrum.peakLists: +- if peakList.findFirstPeak(): +- peakLists.append(peakList) ++ for peakList in spectrum.sortedPeakLists(): ++ if excludeSimulated and peakList.isSimulated: ++ continue ++ peakLists.append(peakList) + + + return peakLists +@@ -952,8 +943,6 @@ def makeAriaSpectrum(peakList, ariaMolecule, filterRejected=True): + expDimRefDict = {} + + for expDimRef in transfer.sortedExpDimRefs(): +- if expDimRef.isotopeCodes != ('1H',): +- raise Exception('Not an H-H experiment') + + onebondTransfer = expDimRef.findFirstExpTransfer(transferType='onebond') + +@@ -1095,7 +1084,7 @@ def getAriaAtomsFromResonance(resonance, ariaMolecule, cache={}): + + # TJS modify to return just a list of atoms, rather than a list of list + ariaAtoms = [] +- for atom in atomSet.sortedAtoms(): ++ for atom in atomSet.atoms: + ariaAtom = ariaResidue.atoms.get(atom.name) + if not ariaAtom: + messager.warning('Could not find ARIA Atom for CCPN atom %d%s %s' % (residue.seqCode,residue.ccpCode, atom.name)) +@@ -1256,9 +1245,9 @@ def getAriaDistanceRestraintsList(constraint_list, constraint_type, aria_mol): + restraint.setWeight(weight) + + +- for constrItem in distConstr.sortedItems(): ++ for constrItem in distConstr.items: + +- reso1, reso2 = constrItem.sortedResonances() ++ reso1, reso2 = constrItem.resonances + + # TJS fix for mapping prochirals + # always use real resonnances where possible diff --git a/sci-chemistry/aria/metadata.xml b/sci-chemistry/aria/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/aria/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/arp-warp-bin/Manifest b/sci-chemistry/arp-warp-bin/Manifest new file mode 100644 index 000000000000..739b86dac839 --- /dev/null +++ b/sci-chemistry/arp-warp-bin/Manifest @@ -0,0 +1 @@ +DIST arp_warp_7.5.tar.gz 198643246 SHA256 d16fc6775905e56e5159f4a658f654b98d94f78143a2537ba67bffaed7ef1ad8 SHA512 351ed4bad863bac63005d128c693b7dde60c03ca5e8bd449ea602646f7f856c022070e542bcacae2793fbde88d67e7b5639bedeec55eeb191017a2ec19d03768 WHIRLPOOL d4ea42179a8a406508c82320567dc39ce419a2cba8b9e6ed05739dbbf0c9aba072b720c56987c4c94806ba2772f9c8787bde898f7c76543cc4702f00b7f16532 diff --git a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild new file mode 100644 index 000000000000..ef10d0ab3d5d --- /dev/null +++ b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils prefix + +MY_P="arp_warp_${PV}" + +DESCRIPTION="Improvement and interpretation of crystallographic electron density maps" +SRC_URI="${MY_P}.tar.gz" +HOMEPAGE="http://www.embl-hamburg.de/ARP/" + +LICENSE="ArpWarp" +SLOT="0" +KEYWORDS="-* amd64 x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_sse2" + +REQUIRED_USE="cpu_flags_x86_sse2" + +RDEPEND=" + app-shells/tcsh + sci-chemistry/refmac + virtual/awk + virtual/jre + virtual/opengl + x11-libs/libX11" +DEPEND="" + +RESTRICT="fetch" + +S="${WORKDIR}/${MY_P}" + +QA_PREBUILT="opt/arp-warp-bin/bin/*" + +pkg_nofetch(){ + elog "Fill out the form at http://www.embl-hamburg.de/ARP/" + elog "and place ${A} in ${DISTDIR}" +} + +src_prepare() { + epatch "${FILESDIR}"/7.3-setup.patch + eprefixify "${S}"/share/arpwarp_setup_base.* + + sed -e '/exit/d' -i "${S}"/share/arpwarp_setup_base.* || die +} + +src_install(){ + m_type=$(uname -m) + os_type=$(uname) + + exeinto /opt/${PN}/bin/bin-${m_type}-${os_type} + doexe "${S}"/bin/bin-${m_type}-${os_type}/* "${S}"/share/*{pl,sh} + + insinto /opt/${PN}/bin/bin-${m_type}-${os_type} + doins "${S}"/share/*{gif,bmp,XYZ,bash,csh,dat,lib,tbl,llh,prm} + + insinto /etc/profile.d/ + newins "${S}"/share/arpwarp_setup_base.csh 90arpwarp_setup.csh + newins "${S}"/share/arpwarp_setup_base.bash 90arpwarp_setup.sh + + dodoc "${S}"/README manual/UserGuide${PV}.pdf + dohtml -r "${S}"/manual/html/* +} + +pkg_postinst(){ + testcommand=$(echo 3 2 | awk '{printf"%3.1f",$1/$2}') + if [ $testcommand == "1,5" ];then + ewarn "*** ERROR ***" + ewarn " 3/2=" $testcommand + ewarn "Invalid decimal separator (must be ".")" + ewarn "You need to set this correctly!!!" + echo + ewarn "One way of setting the decimal separator is:" + ewarn "setenv LC_NUMERIC C' in your .cshrc file" + ewarn "\tor" + ewarn "export LC_NUMERIC=C' in your .bashrc file" + ewarn "Otherwise please consult your system manager" + fi +} diff --git a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch b/sci-chemistry/arp-warp-bin/files/7.3-setup.patch new file mode 100644 index 000000000000..faed9c1102fd --- /dev/null +++ b/sci-chemistry/arp-warp-bin/files/7.3-setup.patch @@ -0,0 +1,30 @@ +diff --git a/share/arpwarp_setup_base.bash b/share/arpwarp_setup_base.bash +index 29e769c..0b8a51e 100644 +--- a/share/arpwarp_setup_base.bash ++++ b/share/arpwarp_setup_base.bash +@@ -13,10 +13,10 @@ else + identifier=${nameprocessor}'-'${namesystem} + fi + # +-arpwarphome="$1X" ++arpwarphome="@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin" + # + export warpbin=${arpwarphome}/bin/bin-${identifier} +-export warpdoc=${arpwarphome}/manual ++export warpdoc=@GENTOO_PORTAGE_EPREFIX@/usr/share/doc/arp-warp-bin-7.1/html/ + export PATH=${warpbin}:${PATH} + # + # Checks for existence of $warpbin directory +diff --git a/share/arpwarp_setup_base.csh b/share/arpwarp_setup_base.csh +index 41b11e9..a4edcff 100644 +--- a/share/arpwarp_setup_base.csh ++++ b/share/arpwarp_setup_base.csh +@@ -13,7 +13,7 @@ else + set identifier = ${nameprocessor}'-'${namesystem} + endif + # +-set arpwarphome = '$1X' ++set arpwarphome = '@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin' + # + setenv warpbin ${arpwarphome}/bin/bin-${identifier} + # diff --git a/sci-chemistry/arp-warp-bin/metadata.xml b/sci-chemistry/arp-warp-bin/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/arp-warp-bin/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest new file mode 100644 index 000000000000..422cb216787f --- /dev/null +++ b/sci-chemistry/autodock/Manifest @@ -0,0 +1 @@ +DIST autodocksuite-4.2.6-src.tar.gz 35438010 SHA256 4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4 SHA512 75b8878f948c4f6bc28adb442997192dad0c36bbede2fd698623903cb27b06b4df3ba038bfc70fc13b4bdee864fd2344f0f7208be2020da4e01a00b842b46bbb WHIRLPOOL 18230783d13c2d82ad6427711a48dec0c6695301a52dcf419cf4feefb0b5f41bac5de53824313e75d9040ac8623915ba266e764e92ecad9869d845053ec60b93 diff --git a/sci-chemistry/autodock/autodock-4.2.6.ebuild b/sci-chemistry/autodock/autodock-4.2.6.ebuild new file mode 100644 index 000000000000..10d018292e93 --- /dev/null +++ b/sci-chemistry/autodock/autodock-4.2.6.ebuild @@ -0,0 +1,102 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools eutils python-any-r1 versionator + +MY_PN="autodocksuite" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="A suite of automated docking tools" +HOMEPAGE="http://autodock.scripps.edu/" +SRC_URI="http://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(delete_all_version_separators)/${MY_P}-src.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples openmp test" + +RDEPEND="" +DEPEND="test? ( ${PYTHON_DEPS} )" + +S="${WORKDIR}/src" + +PATCHES=( + "${FILESDIR}"/${P}-buildsystem.patch +) + +src_prepare() { + local i + + epatch ${PATCHES[@]} + + sed \ + -e "s/\tcsh/\tsh/" \ + -i auto{dock,grid}/Makefile.am || die + for i in autodock autogrid; do + pushd $i &>/dev/null + eautoreconf + popd &>/dev/null + done +} + +src_configure() { + local i + for i in autodock autogrid; do + pushd $i &>/dev/null + econf $(use_enable openmp) + popd &>/dev/null + done +} + +src_compile() { + emake -C autodock + emake -C autogrid +} + +src_test() { + elog "Testing autodock" + cd "${S}/autodock/Tests" || die + cp ../*.dat . || die + ${EPYTHON} test_autodock4.py || die "AutoDock tests failed." + einfo "Testing autogrid" + cd "${S}/autogrid/Tests" || die + ${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed." +} + +src_install() { + if use openmp; then + newbin autodock/autodock4.omp ${PN}4 + dobin autogrid/autogrid4 + else + dobin autodock/autodock4 autogrid/autogrid4 + fi + + insinto /usr/share/${PN} + doins -r \ + autodock/{AD4_parameters.dat,AD4_PARM99.dat} \ + $(usex examples "autodoc/EXAMPLES" "") + + DOCS=( + RELEASENOTES + autodock/{AUTHORS,README} + autodock/USERGUIDES/AutoDock4.{0,1,2}_UserGuide.doc + autodock/USERGUIDES/AutoDock4.2_UserGuide.pdf + ) + einstalldocs +} + +pkg_postinst() { + elog "The AutoDock development team requests all users to fill out the" + elog "registration form at:" + echo + elog "\thttp://autodock.scripps.edu/downloads/autodock-registration" + echo + elog "The number of unique users of AutoDock is used by Prof. Arthur J." + elog "Olson and the Scripps Research Institude to support grant" + elog "applications." +} diff --git a/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch b/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch new file mode 100644 index 000000000000..b9eb3c409c64 --- /dev/null +++ b/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch @@ -0,0 +1,10 @@ +--- autodocksuite-4.0.1.orig/src/autogrid/check_size.cpp 2008-08-04 22:44:46.000000000 -0700 ++++ autodocksuite-4.0.1/src/autogrid/check_size.cpp 2008-08-04 22:45:12.000000000 -0700 +@@ -27,6 +27,7 @@ + + #include <iostream> + #include <math.h> ++#include <cstdlib> + #include "autogrid.h" + + diff --git a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch new file mode 100644 index 000000000000..ae44ffeb3159 --- /dev/null +++ b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch @@ -0,0 +1,44 @@ + src/autodock/Makefile.am | 6 +++--- + src/autogrid/Makefile.am | 4 ++-- + 2 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/src/autodock/Makefile.am b/src/autodock/Makefile.am +index 799a3c4..911897b 100644 +--- a/src/autodock/Makefile.am ++++ b/src/autodock/Makefile.am +@@ -459,7 +459,8 @@ endif + + BUILT_SOURCES = $(autodock4_SOURCES) default_parameters.h + +-AM_CXXFLAGS = -O3 # Agressive optimization ++AM_CXXFLAGS = ++#AM_CXXFLAGS = -O3 # Agressive optimization + #AM_CXXFLAGS = -g # debug + + # if gnu c++ compiler +@@ -488,8 +489,7 @@ endif + AM_CPPFLAGS = -DNOSQRT \ + -DUSE_DOUBLE \ + -DUSE_8A_NBCUTOFF \ +- -DUSE_INT_AS_FOURBYTELONG \ +- -O3 ++ -DUSE_INT_AS_FOURBYTELONG + # AM_LDFLAGS = -g # -g is MP debug + + +diff --git a/src/autogrid/Makefile.am b/src/autogrid/Makefile.am +index b531099..b78b380 100644 +--- a/src/autogrid/Makefile.am ++++ b/src/autogrid/Makefile.am +@@ -94,9 +94,9 @@ autogrid4_SOURCES = main.cpp \ + BUILT_SOURCES = default_parameters.h + + +-AM_CFLAGS = -Wall -O3 # All warnings, Agressive optimization ++AM_CFLAGS = -Wall # All warnings, Agressive optimization + +-AM_CPPFLAGS = -Wall -O3 -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization ++AM_CPPFLAGS = -Wall -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization + AM_CPPFLAGS += -Wno-write-strings # increase compatibility with pre 4.x compilers for string handling + # M Pique - add USE_8A_NBCUTOFF + AM_CPPFLAGS += -DUSE_8A_NBCUTOFF diff --git a/sci-chemistry/autodock/metadata.xml b/sci-chemistry/autodock/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/autodock/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest new file mode 100644 index 000000000000..a2f7882e9d79 --- /dev/null +++ b/sci-chemistry/autodock_vina/Manifest @@ -0,0 +1 @@ +DIST autodock_vina_1_1_2.tgz 67366 SHA256 b86412d316960b1e4e319401719daf57ff009229d91654d623c3cf09339f6776 SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9 WHIRLPOOL b68f3bb81fe957fddb6674f71e0c63d1425eb5b4de0615258545ba8e241b347380c8745ee47bd2ee2257f29916191773440e3dd4e9ce857b83a947074eae8d45 diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild new file mode 100644 index 000000000000..aea218f8faf9 --- /dev/null +++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils flag-o-matic versionator + +MY_P="${PN}_$(replace_all_version_separators _)" + +DESCRIPTION="Program for drug discovery, molecular docking and virtual screening" +HOMEPAGE="http://vina.scripps.edu/" +SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz" + +SLOT="0" +KEYWORDS="amd64 x86" +LICENSE="Apache-2.0" +IUSE="debug" + +RDEPEND="dev-libs/boost" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_P}/build/linux/release + +src_prepare() { + cd "${WORKDIR}"/${MY_P} || die + epatch \ + "${FILESDIR}"/${PV}-gentoo.patch \ + "${FILESDIR}"/${P}-boost-filesystem.patch +} + +src_compile() { + local c_options + + use debug || c_options="-DNDEBUG" + + append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 + + emake \ + BASE="${EPREFIX}"/usr/ \ + GPP="$(tc-getCXX)" \ + C_OPTIONS="${c_options}" +} + +src_install() { + dobin vina{,_split} +} diff --git a/sci-chemistry/autodock_vina/files/1.1.1-gentoo.patch b/sci-chemistry/autodock_vina/files/1.1.1-gentoo.patch new file mode 100644 index 000000000000..356ae2ee547d --- /dev/null +++ b/sci-chemistry/autodock_vina/files/1.1.1-gentoo.patch @@ -0,0 +1,68 @@ +diff --git a/build/linux/debug/Makefile b/build/linux/debug/Makefile +index d2c2d3b..d1f02e5 100644 +--- a/build/linux/debug/Makefile ++++ b/build/linux/debug/Makefile +@@ -1,6 +1,6 @@ + BASE=/usr/local + BOOST_VERSION=1_41 +-C_PLATFORM=-static-libgcc -pthread ++C_PLATFORM=-pthread + GPP=/usr/bin/g++ + C_OPTIONS= -g + BOOST_LIB_VERSION= +diff --git a/build/linux/release/Makefile b/build/linux/release/Makefile +index bfbcc1e..c9fd630 100644 +--- a/build/linux/release/Makefile ++++ b/build/linux/release/Makefile +@@ -1,6 +1,6 @@ + BASE=/usr/local + BOOST_VERSION=1_41 +-C_PLATFORM=-static-libgcc -pthread ++C_PLATFORM=-pthread + GPP=/usr/bin/g++ + C_OPTIONS= -O3 -DNDEBUG + BOOST_LIB_VERSION= +diff --git a/build/makefile_common b/build/makefile_common +index 885935c..e72142d 100644 +--- a/build/makefile_common ++++ b/build/makefile_common +@@ -1,30 +1,30 @@ +-BOOST_INCLUDE = $(BASE)/include/boost-${BOOST_VERSION} ++BOOST_INCLUDE = $(BASE)/include/boost + + LIBOBJ = cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manifold.o model.o monte_carlo.o mutate.o my_pid.o naive_non_cache.o non_cache.o parallel_mc.o parse_pdbqt.o pdb.o quasi_newton.o quaternion.o random.o ssd.o terms.o weighted_terms.o + MAINOBJ = main.o + SPLITOBJ = split.o + +-INCFLAGS = -I $(BOOST_INCLUDE) ++INCFLAGS = -I$(BOOST_INCLUDE) + +-CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS) ++CC = ${GPP} ${C_PLATFORM} ${C_OPTIONS} $(INCFLAGS) + +-LDFLAGS = -L$(BASE)/lib -L. ++LDFLAGS += -L. + +-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread ++LIBS = -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem -lboost_program_options -lpthread + + .SUFFIXES: .cpp .o + + %.o : ../../../src/lib/%.cpp +- $(CC) $(CFLAGS) -o $@ -c $< ++ $(CC) $(CXXFLAGS) -o $@ -c $< + + %.o : ../../../src/design/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + %.o : ../../../src/main/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + %.o : ../../../src/split/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + all: vina vina_split + diff --git a/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch new file mode 100644 index 000000000000..61ae8bec36f5 --- /dev/null +++ b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch @@ -0,0 +1,72 @@ + build/linux/debug/Makefile | 2 +- + build/linux/release/Makefile | 2 +- + build/makefile_common | 14 +++++++------- + 3 files changed, 9 insertions(+), 9 deletions(-) + +diff --git a/build/linux/debug/Makefile b/build/linux/debug/Makefile +index 6a41cfc..8097fb9 100644 +--- a/build/linux/debug/Makefile ++++ b/build/linux/debug/Makefile +@@ -1,7 +1,7 @@ + BASE=/usr/local + BOOST_VERSION=1_41 + BOOST_INCLUDE = $(BASE)/include +-C_PLATFORM=-static -pthread ++C_PLATFORM=-pthread + GPP=/usr/local/bin/g++ + C_OPTIONS= -g + BOOST_LIB_VERSION= +diff --git a/build/linux/release/Makefile b/build/linux/release/Makefile +index 1de1063..ded8133 100644 +--- a/build/linux/release/Makefile ++++ b/build/linux/release/Makefile +@@ -1,7 +1,7 @@ + BASE=/usr/local + BOOST_VERSION=1_41 + BOOST_INCLUDE = $(BASE)/include +-C_PLATFORM=-static -pthread ++C_PLATFORM=-pthread + GPP=/usr/local/bin/g++ + C_OPTIONS= -O3 -DNDEBUG + BOOST_LIB_VERSION= +diff --git a/build/makefile_common b/build/makefile_common +index a940329..96336e8 100644 +--- a/build/makefile_common ++++ b/build/makefile_common +@@ -2,29 +2,29 @@ LIBOBJ = cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manif + MAINOBJ = main.o + SPLITOBJ = split.o + +-INCFLAGS = -I $(BOOST_INCLUDE) ++INCFLAGS = -I$(BOOST_INCLUDE) + + # -pedantic fails on Mac with Boost 1.41 (syntax problems in their headers) + #CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS) + CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS) + +-LDFLAGS = -L$(BASE)/lib -L. ++LDFLAGS += -L. + +-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread ++LIBS = -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem -lboost_program_options -lpthread + + .SUFFIXES: .cpp .o + + %.o : ../../../src/lib/%.cpp +- $(CC) $(CFLAGS) -o $@ -c $< ++ $(CC) $(CXXFLAGS) -o $@ -c $< + + %.o : ../../../src/design/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + %.o : ../../../src/main/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + %.o : ../../../src/split/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + all: vina vina_split + diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch new file mode 100644 index 000000000000..298aaa9ab993 --- /dev/null +++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch @@ -0,0 +1,79 @@ + src/main/main.cpp | 10 +++++++++- + src/split/split.cpp | 11 ++++++++++- + 2 files changed, 19 insertions(+), 2 deletions(-) + +diff --git a/src/main/main.cpp b/src/main/main.cpp +index f49c8f5..b566aa2 100644 +--- a/src/main/main.cpp ++++ b/src/main/main.cpp +@@ -47,7 +47,7 @@ + using boost::filesystem::path;
+
+ path make_path(const std::string& str) {
+- return path(str, boost::filesystem::native);
++ return path(str);
+ }
+
+ void doing(int verbosity, const std::string& str, tee& log) {
+@@ -661,7 +661,11 @@ Thank you!\n"; + cpu, seed, verbosity, max_modes_sz, energy_range, log);
+ }
+ catch(file_error& e) {
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#else
+ std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#endif
+ return 1;
+ }
+ catch(boost::filesystem::filesystem_error& e) {
+@@ -673,7 +677,11 @@ Thank you!\n"; + return 1;
+ }
+ catch(parse_error& e) {
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n';
++#else
+ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++#endif
+ return 1;
+ }
+ catch(std::bad_alloc&) {
+diff --git a/src/split/split.cpp b/src/split/split.cpp +index 54c614b..bc5530e 100644 +--- a/src/split/split.cpp ++++ b/src/split/split.cpp +@@ -38,7 +38,7 @@ + using boost::filesystem::path;
+
+ path make_path(const std::string& str) {
+- return path(str, boost::filesystem::native);
++ return path(str);
+ }
+
+ std::string default_prefix(const std::string& input_name, const std::string& add) {
+@@ -208,7 +208,12 @@ Thank you!\n"; + write_multimodel_pdbqt(tmp, ligand_prefix, flex_prefix);
+ }
+ catch(file_error& e) {
++
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#else
+ std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#endif
+ return 1;
+ }
+ catch(boost::filesystem::filesystem_error& e) {
+@@ -220,7 +225,11 @@ Thank you!\n"; + return 1;
+ }
+ catch(parse_error& e) {
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n';
++#else
+ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++#endif
+ return 1;
+ }
+ catch(std::bad_alloc&) {
diff --git a/sci-chemistry/autodock_vina/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml new file mode 100644 index 000000000000..3f44e973345a --- /dev/null +++ b/sci-chemistry/autodock_vina/metadata.xml @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +AutoDock Vina is a new open-source program for drug discovery, molecular +docking and virtual screening, offering multi-core capability, high +performance and enhanced accuracy and ease of use. [1] +AutoDock Vina has been designed and implemented by Dr. Oleg Trott +in the Molecular Graphics Lab at The Scripps Research Institute. +If you used AutoDock Vina in your work, please cite: +O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy +of docking with a new scoring function, efficient optimization and +multithreading +Journal of Computational Chemistry 31 (2010) 455-461 +</longdescription> + <!-- +<use> + <flag name='flag'>Description of how USE='flag' affects this package</flag> + <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this + package</flag> + <flag name='aspell'>Uses <pkg>app-text/aspell</pkg> for spell checking. + Requires an installed dictionary from <cat>app-dicts</cat></flag> +</use> +--> +</pkgmetadata> diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest new file mode 100644 index 000000000000..aad0cb8f1ba9 --- /dev/null +++ b/sci-chemistry/avogadro/Manifest @@ -0,0 +1,2 @@ +DIST avogadro-1.0.3.tar.bz2 4971989 SHA256 efb6fda223da3c027436f0c218a47ce804f7469c58b41134230e9ebad1c98468 SHA512 49e7b8ca43f0f52a65efc7bf9dc45670ae5a5de5d1aa6bf7b58b8368e816be30fe6529c45fa658d7337d4a69327bb0aa8799d8d4b4805860aace28011cc74210 WHIRLPOOL c835ac24b317a1fa310bf3ea75bae4002d01f364d4754e6a7d841594dcce321435c827d60e125d9410f05670a94c887cc250bf49759d02cde34a5839d2324c92 +DIST avogadro-1.1.0.tar.bz2 10741835 SHA256 6b4eaf57ae52bf43df9b103c77e6abae71e067053d5c99f82acbce9855ecceb0 SHA512 d621dd3ea9e9223d3a29c6b0c0eec89a935837d0c587fcaaa549f91274a76f78a8c60c2a68a67d2f3aa2e107826befb6658be601c46c5bc0760c95bf7284540a WHIRLPOOL c81e866e60b3383a58de515317c754e3982e716c27974ce43ca0c1209d24544949361a7f2f93a4a940d73fd7a18b184f68c7a1856fea89ae5eba75db74b1012d diff --git a/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild b/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild new file mode 100644 index 000000000000..ae73ee50ac4e --- /dev/null +++ b/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils eutils python-single-r1 + +DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" +HOMEPAGE="http://avogadro.openmolecules.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~ppc ~x86" +IUSE="+glsl python cpu_flags_x86_sse2" + +RDEPEND=" + >=sci-chemistry/openbabel-2.2.3 + >=dev-qt/qtgui-4.5.3:4 + >=dev-qt/qtopengl-4.5.3:4 + x11-libs/gl2ps + glsl? ( >=media-libs/glew-1.5.0 ) + python? ( + >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND} + dev-cpp/eigen:2" + +PATCHES=( + "${FILESDIR}"/1.0.1-gl2ps.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DENABLE_THREADGL=OFF + -DENABLE_RPATH=OFF + -DENABLE_UPDATE_CHECKER=OFF + -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs" + -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs + $(cmake-utils_use_enable glsl) + $(cmake-utils_use_with cpu_flags_x86_sse2 SSE2) + $(cmake-utils_use_enable python) + ) + + cmake-utils_src_configure +} diff --git a/sci-chemistry/avogadro/avogadro-1.1.0.ebuild b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild new file mode 100644 index 000000000000..0de1b83085b6 --- /dev/null +++ b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils eutils python-single-r1 + +DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" +HOMEPAGE="http://avogadro.openmolecules.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86" +IUSE="+glsl python cpu_flags_x86_sse2 test" + +RDEPEND=" + >=sci-chemistry/openbabel-2.3.0 + >=dev-qt/qtgui-4.5.3:4 + >=dev-qt/qtopengl-4.5.3:4 + x11-libs/gl2ps + glsl? ( >=media-libs/glew-1.5.0 ) + python? ( + >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND} + dev-cpp/eigen:2" + +# https://sourceforge.net/p/avogadro/bugs/653/ +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/${P}-textrel.patch + "${FILESDIR}"/${P}-xlibs.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DENABLE_THREADGL=OFF + -DENABLE_RPATH=OFF + -DENABLE_UPDATE_CHECKER=OFF + -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs" + -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs + $(cmake-utils_use_enable glsl) + $(cmake-utils_use_enable test TESTS) + $(cmake-utils_use_with cpu_flags_x86_sse2 SSE2) + $(cmake-utils_use_enable python) + ) + + cmake-utils_src_configure +} diff --git a/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch new file mode 100644 index 000000000000..d8a0c0f758e1 --- /dev/null +++ b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch @@ -0,0 +1,39 @@ +diff --git a/avogadro/src/CMakeLists.txt b/avogadro/src/CMakeLists.txt +index 75b6dfb..d87ac2c 100644 +--- a/avogadro/src/CMakeLists.txt ++++ b/avogadro/src/CMakeLists.txt +@@ -45,7 +45,7 @@ endif(ENABLE_UPDATE_CHECKER) + FILE(GLOB projectDelegates_SRCS "projectdelegates/*.cpp") + set(avogadro_SRCS ${avogadro_SRCS} ${projectDelegates_SRCS}) + # Add GL2PS to the executable +-set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c") ++#set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c") + + if( WIN32 ) + set(avogadro_SRCS ${avogadro_SRCS} windows/avogadro.rc) +diff --git a/avogadro/src/mainwindow.cpp b/avogadro/src/mainwindow.cpp +index 66785fd..2933953 100644 +--- a/avogadro/src/mainwindow.cpp ++++ b/avogadro/src/mainwindow.cpp +@@ -51,7 +51,7 @@ + //#endif + + // Include the GL2PS header +-#include "../gl2ps/gl2ps.h" ++#include <gl2ps.h> + + #include <avogadro/pluginmanager.h> + +diff --git a/libavogadro/src/CMakeLists.txt b/libavogadro/src/CMakeLists.txt +index cce8ece..cc084fb 100644 +--- a/libavogadro/src/CMakeLists.txt ++++ b/libavogadro/src/CMakeLists.txt +@@ -152,7 +152,7 @@ endforeach(headerFile ${libavogadro_HDRS}) + add_library(avogadro SHARED ${libavogadro_SRCS} ${libavogadro_QM} ${pythontool_RC_SRCS}) + set_target_properties(avogadro + PROPERTIES VERSION ${Avogadro_VERSION_FULL} SOVERSION 1 ) +-target_link_libraries(avogadro ${AVO_LINK_LIBRARIES}) ++target_link_libraries(avogadro ${AVO_LINK_LIBRARIES} gl2ps) + + install(TARGETS avogadro DESTINATION ${LIB_INSTALL_DIR}) + install(FILES ${libavogadro_HDRS} diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch new file mode 100644 index 000000000000..6d4536ef7c9b --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch @@ -0,0 +1,29 @@ + libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt | 2 +- + libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt +index fb88316..2ddcfdf 100644 +--- a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt ++++ b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt +@@ -20,6 +20,6 @@ add_library(spglib STATIC ${spglib_SRCS}) + set_target_properties(spglib PROPERTIES COMPILE_FLAGS "-w") + + # Set -fPIC on x86_64 +-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") ++if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" ) + endif() +diff --git a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt +index 0cd0c3e..9e89daf 100644 +--- a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt ++++ b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt +@@ -19,7 +19,7 @@ add_library(tubegen STATIC ${tubegen_SRCS}) + set_target_properties(tubegen PROPERTIES COMPILE_FLAGS "-w") + + # Set -fPIC on x86_64 +-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") ++if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" ) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC" ) + endif() diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch new file mode 100644 index 000000000000..74a5889ec8ae --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch @@ -0,0 +1,16 @@ + * Info: Using [gentoo] (https://bugs.gentoo.org/xmlrpc.cgi) + * Info: Getting attachment 403034 + * Info: Viewing attachment: "X11.patch" +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 60ec98f..03443a7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -225,6 +225,7 @@ set(I18N_LANGUAGE "" CACHE STRING "Build i18n only for selected language") + + find_package(Qt4 4.6.0 REQUIRED) # find and setup Qt4 for this project + find_package(OpenGL REQUIRED) # find and setup OpenGL ++find_package(X11 REQUIRED) + find_package(Linguist) # find and setup Linguist + if(NOT Linguist_FOUND) + message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations") + diff --git a/sci-chemistry/avogadro/metadata.xml b/sci-chemistry/avogadro/metadata.xml new file mode 100644 index 000000000000..bacd1480b120 --- /dev/null +++ b/sci-chemistry/avogadro/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> + Avogadro is an advanced molecular editor designed for cross-platform use in + computational chemistry, molecular modeling, bioinformatics, materials + science, and related areas. It offers flexible rendering and a powerful + plugin architecture. + </longdescription> + <use> + <flag name="glsl">Enable glsl features via GLEW.</flag> + </use> + <upstream> + <remote-id type="sourceforge">avogadro</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/azara/Manifest b/sci-chemistry/azara/Manifest new file mode 100644 index 000000000000..700d6abb6ece --- /dev/null +++ b/sci-chemistry/azara/Manifest @@ -0,0 +1 @@ +DIST azara-2.8-src.tgz 638120 SHA256 1f9b86d368ca3b4818c88490c40b2055c7a6d1732e746e4c117e045a73269a98 SHA512 61a913b041f8ed7dade9d452ca0d99804ffcea0c678f23ad8357c1e7188996eecde9402201399306fcb32a504b17c3d61997f50ce57794f876c9f8d492ca500c WHIRLPOOL b7512fe29ad97830d2f96811e71c2ab74e9e71c62354f65a499484a1a57fbe8b74a8ecd27a0b72c48cf0ec5bb48c78148433e32f4f2a880c6317d516f3aa644a diff --git a/sci-chemistry/azara/azara-2.8-r4.ebuild b/sci-chemistry/azara/azara-2.8-r4.ebuild new file mode 100644 index 000000000000..2b5f3bd6f0b8 --- /dev/null +++ b/sci-chemistry/azara/azara-2.8-r4.ebuild @@ -0,0 +1,98 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="python? 2" +SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.* *-jython 2.7-pypy-*" + +inherit eutils python toolchain-funcs + +DESCRIPTION="A suite of programmes to process and view NMR data" +HOMEPAGE="http://www.bio.cam.ac.uk/azara/" +SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${PN}/${P}-src.tgz" + +LICENSE="AZARA" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="python xpm X" + +RDEPEND=" + x11-libs/libX11 + x11-libs/motif:0 + xpm? ( x11-libs/libXpm )" +DEPEND="${RDEPEND}" + +src_prepare() { + cat > ENVIRONMENT <<- EOF + CC=$(tc-getCC) + CFLAGS = ${CFLAGS} + LFLAGS = ${LDFLAGS} + MATH_LIB = -lm + X11_INCLUDE_DIR = -I"${EPREFIX}/usr/X11R6/include" + MOTIF_INCLUDE_DIR = -I"${EPREFIX}/usr/include" -I../global + X11_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)" + MOTIF_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)" + X11_LIB = -lX11 + MOTIF_LIB = -lXm -lXt + SHARED_FLAGS = -shared + ENDIAN_FLAG = -DBIG_ENDIAN_DATA -DWRITE_ENDIAN_PAR + PIC = -fPIC + EOF + + use xpm && echo "XPMUSE=\"XPM_FLAG=-DUSE_XPM XPM_LIB=-lXpm\"" >> ENVIRONMENT + + epatch \ + "${FILESDIR}"/${PV}-prll.patch \ + "${FILESDIR}"/${PV}-impl-dec.patch \ + "${FILESDIR}"/${PV}-python.patch \ + "${FILESDIR}"/${PV}-64bit.patch +} + +src_compile() { + local mymake + local makeflags + + mymake="${mymake} help nongui" + use X && mymake="${mymake} gui" + + emake ${mymake} || die + + compilation() { + emake DataRows_clean || die + emake \ + PYTHON_INCLUDE_DIR="-I${EPREFIX}/$(python_get_includedir)" \ + PYTHON_LIB="$(python_get_library -l)" \ + DataRows || die + } + use python && python_execute_function compilation +} + +src_install() { + rm bin/pythonAzara || die + if ! use X; then + rm bin/plot* || die + fi + + dodoc CHANGES* README* || die + dohtml -r html/* || die + + installation() { + insinto $(python_get_sitedir) + doins lib/DataRows.so || die + } + use python && python_execute_function installation + + cd bin + dobin ${PN}|| die + rm ${PN} + for bin in *; do + newbin ${bin} ${bin}-${PN} || die "failed to install ${bin}" + done +} + +pkg_postinst() { + einfo "Due to collision we moved all binary to *-${PN}" +} diff --git a/sci-chemistry/azara/azara-2.8-r5.ebuild b/sci-chemistry/azara/azara-2.8-r5.ebuild new file mode 100644 index 000000000000..4b90f2ccbd2b --- /dev/null +++ b/sci-chemistry/azara/azara-2.8-r5.ebuild @@ -0,0 +1,99 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 toolchain-funcs + +DESCRIPTION="A suite of programmes to process and view NMR data" +HOMEPAGE="http://www.bio.cam.ac.uk/azara/" +SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${PN}/${P}-src.tgz" + +LICENSE="AZARA" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="xpm X" + +RDEPEND=" + x11-libs/libX11 + x11-libs/motif:0 + xpm? ( x11-libs/libXpm )" +DEPEND="${RDEPEND}" + +src_prepare() { + cat > ENVIRONMENT <<- EOF + CC=$(tc-getCC) + CFLAGS = ${CFLAGS} + LFLAGS = ${LDFLAGS} + MATH_LIB = -lm + X11_INCLUDE_DIR = -I"${EPREFIX}/usr/X11R6/include" + MOTIF_INCLUDE_DIR = -I"${EPREFIX}/usr/include" -I../global + X11_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)" + MOTIF_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)" + X11_LIB = -lX11 + MOTIF_LIB = -lXm -lXt + SHARED_FLAGS = -shared + ENDIAN_FLAG = -DBIG_ENDIAN_DATA -DWRITE_ENDIAN_PAR + PIC = -fPIC + EOF + + use xpm && echo "XPMUSE=\"XPM_FLAG=-DUSE_XPM XPM_LIB=-lXpm\"" >> ENVIRONMENT + + epatch \ + "${FILESDIR}"/${PV}-prll.patch \ + "${FILESDIR}"/${PV}-impl-dec.patch \ + "${FILESDIR}"/${PV}-python.patch \ + "${FILESDIR}"/${PV}-64bit.patch +} + +src_compile() { + local mymake + local makeflags + + mymake="${mymake} help nongui" + use X && mymake="${mymake} gui" + + emake ${mymake} + + compilation() { + python_export PYTHON_CFLAGS PYTHON_LIBS + cd "${BUILD_DIR}" || die + emake DataRows_clean + emake \ + PYTHON_INCLUDE_DIR="${PYTHON_CFLAGS}" \ + PYTHON_LIB="${PYTHON_LIBS}" \ + DataRows + } + python_copy_sources + python_foreach_impl compilation +} + +src_install() { + rm bin/pythonAzara || die + if ! use X; then + rm bin/plot* || die + fi + + dodoc CHANGES* README* + dohtml -r html/* + + cd bin || die + dobin ${PN} + rm ${PN} || die + for bin in *; do + newbin ${bin} ${bin}-${PN} + done + + installation() { + cd "${BUILD_DIR}" || die + python_domodule lib/DataRows.so + } + python_foreach_impl installation +} + +pkg_postinst() { + einfo "Due to collision we moved all binary to *-${PN}" +} diff --git a/sci-chemistry/azara/files/2.8-64bit.patch b/sci-chemistry/azara/files/2.8-64bit.patch new file mode 100644 index 000000000000..c65e075c1d30 --- /dev/null +++ b/sci-chemistry/azara/files/2.8-64bit.patch @@ -0,0 +1,85 @@ +diff --git a/global/par.c b/global/par.c +index ac87c88..fecfe35 100644 +--- a/global/par.c ++++ b/global/par.c +@@ -562,9 +562,9 @@ static Status get_varian_header(FILE *fp, String error_msg) + return OK; + } + +-static long get_varian_long(int offset) ++static int get_varian_int(int offset) + { +- long x; ++ int x; + + if (swapped) + { +@@ -572,7 +572,7 @@ static long get_varian_long(int offset) + SWAP(varian_header[offset+1], varian_header[offset+2], char); + } + +- x = *((long *) (varian_header + offset)); ++ x = *((int *) (varian_header + offset)); + + return x; + } +@@ -591,7 +591,7 @@ static short get_varian_short(int offset) + + static Status check_varian_header(String error_msg) + { +- long nblocks, ntraces, np, ebytes, tbytes, /*bbytes,*/ d; ++ int nblocks, ntraces, np, ebytes, tbytes, /*bbytes,*/ d; + short status; + FILE *fp; + +@@ -605,17 +605,19 @@ static Status check_varian_header(String error_msg) + FCLOSE(fp); + + /* numbers in parentheses are offsets into header */ +- nblocks = get_varian_long(0); /* number of blocks in file */ +- ntraces = get_varian_long(4); /* number of traces per block */ +- np = get_varian_long(8); /* number of elements per trace */ +- ebytes = get_varian_long(12); /* number of bytes per element */ +- tbytes = get_varian_long(16); /* number of bytes per trace */ +- /*bbytes = get_varian_long(20);*/ /* number of bytes per block */ ++ nblocks = get_varian_int(0); /* number of blocks in file */ ++ printf("nblocks = %d\n", nblocks); ++ ntraces = get_varian_int(4); /* number of traces per block */ ++ printf("ntraces = %d\n", ntraces); ++ np = get_varian_int(8); /* number of elements per trace */ ++ ebytes = get_varian_int(12); /* number of bytes per element */ ++ tbytes = get_varian_int(16); /* number of bytes per trace */ ++ /*bbytes = get_varian_int(20);*/ /* number of bytes per block */ + /* short starting at 24 is software version */ + status = get_varian_short(26); /* status of whole file */ + /* long starting at 28 is number of block headers */ + +- if (ntraces != 1L) ++ if (ntraces != 1) + RETURN_ERROR_MSG("can only process Varian data with #traces = 1"); + + if (np != npoints[0]) +@@ -646,12 +648,12 @@ static Status check_varian_header(String error_msg) + + if (integer) + { +- if (ebytes == 2L) ++ if (ebytes == 2) + { + if (status & (1<<2)) + RETURN_ERROR_MSG("Varian header has inconsistent byte information"); + } +- else if (ebytes == 4L) ++ else if (ebytes == 4) + { + if (!(status & (1<<2))) + RETURN_ERROR_MSG("Varian header has inconsistent byte information"); +@@ -666,7 +668,7 @@ static Status check_varian_header(String error_msg) + } + else /* !integer, i.e. floating point */ + { +- if (ebytes != 4L) ++ if (ebytes != 4) + RETURN_ERROR_MSG("Varian header has inconsistent byte information"); + } + diff --git a/sci-chemistry/azara/files/2.8-impl-dec.patch b/sci-chemistry/azara/files/2.8-impl-dec.patch new file mode 100644 index 000000000000..62e8c7d6873b --- /dev/null +++ b/sci-chemistry/azara/files/2.8-impl-dec.patch @@ -0,0 +1,226 @@ +diff --git a/DataRows/data_rows.c b/DataRows/data_rows.c +index 054fa1f..a07eedc 100644 +--- a/DataRows/data_rows.c ++++ b/DataRows/data_rows.c +@@ -1,4 +1,5 @@ + #include "data_rows.h" ++#include "utility.h" + + #include "par.h" + +diff --git a/DataRows/py_data_rows.c b/DataRows/py_data_rows.c +index fc8b3c8..985e6c3 100644 +--- a/DataRows/py_data_rows.c ++++ b/DataRows/py_data_rows.c +@@ -1,4 +1,6 @@ + #include "Python.h" /* Python header files */ ++#include "modsupport.h" ++#include "intobject.h" + + #include "data_rows.h" + +diff --git a/connect/crosspeak.c b/connect/crosspeak.c +index 0de57bf..7b016e1 100644 +--- a/connect/crosspeak.c ++++ b/connect/crosspeak.c +@@ -1,4 +1,5 @@ + #include "crosspeak.h" ++#include "utility.h" + + #include "atom.h" + #include "table.h" +diff --git a/connect/shift.c b/connect/shift.c +index f54ba9f..a880001 100644 +--- a/connect/shift.c ++++ b/connect/shift.c +@@ -1,4 +1,5 @@ + #include "shift.h" ++#include "utility.h" + + #include "atom.h" + #include "table.h" +diff --git a/global/macros.h b/global/macros.h +index 43fc43e..bb1d267 100644 +--- a/global/macros.h ++++ b/global/macros.h +@@ -8,6 +8,7 @@ + #include <math.h> + #include <string.h> + #include <stdlib.h> ++#include <ctype.h> + + #ifdef WIN32 + #include <ctype.h> +diff --git a/global/parser.c b/global/parser.c +index 007d926..0f19575 100644 +--- a/global/parser.c ++++ b/global/parser.c +@@ -1,4 +1,5 @@ + #include "parser.h" ++#include "utility.h" + + #define MAX_NARGS 20 + +diff --git a/peak/fitter.c b/peak/fitter.c +index ba6b175..b58f573 100644 +--- a/peak/fitter.c ++++ b/peak/fitter.c +@@ -1,4 +1,5 @@ + #include "fitter.h" ++#include "data.h" + + #include "nonlinear_model.h" + +diff --git a/peak/peak_fit.c b/peak/peak_fit.c +index 92c69a8..5b9791f 100644 +--- a/peak/peak_fit.c ++++ b/peak/peak_fit.c +@@ -6,6 +6,7 @@ + #include "output.h" + #include "ref.h" + #include "script_fit.h" ++#include "fitter.h" + + #define MEGAWORD (1024 * 1024) + #define DEFAULT_STORE (2 * MEGAWORD) +diff --git a/plot1/draw.c b/plot1/draw.c +index 4fdce96..a2a2e8a 100644 +--- a/plot1/draw.c ++++ b/plot1/draw.c +@@ -1,4 +1,5 @@ + #include "draw.h" ++#include "ticks.h" + + #include "color.h" + #include "data.h" +diff --git a/plot1/object.c b/plot1/object.c +index 973897c..e043a53 100644 +--- a/plot1/object.c ++++ b/plot1/object.c +@@ -1,4 +1,5 @@ + #include "object.h" ++#include "script.h" + + #include "color.h" + #include "parser.h" +diff --git a/plot1/output_popup.c b/plot1/output_popup.c +index 0794584..e73976e 100644 +--- a/plot1/output_popup.c ++++ b/plot1/output_popup.c +@@ -1,4 +1,5 @@ + #include "output_popup.h" ++#include "script.h" + + #include "output.hlp" + +diff --git a/plot1/plots.c b/plot1/plots.c +index 3790f5b..7ac58df 100644 +--- a/plot1/plots.c ++++ b/plot1/plots.c +@@ -1,4 +1,5 @@ + #include "plots.h" ++#include "script.h" + + #include "data.h" + #include "input.h" +diff --git a/plot1/region_popup.c b/plot1/region_popup.c +index 68b3930..f049d29 100644 +--- a/plot1/region_popup.c ++++ b/plot1/region_popup.c +@@ -1,4 +1,5 @@ + #include "region_popup.h" ++#include "data.h" + + #include "region.hlp" + +diff --git a/plot2/data_popup.c b/plot2/data_popup.c +index 851b1d4..1c9026e 100644 +--- a/plot2/data_popup.c ++++ b/plot2/data_popup.c +@@ -1,4 +1,5 @@ + #include "data_popup.h" ++#include "rowcol_popup.h" + + #include "data.hlp" + +diff --git a/plot2/extract_popup.c b/plot2/extract_popup.c +index 416aab0..a7fcbf3 100644 +--- a/plot2/extract_popup.c ++++ b/plot2/extract_popup.c +@@ -1,4 +1,5 @@ + #include "extract_popup.h" ++#include "script.h" + + #include "extract.hlp" + +diff --git a/plot2/levels_popup.c b/plot2/levels_popup.c +index 197cf2c..e1ac22c 100644 +--- a/plot2/levels_popup.c ++++ b/plot2/levels_popup.c +@@ -1,4 +1,5 @@ + #include "levels_popup.h" ++#include "levels_func.h" + + #include "levels.hlp" + +diff --git a/plot2/plot2.c b/plot2/plot2.c +index 9ca91c3..0c10d5a 100644 +--- a/plot2/plot2.c ++++ b/plot2/plot2.c +@@ -1,4 +1,6 @@ + #include "plot2.h" ++#include "object_popup.h" ++#include "prop_popup.h" + + #include "baseline_popup.h" + #include "callback.h" +diff --git a/plot2/rowcol_popup.c b/plot2/rowcol_popup.c +index e9f4843..6c50426 100644 +--- a/plot2/rowcol_popup.c ++++ b/plot2/rowcol_popup.c +@@ -1,4 +1,5 @@ + #include "rowcol_popup.h" ++#include "ref_popup.h" + + #include "rowcol.hlp" + +diff --git a/plot2/script.c b/plot2/script.c +index 2f55182..d7d886f 100644 +--- a/plot2/script.c ++++ b/plot2/script.c +@@ -1,4 +1,5 @@ + #include "script.h" ++#include "macros.h" + + #include "param.h" + #include "stack.h" +diff --git a/plot2/slice_popup.c b/plot2/slice_popup.c +index b601834..1b1e686 100644 +--- a/plot2/slice_popup.c ++++ b/plot2/slice_popup.c +@@ -1,4 +1,5 @@ + #include "slice_popup.h" ++#include "rowcol_func.h" + + #include "baseline.h" + #include "baseline_popup.h" +diff --git a/process/files.c b/process/files.c +index e09127e..d95d681 100644 +--- a/process/files.c ++++ b/process/files.c +@@ -1,4 +1,5 @@ + #include "files.h" ++#include "macros.h" + + #include <sys/types.h> + #include <sys/stat.h> +diff --git a/project/project.c b/project/project.c +index 92b70e3..a3e6d94 100644 +--- a/project/project.c ++++ b/project/project.c +@@ -1,4 +1,5 @@ + #include "project.h" ++#include "utility.h" + + #include "block.h" + #include "par.h" diff --git a/sci-chemistry/azara/files/2.8-prll.patch b/sci-chemistry/azara/files/2.8-prll.patch new file mode 100644 index 000000000000..4720bb659445 --- /dev/null +++ b/sci-chemistry/azara/files/2.8-prll.patch @@ -0,0 +1,387 @@ +diff --git a/DataRows/makefile b/DataRows/makefile +index 587e710..4e0a312 100644 +--- a/DataRows/makefile ++++ b/DataRows/makefile +@@ -28,7 +28,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-DataRows.so: locals globals ++DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) +diff --git a/azara/makefile b/azara/makefile +index 3ba0cd9..f7b4ce5 100644 +--- a/azara/makefile ++++ b/azara/makefile +@@ -12,7 +12,7 @@ LOCAL_OBJS = \ + GLOBAL_OBJS = \ + $(GLOBAL_DIR)/help.o + +-azara: locals globals ++azara: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/combine/makefile b/combine/makefile +index a855236..7a83d8f 100644 +--- a/combine/makefile ++++ b/combine/makefile +@@ -20,7 +20,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-combine: locals globals ++combine: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/connect/makefile b/connect/makefile +index d75e7da..d238507 100644 +--- a/connect/makefile ++++ b/connect/makefile +@@ -23,7 +23,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-connect: locals globals ++connect: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/contours/makefile b/contours/makefile +index 5b832b8..49175dd 100644 +--- a/contours/makefile ++++ b/contours/makefile +@@ -19,7 +19,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-contours: locals globals ++contours: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/deflate/makefile b/deflate/makefile +index 4c4e02e..42d5c30 100644 +--- a/deflate/makefile ++++ b/deflate/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-deflate: locals globals ++deflate: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/extract/makefile b/extract/makefile +index 3212cb9..fed874b 100644 +--- a/extract/makefile ++++ b/extract/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-extract: locals globals ++extract: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/global/makefile b/global/makefile +index 364fa41..5272a31 100644 +--- a/global/makefile ++++ b/global/makefile +@@ -42,6 +42,31 @@ LINPACK_OBJS = \ + AZARA_OBJS = \ + help.o + ++all: \ ++ azara_objects \ ++ decay_objects \ ++ simulate_objects \ ++ viewer_objects \ ++ components_objects \ ++ shuffle_objects \ ++ connect_objects \ ++ slides_objects \ ++ peak_find_objects \ ++ peak_fit_objects \ ++ plot1_objects \ ++ reflate_objects \ ++ deflate_objects \ ++ combine_objects \ ++ unblock_objects \ ++ extract_objects \ ++ project_objects \ ++ contours_objects \ ++ plot2_nog_objects \ ++ plot2_objects \ ++ process_objects \ ++ python_objects \ ++ integrate_objects ++ + azara_objects: $(AZARA_OBJS) + + DECAY_OBJS = \ +diff --git a/help/makefile b/help/makefile +index 9e99a7c..59a86a3 100644 +--- a/help/makefile ++++ b/help/makefile +@@ -39,7 +39,7 @@ globals: + + .c.o:; $(CC) -c $(CFLAGS) $< + +-hlp: ++hlp: txt2hlp + $(TXT2HLP) azara + $(TXT2HLP) combine + $(TXT2HLP) connect +@@ -78,7 +78,7 @@ hlp: + $(TXT2HLP) plot1/text + $(TXT2HLP) DataRows + +-html: ++html: txt2html + $(TXT2HTML) azara + $(TXT2HTML) combine + $(TXT2HTML) connect +diff --git a/makefile b/makefile +index 9965b07..f4383af 100644 +--- a/makefile ++++ b/makefile +@@ -14,7 +14,7 @@ all: help nongui DataRows gui + help: \ + help_program + +-nongui: \ ++nongui: help \ + process_program \ + plot2_nog_program \ + peak_program \ +@@ -29,63 +29,66 @@ nongui: \ + connect_program \ + azara_program + +-gui: \ ++gui: help \ + plot2_program \ + plot1_program + +-DataRows: \ ++DataRows: help \ + DataRows + +-process_program: +- cd process; $(MAKE) ++global: ++ $(MAKE) -C global + +-plot2_program: +- cd plot2; $(MAKE) plot2 ++process_program: global ++ $(MAKE) -C process + +-plot2_nog_program: +- cd plot2; $(MAKE) plot2_nog ++plot2_program: global ++ $(MAKE) -C plot2 + +-plot1_program: +- cd plot1; $(MAKE) ++plot2_nog_program: global ++ $(MAKE) -C plot2 plot2_nog + +-peak_program: +- cd peak; $(MAKE) ++plot1_program: global ++ $(MAKE) -C plot1 + +-extract_program: +- cd extract; $(MAKE) ++peak_program: global process_program ++ $(MAKE) -C peak + +-project_program: +- cd project; $(MAKE) ++extract_program: global ++ $(MAKE) -C extract + +-unblock_program: +- cd unblock; $(MAKE) ++project_program: global ++ $(MAKE) -C project + +-contours_program: +- cd contours; $(MAKE) ++unblock_program: global ++ $(MAKE) -C unblock + +-combine_program: +- cd combine; $(MAKE) ++contours_program: global ++ $(MAKE) -C contours + +-deflate_program: +- cd deflate; $(MAKE) ++combine_program: global ++ $(MAKE) -C combine + +-reflate_program: +- cd reflate; $(MAKE) ++deflate_program: global ++ $(MAKE) -C deflate + +-utility_program: +- cd utility; $(MAKE) ++reflate_program: global ++ $(MAKE) -C reflate + +-connect_program: +- cd connect; $(MAKE) ++utility_program: global ++ $(MAKE) -C utility + +-help_program: +- cd help; $(MAKE) ++connect_program: global ++ $(MAKE) -C connect + +-azara_program: +- cd azara; $(MAKE) ++help_program: global ++ $(MAKE) -C help + +-DataRows: +- cd DataRows; $(MAKE) ++azara_program: global ++ $(MAKE) -C azara ++ ++DataRows: global ++ $(MAKE) -C DataRows + + clean: \ + global_clean \ +@@ -227,3 +230,5 @@ azara_realclean: + DataRows_realclean: + cd DataRows; $(MAKE) realclean + ++ ++.PHONY: global process_program +diff --git a/peak/makefile b/peak/makefile +index f3c13b7..4211221 100644 +--- a/peak/makefile ++++ b/peak/makefile +@@ -97,13 +97,13 @@ COMMAND_OBJS = \ + + all: peak_find peak_fit + +-peak_find: local_find global_find ++peak_find: $(LOCAL_FIND_OBJS) $(GLOBAL_FIND_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_FIND_OBJS) \ + $(GLOBAL_FIND_OBJS) \ + $(LIB) $(MATH_LIB) + +-peak_fit: local_fit global_fit commands ++peak_fit: $(LOCAL_FIT_OBJS) $(GLOBAL_FIT_OBJS) $(COMMAND_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_FIT_OBJS) \ + $(GLOBAL_FIT_OBJS) \ +diff --git a/plot1/makefile b/plot1/makefile +index d1dce2d..e729443 100644 +--- a/plot1/makefile ++++ b/plot1/makefile +@@ -95,7 +95,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/utility.o \ + $(GLOBAL_DIR)/window.o + +-plot1: locals globals ++plot1: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +@@ -110,7 +110,7 @@ locals: + globals: + cd $(GLOBAL_DIR); $(MAKE) plot1_objects + +-.c.o:; $(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) $< ++.c.o:; $(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) -I../plot2 $< + + clean: + rm -f *.o +diff --git a/plot2/makefile b/plot2/makefile +index a6b7b4a..98e286e 100644 +--- a/plot2/makefile ++++ b/plot2/makefile +@@ -129,7 +129,7 @@ GLOBAL_PLOT2_NOG_OBJS = \ + + all: plot2 plot2_nog + +-plot2: local_plot2 global_plot2 ++plot2: $(LOCAL_PLOT2_OBJS) $(GLOBAL_PLOT2_OBJS) + $(CC) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_PLOT2_OBJS) \ + $(GLOBAL_PLOT2_OBJS) \ +@@ -137,7 +137,7 @@ plot2: local_plot2 global_plot2 + $(LIB) $(MATH_LIB) \ + $(MOTIF_LIB) $(X11_LIB) $(XPM_LIB) + +-plot2_nog: local_plot2_nog global_plot2_nog ++plot2_nog: $(LOCAL_PLOT2_NOG_OBJS) $(GLOBAL_PLOT2_NOG_OBJS) + $(CC) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_PLOT2_NOG_OBJS) \ + $(GLOBAL_PLOT2_NOG_OBJS) \ +diff --git a/process/makefile b/process/makefile +index 22ceeed..72d587b 100644 +--- a/process/makefile ++++ b/process/makefile +@@ -72,7 +72,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/utility.o \ + $(LINPACK_OBJS) + +-process: locals globals ++process: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/project/makefile b/project/makefile +index 78143fc..ed0f296 100644 +--- a/project/makefile ++++ b/project/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-project: locals globals ++project: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/reflate/makefile b/reflate/makefile +index 079a3fc..01ec311 100644 +--- a/reflate/makefile ++++ b/reflate/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-reflate: locals globals ++reflate: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/unblock/makefile b/unblock/makefile +index 510dc9e..d9a0f2b 100644 +--- a/unblock/makefile ++++ b/unblock/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-unblock: locals globals ++unblock: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ diff --git a/sci-chemistry/azara/files/2.8-python.patch b/sci-chemistry/azara/files/2.8-python.patch new file mode 100644 index 000000000000..9834c77a77dc --- /dev/null +++ b/sci-chemistry/azara/files/2.8-python.patch @@ -0,0 +1,44 @@ +diff --git a/DataRows/makefile b/DataRows/makefile +index 4e0a312..ce261ab 100644 +--- a/DataRows/makefile ++++ b/DataRows/makefile +@@ -22,16 +22,17 @@ LOCAL_OBJS = \ + data_rows.o + + GLOBAL_OBJS = \ +- $(GLOBAL_DIR)/block_io.o \ +- $(GLOBAL_DIR)/par.o \ +- $(GLOBAL_DIR)/parse.o \ +- $(GLOBAL_DIR)/ref.o \ +- $(GLOBAL_DIR)/utility.o ++ block_io.o \ ++ par.o \ ++ parse.o \ ++ ref.o \ ++ utility.o + + DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_OBJS) \ +- $(GLOBAL_OBJS) ++ $(GLOBAL_OBJS) \ ++ $(PYTHON_LIB) + + local_objects: $(LOCAL_OBJS) + +@@ -42,9 +43,13 @@ globals: + cd $(GLOBAL_DIR); $(MAKE) python_objects + + py_data_rows.o: py_data_rows.c +- $(CC) -c $(CFLAGS) $(PYTHON_INCLUDE_DIR) $< ++ $(CC) -c $(CFLAGS) $(PIC) $(PYTHON_INCLUDE_DIR) $< + +-.c.o:; $(CC) -c $(CFLAGS) $< ++data_rows.o: data_rows.c ++ $(CC) -c $(CFLAGS) $(PIC) $< ++ ++%.o: $(GLOBAL_DIR)/%.c ++ $(CC) -c $(CFLAGS) $(PIC) $< + + clean: + rm -f *.o diff --git a/sci-chemistry/azara/metadata.xml b/sci-chemistry/azara/metadata.xml new file mode 100644 index 000000000000..c0432fefe855 --- /dev/null +++ b/sci-chemistry/azara/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher (jlec)</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/babel/Manifest b/sci-chemistry/babel/Manifest new file mode 100644 index 000000000000..c710a51eca7e --- /dev/null +++ b/sci-chemistry/babel/Manifest @@ -0,0 +1 @@ +DIST babel-1.6.tar.Z 242341 SHA256 132a800cfe0c15b47391c809481a7ca174bbd1402aac7486e0973da0fd4db948 SHA512 60336f695b8ee3ec87433b003da38d55365162bbe87244cb175eabec6c0a470c475dac66f85f24525a61b16fa933bdc3eea5ddd0452b6573bcb046ab774b3229 WHIRLPOOL f6dee4fe6409aed0dfae3f672c826ccdb45f0f5d743421faf6622e1258435caf7d9259ece83ab711754a7964bca0c21af42ed179af23b056329d8b800bd95e80 diff --git a/sci-chemistry/babel/babel-1.6-r1.ebuild b/sci-chemistry/babel/babel-1.6-r1.ebuild new file mode 100644 index 000000000000..1905b34846f0 --- /dev/null +++ b/sci-chemistry/babel/babel-1.6-r1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils + +DESCRIPTION="Interconvert file formats used in molecular modeling" +HOMEPAGE="http://smog.com/chem/babel/" +SRC_URI="http://smog.com/chem/babel/files/${P}.tar.Z" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="amd64 ppc x86" +RESTRICT="mirror bindist" + +#Doesn't really seem to depend on anything (?) +DEPEND="!sci-chemistry/openbabel" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-gcc32.diff \ + "${FILESDIR}"/${P}-makefile.patch + tc-export CC +} + +src_install () { + emake DESTDIR="${D}"/usr/bin install + + insinto /usr/share/${PN} + doins *.lis + + doenvd "${FILESDIR}"/10babel + dodoc README.1ST +} diff --git a/sci-chemistry/babel/files/10babel b/sci-chemistry/babel/files/10babel new file mode 100644 index 000000000000..69f3397638dd --- /dev/null +++ b/sci-chemistry/babel/files/10babel @@ -0,0 +1 @@ +BABEL_DIR=/usr/share/babel diff --git a/sci-chemistry/babel/files/babel-1.6-gcc32.diff b/sci-chemistry/babel/files/babel-1.6-gcc32.diff new file mode 100644 index 000000000000..ba0964af5352 --- /dev/null +++ b/sci-chemistry/babel/files/babel-1.6-gcc32.diff @@ -0,0 +1,28 @@ +--- block.c.orig Sun Sep 15 04:51:13 2002 ++++ block.c Sun Sep 15 04:58:04 2002 +@@ -99,7 +99,12 @@ + void *array; + + /* calc how much space we are gonna need */ ++#ifdef __va_copy ++ __va_copy (ap, initap); ++#else + ap = initap; ++#endif ++ + size = 0; + for(i=0; types[i] != '\0'; i++) + { +@@ -116,7 +121,12 @@ + /* set up the ptrs if we can alloc the memory */ + if(*handle != NULL) + { ++#ifdef __va_copy ++ __va_copy (ap, initap); ++#else + ap = initap; ++#endif ++ + ptr = 0; + for(i=0; types[i] != '\0'; i++) + { diff --git a/sci-chemistry/babel/files/babel-1.6-gentoo.diff b/sci-chemistry/babel/files/babel-1.6-gentoo.diff new file mode 100644 index 000000000000..77e2cb47ef03 --- /dev/null +++ b/sci-chemistry/babel/files/babel-1.6-gentoo.diff @@ -0,0 +1,28 @@ +--- Makefile.orig Tue Oct 23 00:20:54 2001 ++++ Makefile Tue Oct 23 00:33:36 2001 +@@ -1,11 +1,15 @@ +-CFLAGS = -O ++#Commented out to pull CFLAGS from make.conf ++#CFLAGS = -O + + LIBFLAGS = -O -DLIBRARY + +-CC = cc ++#Probably not necessary to specify gcc ++CC = gcc + + PROGRAM = babel + ++DEST = ${DESTDIR}/$(PROGRAM) ++ + LDFLAGS = + + LIBS = +@@ -334,6 +338,7 @@ + index:; ctags -wx $(HDRS) $(SRCS) + + install: $(PROGRAM) ++ install -d ${DESTDIR} + install -s $(PROGRAM) $(DEST) + + print:; $(PRINT) $(HDRS) $(SRCS) diff --git a/sci-chemistry/babel/files/babel-1.6-makefile.patch b/sci-chemistry/babel/files/babel-1.6-makefile.patch new file mode 100644 index 000000000000..33b158d1b2cf --- /dev/null +++ b/sci-chemistry/babel/files/babel-1.6-makefile.patch @@ -0,0 +1,33 @@ +diff -Naur babel-1.6/Makefile babel-1.6.new/Makefile +--- babel-1.6/Makefile 1997-01-21 10:53:05.000000000 -0500 ++++ babel-1.6.new/Makefile 2008-10-19 10:41:42.000000000 -0400 +@@ -1,12 +1,16 @@ +-CFLAGS = -O ++#Commented out to pull CFLAGS from make.conf ++#CFLAGS = -O + + LIBFLAGS = -O -DLIBRARY + +-CC = cc ++#Probably not necessary to specify gcc ++#CC = gcc + + PROGRAM = babel + +-LDFLAGS = ++DEST = ${DESTDIR}/$(PROGRAM) ++ ++#LDFLAGS = + + LIBS = + +@@ -334,7 +338,8 @@ + index:; ctags -wx $(HDRS) $(SRCS) + + install: $(PROGRAM) +- install -s $(PROGRAM) $(DEST) ++ install -d ${DESTDIR} ++ install $(PROGRAM) $(DEST) + + print:; $(PRINT) $(HDRS) $(SRCS) + diff --git a/sci-chemistry/babel/metadata.xml b/sci-chemistry/babel/metadata.xml new file mode 100644 index 000000000000..e42d0af60f42 --- /dev/null +++ b/sci-chemistry/babel/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/balbes/Manifest b/sci-chemistry/balbes/Manifest new file mode 100644 index 000000000000..ac3f2cd87d87 --- /dev/null +++ b/sci-chemistry/balbes/Manifest @@ -0,0 +1,2 @@ +DIST balbes-1.0.0_p100317.tar.gz 506464 SHA256 c5bf6c2086e1a3d7d380e5501c0cffdb91cbf77c74d2951dd345273f21921d0c +DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 diff --git a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild new file mode 100644 index 000000000000..5334207c0229 --- /dev/null +++ b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +CCP4VER="6.1.3" +PYTHON_DEPEND="2" + +inherit eutils fortran-2 python toolchain-funcs + +DESCRIPTION="Automated molecular replacement (MR) pipeline" +HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/index.html" +SRC_URI=" + mirror://gentoo/${P}.tar.gz + ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-core-src.tar.gz" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +# bundled PyXML is modified and cannot be replaced + +COMMON_DEPEND="sci-libs/ccp4-libs" +RDEPEND="${COMMON_DEPEND} + ~sci-libs/balbes-db-${CCP4VER} + !<=sci-chemistry/ccp4-apps-6.1.3-r1" +DEPEND="${COMMON_DEPEND}" + +S="${WORKDIR}"/src + +pkg_setup() { + fortran-2_pkg_setup + python_set_active_version 2 +} + +src_unpack() { + unpack ${P}.tar.gz + tar xvzf "${DISTDIR}"/ccp4-${CCP4VER}-core-src.tar.gz \ + ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \ + ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 + python_convert_shebangs 2 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes +} + +src_prepare() { + mkdir "${WORKDIR}"/bin || die + epatch "${FILESDIR}"/${PV}-makefile.patch + cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/ + epatch "${FILESDIR}"/pyxml-0.8.4-python-2.6.patch +} + +src_compile() { + emake \ + BLANC_FORT="$(tc-getFC) ${FFLAGS}" || die + cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 + find build -delete + $(PYTHON) setup.py build + find xml/xslt test -delete +} + +src_install() { + insinto /usr/share/balbes/BALBES_0.0.1/ + doins -r \ + "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \ + "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 || die + dobin \ + "${WORKDIR}"/bin/* \ + "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes \ + || die +} + +pkg_postinst() { + python_mod_optimize /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4} +} + +pkg_postrm() { + python_mod_cleanup /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4} +} diff --git a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch b/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch new file mode 100644 index 000000000000..da17240642d7 --- /dev/null +++ b/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch @@ -0,0 +1,107 @@ +diff --git a/makefile b/makefile +index baaceb5..85a7baf 100755 +--- a/makefile ++++ b/makefile +@@ -70,6 +70,15 @@ OBJDB_G = get_pdb_list.o + + #OBJDB_Z = blanc2mtz.o libutils.o + ++# incomplete targets: ++# dimer_search_db domain_search_db domain align3 ++all: search_db get_structure_db manage_db search_dm dom2ch \ ++ save_si get_pdb_list_db update_db \ ++ update_dom_db bl2mtz check_file_db fobs2cif sol_check \ ++ get_trns p2s check_cell alt_sg \ ++ align cell_list create_bins \ ++ get_pdb_list_db get_ch get_nm get_mod ++ + search_db: sdb_l + + get_structure_db: tdb_l +@@ -201,58 +210,58 @@ save_seg_id.o: save_seg_id.f + $(BLANC_FORT) -c save_seg_id.f + + sdb_l: $(OBJDB_S) +- $(BLANC_FORT) -o ../bin/search_DB $(OBJDB_S) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DB $(OBJDB_S) + tdb_l: $(OBJDB_T) +- $(BLANC_FORT) -o ../bin/get_structure_DB $(OBJDB_T) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_structure_DB $(OBJDB_T) + mdb_l: $(OBJDB_M) +- $(BLANC_FORT) -o ../bin/manage_DB $(OBJDB_M) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/manage_DB $(OBJDB_M) + mdm_l: $(OBJDB_MD) +- $(BLANC_FORT) -o ../bin/search_DOM $(OBJDB_MD) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DOM $(OBJDB_MD) + d2c_l: $(OBJDB_A) +- $(BLANC_FORT) -o ../bin/domain2chain $(OBJDB_A) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain2chain $(OBJDB_A) + upd_l: $(OBJDB_U) +- $(BLANC_FORT) -o ../bin/update_DB $(OBJDB_U) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_DB $(OBJDB_U) + dom_l: $(OBJDB_V) +- $(BLANC_FORT) -o ../bin/update_domain_DB $(OBJDB_V) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_domain_DB $(OBJDB_V) + ddb_l: $(OBJDB_D) +- $(BLANC_FORT) -o ../bin/dimer_search $(OBJDB_D) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/dimer_search $(OBJDB_D) + dmdb_l: $(OBJDB_N) +- $(BLANC_FORT) -o ../bin/domain_search $(OBJDB_N) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain_search $(OBJDB_N) + gdb_l: $(OBJDB_G) +- $(BLANC_FORT) -o ../bin/get_pdb_list $(OBJDB_G) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_pdb_list $(OBJDB_G) + b2m_l: blanc2mtz.o libutils.o +- $(BLANC_FORT) -o ../bin/blanc2mtz blanc2mtz.o libutils.o $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/blanc2mtz blanc2mtz.o libutils.o -lccp4f -lccp4c + f2c_l: f2cif.o libutils.o +- $(BLANC_FORT) -o ../bin/f2cif f2cif.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/f2cif f2cif.o libutils.o + chf_l: check_file_DB.o libutils.o +- $(BLANC_FORT) -o ../bin/check_file_DB check_file_DB.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_file_DB check_file_DB.o libutils.o + chc_l: check_cell_sg.o libutils.o +- $(BLANC_FORT) -o ../bin/check_cell_sg check_cell_sg.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_cell_sg check_cell_sg.o libutils.o + asl_l: alt_sg_list.o libutils.o +- $(BLANC_FORT) -o ../bin/alt_sg_list alt_sg_list.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/alt_sg_list alt_sg_list.o libutils.o + sc_l: $(OBJDB_C) +- $(BLANC_FORT) -o ../bin/solution_check $(OBJDB_C) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/solution_check $(OBJDB_C) + gt_l: $(OBJDB_R) +- $(BLANC_FORT) -o ../bin/get_trans $(OBJDB_R) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_trans $(OBJDB_R) + dmn_l: domain.o libutils.o +- $(BLANC_FORT) -o ../bin/domain domain.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain domain.o libutils.o + pack: pdb_pack.o libutils.o +- $(BLANC_FORT) -o ../bin/pdb_pack pdb_pack.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb_pack pdb_pack.o libutils.o + p2s_l: $(OBJDB_P) +- $(BLANC_FORT) -o ../bin/pdb2s $(OBJDB_P) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb2s $(OBJDB_P) + aln_l: align_DB.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/align_DB align_DB.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB align_DB.o DB_subr.o libutils.o + aln3_l: align_DB_new.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o + cell_l: create_cell_list.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o + getch_l: get_chain.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/get_chain get_chain.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_chain get_chain.o DB_subr.o libutils.o + getnmr_l: get_nmr.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o + getmod_l: get_model.o libutils.o +- $(BLANC_FORT) -o ../bin/get_model get_model.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_model get_model.o libutils.o + crb_l: create_binaries.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o + save_si_l: save_seg_id.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o diff --git a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch new file mode 100644 index 000000000000..d29b0b6a9eb2 --- /dev/null +++ b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch @@ -0,0 +1,28 @@ +diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py +--- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:54:36.000000000 +0900 ++++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:57:02.000000000 +0900 +@@ -24,8 +24,8 @@ class ParsedAbbreviatedAbsoluteLocationP + self._rel = rel + nt = ParsedNodeTest.ParsedNodeTest('node', '') + ppl = ParsedPredicateList.ParsedPredicateList([]) +- as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') +- self._step = ParsedStep.ParsedStep(as, nt, ppl) ++ as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') ++ self._step = ParsedStep.ParsedStep(as_, nt, ppl) + return + + def evaluate(self, context): +diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py +--- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:54:36.000000000 +0900 ++++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:58:58.000000000 +0900 +@@ -28,8 +28,8 @@ class ParsedAbbreviatedRelativeLocationP + self._right = right + nt = ParsedNodeTest.ParsedNodeTest('node','') + ppl = ParsedPredicateList.ParsedPredicateList([]) +- as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') +- self._middle = ParsedStep.ParsedStep(as, nt, ppl) ++ as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') ++ self._middle = ParsedStep.ParsedStep(as_, nt, ppl) + + def evaluate(self, context): + res = [] diff --git a/sci-chemistry/balbes/metadata.xml b/sci-chemistry/balbes/metadata.xml new file mode 100644 index 000000000000..4bb6be5e5d0c --- /dev/null +++ b/sci-chemistry/balbes/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> + BALBES is a system for solving protein structures using x-ray + crystalographic data. Molecular Replacement(MR) is its core + scientific method. BALBES aims to integrate all components, + necessary for finding a solution structure by MR, into one system. + It consists of a database, scientific programs and a python + pipeline. The system is automated so that it needs no user's + intervention when running complicated combination of jobs such + as model searching, molecular replacement and refinement. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/ball/Manifest b/sci-chemistry/ball/Manifest new file mode 100644 index 000000000000..f7919da9098f --- /dev/null +++ b/sci-chemistry/ball/Manifest @@ -0,0 +1 @@ +DIST BALL-1.4.2.tar.xz 16080664 SHA256 053931b2e050d7d5bceaa21ad3617a1ad0af00f94de56076ce02d544383cbf91 SHA512 c719af4ef2dc1076818d59b72350b704fbffea06bd44737519fb50d88da113ea509333d407f2330aa59bf1c4e6b81adfd3d28e05459f66d7c9707f8d85db7a87 WHIRLPOOL ba7ae340833ea5703d047a9dbc0ce50d9b9dc2b0047a0c6d9f9a17946956c684a09e0860f25c7214a2aa0adee9beb1d01eac38b0ab08259a2934f97cbef91379 diff --git a/sci-chemistry/ball/ball-1.4.2.ebuild b/sci-chemistry/ball/ball-1.4.2.ebuild new file mode 100644 index 000000000000..bc1005204c0b --- /dev/null +++ b/sci-chemistry/ball/ball-1.4.2.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils python-single-r1 + +DESCRIPTION="Biochemical Algorithms Library" +HOMEPAGE="http://www.ball-project.org/" +SRC_URI="http://www.ball-project.org/Downloads/v${PV}/BALL-${PV}.tar.xz" + +SLOT="0" +LICENSE="LGPL-2 GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda mpi +python sql test +threads +webkit" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/boost + dev-qt/qtcore:4 + dev-qt/qtgui:4 + dev-qt/qtopengl:4 + dev-qt/qttest:4 + dev-qt/qtwebkit:4 + media-libs/glew + sci-libs/fftw:3.0[threads?] + sci-libs/gsl + sci-libs/libsvm + sci-mathematics/lpsolve + virtual/opengl + x11-libs/libX11 + cuda? ( dev-util/nvidia-cuda-toolkit ) + mpi? ( virtual/mpi ) + python? ( ${PYTHON_DEPS} ) + sql? ( dev-qt/qtsql:4 ) + webkit? ( dev-qt/qtwebkit:4 )" +DEPEND="${RDEPEND} + dev-python/sip + sys-devel/bison + virtual/yacc" + +S="${WORKDIR}"/BALL-${PV} + +PATCHES=( + "${FILESDIR}"/${PN}-1.4.1-multilib.patch + "${FILESDIR}"/${PN}-1.4.1-missing-signed.patch + "${FILESDIR}"/${P}-PDBFile-Fix-compilation-with-gcc-4.8.patch + "${FILESDIR}"/${P}-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch + "${FILESDIR}"/${PN}-1.4.1-BondOrder.xml.patch + "${FILESDIR}"/${P}-Fix-compilation-of-sipModularWidget.patch + "${FILESDIR}"/${P}-underlinking.patch + ) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_use threads FFTW_THREADS) + $(cmake-utils_use cuda MT_ENABLE_CUDA) + $(cmake-utils_use mpi MT_ENABLE_MPI) + $(cmake-utils_use sql BALL_HAS_QTSQL) + $(cmake-utils_use_use webkit USE_QTWEBKIT) + $(cmake-utils_use python BALL_PYTHON_SUPPORT) + ) + cmake-utils_src_configure + local i + for i in "${S}"/data/*; do + ln -sf "${i}" "${BUILD_DIR}"/source/TEST/ || die + ln -sf "${i}" "${S}"/source/TEST/ || die + done +} + +src_compile() { + cmake-utils_src_compile + use test && cmake-utils_src_make build_tests +} diff --git a/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch b/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch new file mode 100644 index 000000000000..51e592806999 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch @@ -0,0 +1,30 @@ + source/STRUCTURE/assignBondOrderProcessor.C | 2 +- + source/TEST/AssignBondOrderProcessor_test.C | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/source/STRUCTURE/assignBondOrderProcessor.C b/source/STRUCTURE/assignBondOrderProcessor.C +index f8acc4f..035fffc 100644 +--- a/source/STRUCTURE/assignBondOrderProcessor.C ++++ b/source/STRUCTURE/assignBondOrderProcessor.C +@@ -100,7 +100,7 @@ namespace BALL + const bool AssignBondOrderProcessor::Default::KEKULIZE_RINGS = true; + + const char* AssignBondOrderProcessor::Option::INIFile = "iniFile"; +- const String AssignBondOrderProcessor::Default::INIFile = "/bond_lengths/BondOrder.xml"; ++ const String AssignBondOrderProcessor::Default::INIFile = "bond_lengths/BondOrder.xml"; + + const char* AssignBondOrderProcessor::Option::MAX_BOND_ORDER = "max_bond_order"; + const int AssignBondOrderProcessor::Default::MAX_BOND_ORDER = 3; +diff --git a/source/TEST/AssignBondOrderProcessor_test.C b/source/TEST/AssignBondOrderProcessor_test.C +index 6dfafcc..3405ef5 100644 +--- a/source/TEST/AssignBondOrderProcessor_test.C ++++ b/source/TEST/AssignBondOrderProcessor_test.C +@@ -1834,7 +1834,7 @@ CHECK(Option::INIFile) + // There is really not much we can test here, so we just execute the processor + // to have a chance of catching bugs with valgrind if they sneak in + AssignBondOrderProcessor abop; +- abop.options.set(AssignBondOrderProcessor::Option::INIFile, "/bond_lengths/BondOrderGAFF.xml"); ++ abop.options.set(AssignBondOrderProcessor::Option::INIFile, "bond_lengths/BondOrderGAFF.xml"); + + System sys40; + MOL2File mol40(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_C4_input.mol2), std::ios::in); diff --git a/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch b/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch new file mode 100644 index 000000000000..6868871b3dc4 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch @@ -0,0 +1,26 @@ +Index: ball/include/BALL/DATATYPE/hashGrid.h +=================================================================== +--- ball.orig/include/BALL/DATATYPE/hashGrid.h 2011-12-09 13:49:26.000000000 +0100 ++++ ball/include/BALL/DATATYPE/hashGrid.h 2011-12-09 13:51:09.000000000 +0100 +@@ -37,7 +37,7 @@ + { + namespace __private + { +- extern const char BALL_EXPORT neighbour_table_[27][3]; ++ extern const signed char BALL_EXPORT neighbour_table_[27][3]; + } + + template <typename Item> class HashGrid3; +Index: ball/source/DATATYPE/hashGrid.C +=================================================================== +--- ball.orig/source/DATATYPE/hashGrid.C 2011-12-09 13:49:26.000000000 +0100 ++++ ball/source/DATATYPE/hashGrid.C 2011-12-09 13:50:49.000000000 +0100 +@@ -9,7 +9,7 @@ + { + namespace __private + { +- const char neighbour_table_[27][3] = ++ const signed char neighbour_table_[27][3] = + { + { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 }, + { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 }, diff --git a/sci-chemistry/ball/files/ball-1.4.1-multilib.patch b/sci-chemistry/ball/files/ball-1.4.1-multilib.patch new file mode 100644 index 000000000000..317c4029c678 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.1-multilib.patch @@ -0,0 +1,39 @@ +From 5b8f4e58b4e54bcdfa6f287e01f91d9dfd4e5a14 Mon Sep 17 00:00:00 2001 +From: Justin Lecher <jlec@gentoo.org> +Date: Sun, 25 Mar 2012 14:12:21 +0200 +Subject: [PATCH] Correct path for multilib installation. + +Libraries should go into lib64 not lib on native 64bit. Therefore we can use the LIBDIR detected by cmake. +--- + CMakeLists.txt | 8 ++++---- + 1 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 940ebf4..7eb3db4 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -426,8 +426,8 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin") + ## These variables are used in all install-targets + IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + SET(BALL_RUNTIME_INSTALL_DIRECTORY "bin") +- SET(BALL_LIBRARY_INSTALL_DIRECTORY "lib") +- SET(BALL_ARCHIVE_INSTALL_DIRECTORY "lib") ++ SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) ++ SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) + SET(BALL_HEADER_INSTALL_DIRECTORY ".") + SET(BALL_DATA_INSTALL_DIRECTORY "share/BALL") + SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY "share/BALL/doc") +@@ -435,8 +435,8 @@ IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + SET(BALL_PYTHON_INSTALL_DIRECTORY "bin") + SET(BALL_PLUGIN_INSTALL_DIRECTORY "bin") + ELSE() +- SET(BALL_PYTHON_INSTALL_DIRECTORY "lib") +- SET(BALL_PLUGIN_INSTALL_DIRECTORY "lib") ++ SET(BALL_PYTHON_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) ++ SET(BALL_PLUGIN_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) + ENDIF() + ELSE() + SET(BALL_BUNDLE_INSTALL_DIRECTORY "Applications") +-- +1.7.8.5 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch b/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch new file mode 100644 index 000000000000..3ec2f6e983a8 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch @@ -0,0 +1,40 @@ +From da49802f8620562f91ac2c947520dccd223ee26b Mon Sep 17 00:00:00 2001 +From: Andreas Hildebrandt <andreas.hildebrandt@uni-mainz.de> +Date: Wed, 15 Jan 2014 17:42:01 +0100 +Subject: [PATCH] Fix compilation of sipModularWidget + +--- + source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip | 10 +++++----- + 1 file changed, 5 insertions(+), 5 deletions(-) + +diff --git a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip +index 522b0ed..7b8ba3e 100644 +--- a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip ++++ b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip +@@ -22,18 +22,18 @@ class ModularWidget + static Size countInstances(); + static ModularWidget* getInstance(Position); + +- ModularWidget(const char* = "<ModularWidget>") throw(); +- ModularWidget(const ModularWidget&) throw(); ++ ModularWidget(const char* = "<ModularWidget>"); ++ ModularWidget(const ModularWidget&); + ~ModularWidget() throw(); + +- virtual void destroy() throw(); +- virtual void clear() throw(); ++// virtual void destroy(); ++ virtual void clear(); + + static void registerWidget(ModularWidget*) throw(NullPointer); + // virtual void initializeWidget(MainControl&); + // virtual void finalizeWidget(MainControl&); + virtual void checkMenu(MainControl&) throw(); +-// virtual void initializePreferencesTab(Preferences&) throw(); ++// virtual void initializePreferencesTab(Preferences&); + // virtual void finalizePreferencesTab(Preferences&) throw(); + virtual void applyPreferences() throw(); + virtual void fetchPreferences(INIFile&) throw(); +-- +1.9.1 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch b/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch new file mode 100644 index 000000000000..f6b8ff45fa7f --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch @@ -0,0 +1,28 @@ +From e7cc50705bed20e160bd4b637b23f57270f580a8 Mon Sep 17 00:00:00 2001 +From: Daniel Stoeckel <dstoeckel@bioinf.uni-sb.de> +Date: Sat, 6 Apr 2013 01:06:55 +0200 +Subject: [PATCH] PDBFile:Fix compilation with gcc 4.8 + +Apparently the automatic conversion from boost::shared_ptr<CrystalInfo> +to boost::shared_ptr<PersistentObject> is no longer supported. +Just change the type of the pointer and work around this issue. +--- + source/FORMAT/PDBFileDetails.C | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/source/FORMAT/PDBFileDetails.C b/source/FORMAT/PDBFileDetails.C +index 97c2572..aedc5db 100644 +--- a/source/FORMAT/PDBFileDetails.C ++++ b/source/FORMAT/PDBFileDetails.C +@@ -901,7 +901,7 @@ namespace BALL + { + if (!(current_protein_->hasProperty("CRYSTALINFO"))) + { +- boost::shared_ptr<CrystalInfo> temp_ptr(new CrystalInfo()); ++ boost::shared_ptr<PersistentObject> temp_ptr(new CrystalInfo()); + current_protein_->setProperty(NamedProperty("CRYSTALINFO", temp_ptr)); + } + +-- +1.9.1 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch b/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch new file mode 100644 index 000000000000..615a92290805 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch @@ -0,0 +1,44 @@ +From 1e76c9cb1920e9176b725269985c7eb43126d188 Mon Sep 17 00:00:00 2001 +From: Luis de la Garza <delagarza@informatik.uni-tuebingen.de> +Date: Fri, 22 Nov 2013 15:18:55 +0100 +Subject: [PATCH] QT4_EXTRACT_OPTIONS CMake macro changed in CMake 2.8.12; + fixed BALLMacros.cmake + +--- + cmake/BALLMacros.cmake | 14 ++++++++++---- + 1 file changed, 10 insertions(+), 4 deletions(-) + +diff --git a/cmake/BALLMacros.cmake b/cmake/BALLMacros.cmake +index f81ab89..0ac1b87 100644 +--- a/cmake/BALLMacros.cmake ++++ b/cmake/BALLMacros.cmake +@@ -6,16 +6,22 @@ + ### minor modifications (marked with ## BALL ###) + ### + MACRO(QT4_WRAP_UI_BALL outfiles ) +- QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN}) +- +- ### BALL ### ++ # since 2.8.12 qt4_extract_options has an additional argument ++ # copied fix from OpenMS ++ IF(${CMAKE_VERSION} VERSION_LESS "2.8.12") ++ QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN}) ++ ELSE() ++ QT4_EXTRACT_OPTIONS(ui_files ui_options ui_target ${ARGN}) ++ ENDIF() ++ ++ ### BALL ### + # create output directory (will not exist for out-of-source builds) + FILE(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/) + + FOREACH (it ${ui_files}) + GET_FILENAME_COMPONENT(outfile ${it} NAME_WE) + GET_FILENAME_COMPONENT(infile ${it} ABSOLUTE) +- ### BALL ### ++ ### BALL ### + SET(outfile ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/ui_${outfile}.h) + ADD_CUSTOM_COMMAND(OUTPUT ${outfile} + COMMAND ${QT_UIC_EXECUTABLE} +-- +1.9.1 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch b/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch new file mode 100644 index 000000000000..825f41978c13 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch @@ -0,0 +1,16 @@ + source/APPLICATIONS/BALLVIEW/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt +index 6d16212..f94ce76 100644 +--- a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt ++++ b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt +@@ -85,7 +85,7 @@ IF (UNIX) + LIST(APPEND BALLVIEW_SUPPORT_LIBRARIES "pthread") + ENDIF () + +-TARGET_LINK_LIBRARIES(BALLView BALL VIEW ${BALLVIEW_SUPPORT_LIBRARIES}) ++TARGET_LINK_LIBRARIES(BALLView BALL VIEW ${BALLVIEW_SUPPORT_LIBRARIES} X11) + + #Setup the translations + INCLUDE(${CMAKE_SOURCE_DIR}/cmake/BALLViewTranslations.cmake) diff --git a/sci-chemistry/ball/metadata.xml b/sci-chemistry/ball/metadata.xml new file mode 100644 index 000000000000..066e13dd4a53 --- /dev/null +++ b/sci-chemistry/ball/metadata.xml @@ -0,0 +1,32 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +Rapid Software Prototyping can significantly reduce development times in the +field of Computational Molecular Biology and Molecular Modeling. +BALL (Biochemical Algorithms Library) is an application framework in C++ that +has been specifically designed for this purpose. It provides an extensive set +of data structures as well as classes for Molecular Mechanics, advanced +solvation methods, comparison and analysis of protein structures, file +import/export, and visualization . + +BALL has been carefully designed to be robust, easy to use, and open to +extensions. Especially its extensibility which results from an object-oriented +and generic programming approach distinguishes it from other software packages. +BALL is well suited to serve as a public repository for reliable data +structures and algorithms. + +Based on BALL we have developed a stand-alone tool for molecular visualization, +BALLView . BALLView makes the broad functionality available through an +integrated user-friendly GUI. +</longdescription> + <use> + <flag name="sql">Include SQL database support</flag> + <flag name="cuda">Include cuda support</flag> + <flag name="webkit">Uses <pkg>dev-qt/qtwebkit</pkg> for drawing</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/bkchem/Manifest b/sci-chemistry/bkchem/Manifest new file mode 100644 index 000000000000..8073e9e6a720 --- /dev/null +++ b/sci-chemistry/bkchem/Manifest @@ -0,0 +1 @@ +DIST bkchem-0.14.0-pre2.tar.gz 998916 SHA256 65b93128932959b394eff8e5a8018a19b30d26ee1ae44345e8bb87167303ed26 SHA512 7fc3bbd7bfe27bc91cf69a98c347a3fb92f4ea25b45a13debd0646a6b02d7a40c5729ae1b2a9ac33c1049d6b90e38355c3cd80e06660a0a2fcc5dafb3514ef20 WHIRLPOOL 732bc45913248aa3df5929933f2072d09d90a46cdc3b3e22f1849adf391d7fd62704e71a98e24649bd74e1ebe96b30d7d398dadabffc0fcd114d8c13922241c6 diff --git a/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r1.ebuild b/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r1.ebuild new file mode 100644 index 000000000000..c5aa86e917a0 --- /dev/null +++ b/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +PYTHON_REQ_USE="tk" + +inherit distutils-r1 eutils versionator + +MY_P="${PN}-$(replace_version_separator 3 -)" + +DESCRIPTION="Chemical drawing program" +HOMEPAGE="http://bkchem.zirael.org/" +SRC_URI="http://bkchem.zirael.org/download/${MY_P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +LICENSE="GPL-2" +IUSE="cairo" + +DEPEND="cairo? ( dev-python/pycairo[svg,${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${MY_P} + +PATCHES=( + "${FILESDIR}"/${P}-nolauncher.patch +) + +python_install() { + distutils-r1_python_install "--strip=${ED}/_${EPYTHON}" +} + +python_install_all() { + distutils-r1_python_install_all + python_foreach_impl python_newscript ${PN}/${PN}.py ${PN} + make_desktop_entry bkchem BKChem "${EPREFIX}"/usr/share/${PN}/images/${PN}.png Science +} diff --git a/sci-chemistry/bkchem/files/0.14.0_pre1-piddle-Fix-assertions.patch b/sci-chemistry/bkchem/files/0.14.0_pre1-piddle-Fix-assertions.patch new file mode 100644 index 000000000000..6270e59d5320 --- /dev/null +++ b/sci-chemistry/bkchem/files/0.14.0_pre1-piddle-Fix-assertions.patch @@ -0,0 +1,48 @@ +diff --git a/bkchem/plugins/piddle/pdfgen.py b/bkchem/plugins/piddle/pdfgen.py +index 5213672..4c056c7 100644 +--- a/bkchem/plugins/piddle/pdfgen.py ++++ b/bkchem/plugins/piddle/pdfgen.py +@@ -639,7 +639,7 @@ class Canvas: + + #use a flate filter and Ascii Base 85 to compress + raw = myimage.tostring() +- assert(len(raw) == imgwidth * imgheight, "Wrong amount of data for image") ++ assert len(raw) == imgwidth * imgheight, "Wrong amount of data for image" + compressed = zlib.compress(raw) #this bit is very fast... + encoded = pdfutils._AsciiBase85Encode(compressed) #...sadly this isn't + +diff --git a/bkchem/plugins/piddle/pdfutils.py b/bkchem/plugins/piddle/pdfutils.py +index ebde677..4a7675d 100644 +--- a/bkchem/plugins/piddle/pdfutils.py ++++ b/bkchem/plugins/piddle/pdfutils.py +@@ -27,7 +27,7 @@ def cacheImageFile(filename): + code.append('ID') + #use a flate filter and Ascii Base 85 + raw = img.tostring() +- assert(len(raw) == imgwidth * imgheight, "Wrong amount of data for image") ++ assert len(raw) == imgwidth * imgheight, "Wrong amount of data for image" + compressed = zlib.compress(raw) #this bit is very fast... + encoded = _AsciiBase85Encode(compressed) #...sadly this isn't + +diff --git a/bkchem/plugins/piddle/piddlePS.py b/bkchem/plugins/piddle/piddlePS.py +index 4d3c327..3afa361 100644 +--- a/bkchem/plugins/piddle/piddlePS.py ++++ b/bkchem/plugins/piddle/piddlePS.py +@@ -866,7 +866,7 @@ translate + # piddlePDF again + + rawimage = myimage.tostring() +- assert(len(rawimage) == imgwidth*imgheight, 'Wrong amount of data for image') ++ assert len(rawimage) == imgwidth*imgheight, 'Wrong amount of data for image' + #compressed = zlib.compress(rawimage) # no zlib at moment + hex_encoded = self._AsciiHexEncode(rawimage) + +@@ -957,7 +957,7 @@ translate + 'image']) + # after image operator just need to dump image dat to file as hexstring + rawimage = myimage.tostring() +- assert(len(rawimage) == imwidth*imheight, 'Wrong amount of data for image') ++ assert len(rawimage) == imwidth*imheight, 'Wrong amount of data for image' + #compressed = zlib.compress(rawimage) # no zlib at moment + hex_encoded = self._AsciiHexEncode(rawimage) + diff --git a/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch b/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch new file mode 100644 index 000000000000..202c47a9c74f --- /dev/null +++ b/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch @@ -0,0 +1,106 @@ + bkchem/bkchem.py | 24 +++++++++++++----------- + setup.py | 23 ----------------------- + 2 files changed, 13 insertions(+), 34 deletions(-) + +diff --git a/bkchem/bkchem.py b/bkchem/bkchem.py +index b336b9c..bcb68b0 100644 +--- a/bkchem/bkchem.py ++++ b/bkchem/bkchem.py +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python2 + #-------------------------------------------------------------------------- + # This file is part of BKChem - a chemical drawing program + # Copyright (C) 2002-2009 Beda Kosata <beda@zirael.org> +@@ -18,18 +19,19 @@ + #-------------------------------------------------------------------------- + + +-"""this is just a starter of the application""" ++#"""this is just a starter of the application""" + + ## support for loading from outside of bkchem dir + +-import os_support, sys ++from bkchem import os_support ++import sys + sys.path.insert( 1, os_support.get_module_path()) + + + ### now starting for real + +-from singleton_store import Store +-import pref_manager ++from bkchem.singleton_store import Store ++from bkchem import pref_manager + + # at first preference manager + Store.pm = pref_manager.pref_manager( +@@ -78,13 +80,13 @@ else: + + + +-import config ++from bkchem import config + + if not config.debug: + # checking of important modules availability + # import modules +- import import_checker +- import messages ++ from bkchem import import_checker ++ from bkchem import messages + + # we need sets from the 2.3 version + if not import_checker.python_version_ok: +@@ -103,16 +105,16 @@ if not config.debug: + + + #import Tkinter +-from main import BKChem +-from splash import Splash +-from singleton_store import Store ++from bkchem.main import BKChem ++from bkchem.splash import Splash ++from bkchem.singleton_store import Store + + myapp = BKChem() + myapp.withdraw() + + if __name__ == '__main__': + +- import messages ++ from bkchem import messages + enc = sys.getfilesystemencoding() + if not enc: + enc = sys.getdefaultencoding() +diff --git a/setup.py b/setup.py +index d4b2a21..2319216 100755 +--- a/setup.py ++++ b/setup.py +@@ -91,26 +91,3 @@ if len( sys.argv) > 1 and sys.argv[1] == 'install' and '--help' not in sys.argv: + print "file %s created" % config_name + + +- # the executable +- if not os.path.isdir( bin_dir): +- try: +- os.mkdir( bin_dir) +- except: +- print "ERROR: could not create directory %s" % bin_dir +- sys.exit( 201) +- exec_name = os.path.join( bin_dir, 'bkchem') +- try: +- file = open( exec_name, 'w') +- except: +- print "ERROR: couldn't open the file %s for write" % exec_name +- sys.exit( 201) +- file.write( "#!/bin/sh\n") +- file.write( 'python %s "$@"\n' % strip_path( os.path.join( py_dir, "bkchem", "bkchem.py"))) +- file.close() +- print "file %s created" % exec_name +- try: +- os.chmod( os.path.join( bin_dir, 'bkchem'), 5+5*8+7*8*8) +- except: +- print "ERROR: failed to make %s executable" % exec_name +- sys.exit( 201) +- print "file %s made executable" % exec_name diff --git a/sci-chemistry/bkchem/metadata.xml b/sci-chemistry/bkchem/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/bkchem/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/bodr/Manifest b/sci-chemistry/bodr/Manifest new file mode 100644 index 000000000000..53b218466c9e --- /dev/null +++ b/sci-chemistry/bodr/Manifest @@ -0,0 +1,2 @@ +DIST bodr-10.tar.bz2 225671 SHA256 738a0f0e263cdc088581d0a67a0ea16ec586ceb424704d0ff73bdb5da5d4ee81 SHA512 a3e0e7195914938d8824127aa4777c4054c302ef7811d82d1e012d9be5d7a13d7f2225d4216f4a30ae7dbf70eb3b0b38571c3ee0dbe1d97af15f04171dd51bec WHIRLPOOL e61db3427f6f994a1a628eec12c1a41cf8d9cdbd1a16814a267363ffe4fa320f3fb9b03f8188c746899774631dc5d0398830b8d779d225f3317158809c182c3e +DIST bodr-9.tar.bz2 210548 SHA256 a7ed30ecc385ff9fe9b2af84710574ac12febea081b5123db6d6337a4a7a4b60 SHA512 5bcdd682729e11a0bc48f9306262e03fa2a3ca3a805633c2b40d7f94608ce6e2e778cc89ed0c57ec3bf6105c2f759204e158ac6f29c9e6ee3aa37190f8f0d772 WHIRLPOOL 78061c24718a4ce5c5694e369d3c97eb90826b2c3b3f694ba9a0f405173ef0efdc565583373b26c96582c853e1606314ee2c5ab3e5cc8e889c0625358f87291b diff --git a/sci-chemistry/bodr/bodr-10.ebuild b/sci-chemistry/bodr/bodr-10.ebuild new file mode 100644 index 000000000000..7958b8c319da --- /dev/null +++ b/sci-chemistry/bodr/bodr-10.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="The Blue Obelisk Data Repository listing element and isotope properties" +HOMEPAGE="http://sourceforge.net/projects/bodr" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos" +IUSE="" + +DEPEND="dev-libs/libxslt" +RDEPEND="" + +DOCS=( "THANKS" "AUTHORS" "README" "ChangeLog" ) + +src_prepare(){ + sed -i -e "s/COPYING//g" Makefile.* || die +} + +src_configure() { + econf --docdir="${EPREFIX}"/usr/share/doc/${PF} +} diff --git a/sci-chemistry/bodr/bodr-9-r1.ebuild b/sci-chemistry/bodr/bodr-9-r1.ebuild new file mode 100644 index 000000000000..7958b8c319da --- /dev/null +++ b/sci-chemistry/bodr/bodr-9-r1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="The Blue Obelisk Data Repository listing element and isotope properties" +HOMEPAGE="http://sourceforge.net/projects/bodr" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos" +IUSE="" + +DEPEND="dev-libs/libxslt" +RDEPEND="" + +DOCS=( "THANKS" "AUTHORS" "README" "ChangeLog" ) + +src_prepare(){ + sed -i -e "s/COPYING//g" Makefile.* || die +} + +src_configure() { + econf --docdir="${EPREFIX}"/usr/share/doc/${PF} +} diff --git a/sci-chemistry/bodr/metadata.xml b/sci-chemistry/bodr/metadata.xml new file mode 100644 index 000000000000..a30a888d000f --- /dev/null +++ b/sci-chemistry/bodr/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> + Blue Obelisk Data Repository (BODR) is a shared data repository. It lists + many important chemoinformatics data such as elemental properties, atomic + radii, etc. including references to original literature. Software developers + can use this repository on online webpages or in chemistry software for + free. + </longdescription> + <upstream> + <remote-id type="sourceforge">bodr</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/burrow-owl/Manifest b/sci-chemistry/burrow-owl/Manifest new file mode 100644 index 000000000000..8b584ea4ad29 --- /dev/null +++ b/sci-chemistry/burrow-owl/Manifest @@ -0,0 +1,2 @@ +DIST burrow-demos.tar 80896000 SHA256 f93e957889adab0521c6e3234f117cf984b7bb18ba6641a3edbdd30202db4b96 SHA512 76948846b4bff2f5c0814e41ee1745122580d6e28f8de217edbf42c4530bc64fb093dc9c96e9c0c083098755c525300b563ee1368caa12be791b2bea7015ee6b WHIRLPOOL 88ca227d8e808814187630c9568e927620a0dc4fb0eba4131ab14cae842aa778fda6294b32e8ec0e23224fca3b5a2a65609ed7f97a34691267439a557bfa0c42 +DIST burrow-owl-1.5.1.tar.gz 1408249 SHA256 76a4ab0746b1b945e0177d441f7ced8042063d4ff2c9171343ea20ddc19a9bbb SHA512 38b428c8b40cdca6caabc7ed9d247118dbf67b537afaec3af14909353d6b138fdf98a33dee6241ce5224631e16c4dbce11b9aadcfe01fecf92f1aae692ce71e1 WHIRLPOOL e165b0508b28e03a47c77ee72ea0d2347ef9088fe33df9788935e3ec0906efd511f77eebe27d74ed79a913f420cde015a39faebdc3195edc1d279ac0d607d39b diff --git a/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild b/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild new file mode 100644 index 000000000000..76018815c9cd --- /dev/null +++ b/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit autotools-utils virtualx + +DESCRIPTION="Visualize multidimensional nuclear magnetic resonance (NMR) spectra" +HOMEPAGE="http://burrow-owl.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${P}.tar.gz + examples? ( mirror://sourceforge/${PN}/burrow-demos.tar )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples static-libs" + +RDEPEND=" + dev-libs/g-wrap + dev-libs/glib:2 + dev-scheme/guile[networking,regex] + dev-scheme/guile-cairo + dev-scheme/guile-gnome-platform + sci-libs/starparse + x11-libs/gtk+:2" +DEPEND="${RDEPEND} + dev-util/indent + virtual/pkgconfig + doc? ( app-doc/doxygen ) +" + +src_configure() { + local myeconfargs=( + $(use_with doc doxygen doxygen) + ) + autotools-utils_src_configure +} + +src_test () { + cd "${AUTOTOOLS_BUILD_DIR}" || die + virtualmake -C test-suite check +} + +src_install() { + use doc && HTML_DOCS=( "${AUTOTOOLS_BUILD_DIR}/doc/api/html/." ) + autotools-utils_src_install + + use examples && \ + insinto /usr/share/${PN} && \ + doins -r "${WORKDIR}"/burrow-demos/* +} diff --git a/sci-chemistry/burrow-owl/files/1.4-glibc-2.12.patch b/sci-chemistry/burrow-owl/files/1.4-glibc-2.12.patch new file mode 100644 index 000000000000..cca640a6347d --- /dev/null +++ b/sci-chemistry/burrow-owl/files/1.4-glibc-2.12.patch @@ -0,0 +1,38 @@ +Fix build with GLIBC-2.12 + +http://bugs.gentoo.org/show_bug.cgi?id=333843 + +--- src/Makefile.am ++++ src/Makefile.am +@@ -82,8 +82,8 @@ + painter.h \ + ticket.c \ + ticket.h \ +-endian.c \ +-endian.h \ ++bo_endian.c \ ++bo_endian.h \ + version.c \ + version.h + +--- src/hosbackingfile.c ++++ src/hosbackingfile.c +@@ -18,6 +18,7 @@ + */ + + #include "hosbackingfile.h" ++#include "bo_endian.h" + + #define DEFAULT_BUF_SIZE 512 + +--- src/nih.c ++++ src/nih.c +@@ -24,7 +24,7 @@ + #include "hosdimensionblock.h" + #include "hosbackingblock.h" + #include "hosbackingfile.h" +-#include "endian.h" ++#include "bo_endian.h" + + /* --- header contents ---- + * diff --git a/sci-chemistry/burrow-owl/files/1.4-include.patch b/sci-chemistry/burrow-owl/files/1.4-include.patch new file mode 100644 index 000000000000..3dc4cbdf8000 --- /dev/null +++ b/sci-chemistry/burrow-owl/files/1.4-include.patch @@ -0,0 +1,12 @@ +diff --git a/src/gw/spectrum-spec.scm b/src/gw/spectrum-spec.scm +index 253464c..605796c 100644 +--- a/src/gw/spectrum-spec.scm ++++ b/src/gw/spectrum-spec.scm +@@ -30,6 +30,7 @@ + "#include <painter_gdk.h>\n" + "#include <burrow/nih.h>\n" + "#include <hosbackingsim.h>\n" ++ "#include <guile-cairo/guile-cairo-smob-types.h>\n" + "\n")) + + ; couple of disabled sources diff --git a/sci-chemistry/burrow-owl/files/burrow-owl-1.5-prll.patch b/sci-chemistry/burrow-owl/files/burrow-owl-1.5-prll.patch new file mode 100644 index 000000000000..340ccd2366e5 --- /dev/null +++ b/sci-chemistry/burrow-owl/files/burrow-owl-1.5-prll.patch @@ -0,0 +1,20 @@ + burrow/canvas/gw/Makefile.am | 4 +++- + 1 files changed, 3 insertions(+), 1 deletions(-) + +diff --git a/burrow/canvas/gw/Makefile.am b/burrow/canvas/gw/Makefile.am +index da50ee3..2ed89bc 100644 +--- a/burrow/canvas/gw/Makefile.am ++++ b/burrow/canvas/gw/Makefile.am +@@ -31,9 +31,11 @@ H2DEF=@top_srcdir@/utils/h2def.py + canvas.defs: $(HEADERS_1) + $(H2DEF) --all $(HEADERS_1) > $@ + +-canvas-gw.c canvas-gw.h canvas-gw.scm: canvas.defs ++canvas-gw.c canvas-gw.h: canvas.defs + GUILE_LOAD_PATH=@srcdir@:@builddir@:@GUILE_GNOME_MODULE_DIR@:@G_WRAP_MODULE_DIR@:$$GUILE_LOAD_PATH $(GUILE) -s @srcdir@/run-g-wrap.scm + ++BUILT_SOURCES=canvas-gw.c canvas-gw.h canvas.defs ++ + INCLUDES=@GTK_CFLAGS@ @G_WRAP_CFLAGS@ @GUILE_GNOME_CFLAGS@ @GUILE_CAIRO_CFLAGS@ @GUILE_CFLAGS@ -I$(headers_dir) -I@top_srcdir@ + + moduledir=$(datadir)/guile/burrow diff --git a/sci-chemistry/burrow-owl/metadata.xml b/sci-chemistry/burrow-owl/metadata.xml new file mode 100644 index 000000000000..9849d77b1370 --- /dev/null +++ b/sci-chemistry/burrow-owl/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">burrow-owl</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/cara-bin/Manifest b/sci-chemistry/cara-bin/Manifest new file mode 100644 index 000000000000..12c0fa6dee54 --- /dev/null +++ b/sci-chemistry/cara-bin/Manifest @@ -0,0 +1,2 @@ +DIST Start1.2.cara.xz 43124 SHA256 c28321b051902bc020ea04a46b33ceb19b1b3d902264956474c90798f2d60d25 SHA512 26874d634491558dc593a0ec32e83d5cfceedc69bbf901f4d25d6b9515b84aebffbf495d1ac34b3664b8b5822954edf62c5b88dcca6bcfcb152715caa88f5f03 WHIRLPOOL 034e8b73354e7244e4fcc21c03da7b99c02019ebef1e0754dd9cb8249fe68b82be1e78db9848912fc48c8625b0f2acf0f41242d83949a117f0b8a648a930445e +DIST cara_1.8.4_linux.gz 6677463 SHA256 5ba34cc8b0782e1791186cde5a02ec036665769df7f5c559db27377b6f3cc6d6 SHA512 e264cfbef640f267132dfd48b940203a319c8f34de71c5b786c6bfc2ab561bdf3fbd79516d619ca52b2aca64a2887f770fabfabedb76433c5f78aa02c65f898f WHIRLPOOL 5619c70bc31dfb328a72233c8fc3e3d8dcfdccc3db4e5a67430f0ebe8a0a474f998abb2a0ec56f4a3c2e6e4b95e324ec3c667864c81cb3531a1e162439c780da diff --git a/sci-chemistry/cara-bin/cara-bin-1.8.4-r1.ebuild b/sci-chemistry/cara-bin/cara-bin-1.8.4-r1.ebuild new file mode 100644 index 000000000000..d17c035cd3bc --- /dev/null +++ b/sci-chemistry/cara-bin/cara-bin-1.8.4-r1.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MY_PN="${PN%%-bin}" +MY_P="${MY_PN}_${PV}" + +DESCRIPTION="Analysis of NMR spectra and Computer Aided Resonance Assignment" +SRC_URI=" + http://www.cara.nmr-software.org/downloads/${MY_P}_linux.gz + http://dev.gentoo.org/~jlec/distfiles//Start1.2.cara.xz" +HOMEPAGE="http://www.nmr.ch" + +LICENSE="CARA" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="lua" + +RDEPEND=" + !prefix? ( + >=media-libs/fontconfig-2.10.92[abi_x86_32(-)] + >=media-libs/freetype-2.5.0.1[abi_x86_32(-)] + >=x11-libs/libICE-1.0.8-r1[abi_x86_32(-)] + >=x11-libs/libSM-1.2.1-r1[abi_x86_32(-)] + >=x11-libs/libX11-1.6.2[abi_x86_32(-)] + >=x11-libs/libXcursor-1.1.14[abi_x86_32(-)] + >=x11-libs/libXext-1.3.2[abi_x86_32(-)] + >=x11-libs/libXi-1.7.2[abi_x86_32(-)] + >=x11-libs/libXrandr-1.4.2[abi_x86_32(-)] + >=x11-libs/libXrender-0.9.8[abi_x86_32(-)] + ) + virtual/libstdc++ + lua? ( dev-lang/lua )" +DEPEND="" + +RESTRICT="mirror" + +QA_PREBUILT="opt/cara/*" + +S="${WORKDIR}" + +src_install() { + exeinto /opt/cara + doexe ${MY_P}_linux + dosym ../cara/${MY_P}_linux /opt/bin/cara + dodoc Start1.2.cara +} diff --git a/sci-chemistry/cara-bin/metadata.xml b/sci-chemistry/cara-bin/metadata.xml new file mode 100644 index 000000000000..4a00a64b40ae --- /dev/null +++ b/sci-chemistry/cara-bin/metadata.xml @@ -0,0 +1,7 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest new file mode 100644 index 000000000000..e56aec5512a2 --- /dev/null +++ b/sci-chemistry/ccp4-apps/Manifest @@ -0,0 +1,2 @@ +DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820 +DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild new file mode 100644 index 000000000000..854cc48db0cf --- /dev/null +++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild @@ -0,0 +1,395 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools eutils fortran-2 flag-o-matic gnuconfig python-single-r1 toolchain-funcs + +MY_P="${PN/-apps}-${PV}" + +#UPDATE="04_03_09" +#PATCHDATE="090511" + +PATCH_TOT="0" + +DESCRIPTION="Protein X-ray crystallography toolkit" +HOMEPAGE="http://www.ccp4.ac.uk/" +SRC="ftp://ftp.ccp4.ac.uk/ccp4" +SRC_URI=" + ${SRC}/${PV}/${MY_P}-core-src.tar.gz + http://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" +# patch tarball from upstream + [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" +# patches created by us + [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" + +for i in $(seq $PATCH_TOT); do + NAME="PATCH${i}[1]" + SRC_URI="${SRC_URI} + ${SRC}/${PV}/patches/${!NAME}" +done + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="examples X" + +X11DEPS=" + x11-libs/libX11 + x11-libs/libXaw + x11-libs/libXt + x11-libs/libxdl_view" + +TKDEPS=" + >=dev-lang/tk-8.3:0= + >=dev-tcltk/blt-2.4 + dev-tcltk/iwidgets + dev-tcltk/itcl + dev-tcltk/itk + >=dev-tcltk/tdom-0.8 + dev-tcltk/tktreectrl" + +SCILIBS=" + ~sci-libs/ccp4-libs-${PV} + >=sci-libs/ccp4-libs-${PV}-r7 + sci-libs/clipper + sci-libs/fftw:2.1 + sci-libs/mmdb:0 + sci-libs/ssm + virtual/blas + virtual/lapack" + +SCIAPPS=" + sci-chemistry/pdb-extract + sci-chemistry/pymol + sci-chemistry/rasmol + >=sci-chemistry/oasis-4.0-r1" + +RDEPEND=" + ${TKDEPS} + ${SCILIBS} + app-shells/tcsh + dev-python/pyxml + dev-libs/libxml2:2 + dev-libs/libjwc_c + dev-libs/libjwc_f + dev-libs/boehm-gc + !app-office/sc + !<sci-chemistry/ccp4-6.1.3 + X? ( ${X11DEPS} )" +DEPEND="${RDEPEND} + X? ( + x11-misc/imake + x11-proto/inputproto + x11-proto/xextproto + )" +PDEPEND="${SCIAPPS}" + +RESTRICT="mirror" + +S="${WORKDIR}/${MY_P}" + +pkg_setup() { + fortran-2_pkg_setup + python-single-r1_pkg_setup +} + +src_prepare() { + tc-export PKG_CONFIG + einfo "Applying upstream patches ..." + for patch in $(seq $PATCH_TOT); do + base="PATCH${patch}" + dir=$(eval echo \${${base}[0]}) + p=$(eval echo \${${base}[1]}) + pushd "${dir}" >& /dev/null + ccp_patch "${DISTDIR}/${p}" + popd >& /dev/null + done + einfo "Done." + echo + + [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch + + einfo "Applying Gentoo patches ..." + + # it tries to create libdir, bindir etc on live system in configure + ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch + + # We already have sci-chemistry/rasmol + # Also remember to create the bindir. + ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch + + # libraries come from sci-libs/ccp4-libs + ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch + + # We have seperate ebuilds for those + for bin in molref xia scala imosflm balbes; do + ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch + done + + # don't configure what is not build + ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-pisa.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch + + # Fix upstreams code + ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch + + # Not renaming, but unbundling libs + ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch + + # Use pkg-config to detect BLAS/LAPCK + ccp_patch "${FILESDIR}"/${PV}-lapack.patch + + # unbundle libs + ccp_patch "${FILESDIR}"/${PV}-unbundle.patch + + # tcl-8.6 + ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch + + # Update things for oasis 4 usage + epatch "${WORKDIR}"/${PV}-oasis4.0.patch + sed 's: oasis : :g' -i src/Makefile.in || die + + einfo "Done." # done applying Gentoo patches + echo + + find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete + + sed \ + -e "s:/usr:${EPREFIX}/usr:g" \ + -e 's:-Wl,-rpath,$CLIB::g' \ + -e 's: -rpath $CLIB::g' \ + -e 's: -I${srcdir}/include/cpp_c_headers::g' \ + -e 's:sleep 1:sleep .2:g' \ + -e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \ + -e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \ + -e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \ + -e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \ + -i configure || die + + sed \ + -e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \ + -i src/Makefile* || die + + find "${S}" -name "Makefile.*" \ + -exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \; + + # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version + sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die + + # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those. + pushd src/rapper 2>/dev/null + eautoreconf + popd 2>/dev/null + + gnuconfig_update + + python_fix_shebang -f . +} + +src_configure() { + # Build system is broken if we set LDFLAGS + export GENTOOLDFLAGS="${LDFLAGS}" + unset LDFLAGS + + # These are broken with ./src/procheck/ps.f + filter-flags "-floop-*" + + # GENTOO_OSNAME can be one of: + # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd + # linux_compaq_compilers linux_intel_compilers generic Darwin + # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers + if [[ "$(tc-getFC)" = "ifort" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + "${S}"/include/ccp4.setup + + # We agree to the license by emerging this, set in LICENSE + sed -i \ + -e "s~^\(^agreed=\).*~\1yes~g" \ + "${S}"/configure || die + + # Fix up variables -- need to reset CCP4_MASTER at install-time + sed -i \ + -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ + -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ + -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ + -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ + -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ + "${S}"/include/ccp4.setup* || die + + # Set up variables for build + source "${S}"/include/ccp4.setup-sh + + export CC=$(tc-getCC) + export CXX=$(tc-getCXX) + export COPTIM=${CFLAGS} + export CXXOPTIM=${CXXFLAGS} + # Default to -O2 if FFLAGS is unset + export FC=$(tc-getFC) + export FOPTIM=${FFLAGS:- -O2} + export BINSORT_SCR="${T}" + export CCP4_MASTER="${WORKDIR}" + export CCP4I_TCLTK="${EPREFIX}/usr/bin" + export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}" + + # Can't use econf, configure rejects unknown options like --prefix + ./configure \ + $(use_enable X x) \ + --with-shared-libs \ + --with-fftw="${EPREFIX}/usr" \ + --with-warnings \ + --disable-pdb_extract \ + --disable-cctbx \ + --disable-phaser \ + --disable-diffractionImg \ + --disable-clipper \ + --disable-ssm \ + --disable-mosflm \ + --disable-mrbump \ + --tmpdir="${TMPDIR}" \ + ${GENTOO_OSNAME} || die "configure failed" + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd src/clipper_progs 2>/dev/null + econf \ + --prefix="${S}" \ + --bindir="${ED}"/usr/libexec/ccp4/bin \ + --with-ccp4="${S}" \ + --with-clipper="${EPREFIX}/usr" \ + --with-fftw="${EPREFIX}/usr" \ + --with-mmdb="${EPREFIX}/usr" \ + CXX=$(tc-getCXX) + popd 2>/dev/null +} + +src_compile() { + # fsplit is required for the programs + pushd lib/src 2>/dev/null + emake fsplit -j1 || die + popd 2>/dev/null + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd src/clipper_progs 2>/dev/null + emake || die + popd 2>/dev/null + + emake -j1 || die "emake failed" +} + +src_install() { + # Set up variables for build + source "${S}"/include/ccp4.setup-sh + + # if we don't make this, a ton of programs fail to install + mkdir "${S}"/bin || die + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd "${S}"/src/clipper_progs 2>/dev/null + emake install || die + popd 2>/dev/null + + einstall || die "install failed" + + # Collision with sci-chemistry/mrbump + rm -f "${S}"/bin/{mrbump,pydbviewer} || die + + # Bins + exeinto /usr/libexec/ccp4/bin/ + doexe "${S}"/bin/* || die + + # Libs + for file in "${S}"/lib/*; do + if [[ -d ${file} ]]; then + continue + elif [[ -x ${file} ]]; then + dolib.so ${file} || die + else + insinto /usr/$(get_libdir) + doins ${file} || die + fi + done + + rm -f "${S}"/include/ccp4.setup* + + # smartie -- log parsing + insinto /usr/share/ccp4 + doins -r "${S}"/share/smartie || die + + # Install docs and examples + local _man + pushd "${S}"/man/cat1 > /dev/null + for _man in *; do + newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2} + done + popd > /dev/null + + mv "${S}"/manual/README "${S}"/manual/README-manual + dodoc manual/* README CHANGES doc/* examples/README || die + + rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.* + rm "${ED}"/usr/share/doc/${PF}/COPYING.* + + dohtml -r "${S}"/html/* + + if use examples; then + for i in data rnase toxd; do + docinto examples/${i} + dodoc "${S}"/examples/${i}/* + done + + docinto examples/tutorial + dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css + for i in data results; do + docinto examples/tutorial/${i} + dodoc "${S}"/examples/tutorial/${i}/* + done + + for i in non-runnable runnable; do + docinto examples/unix/${i} + dodoc "${S}"/examples/unix/${i}/* + done + fi + # Needed for ccp4i docs to work + dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die + + cat >> "${T}"/baubles <<- EOF + #!${EPREFIX}/bin/bash + exec "${EPYTHON}" "\${CCP4}/share/ccp4/smartie/baubles.py" + EOF + + exeinto /usr/libexec/ccp4/bin/ + doexe "${T}"/baubles || die +} + +# Epatch wrapper for bulk patching +ccp_patch() { + EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} +} diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch new file mode 100644 index 000000000000..433a78dbd23b --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch @@ -0,0 +1,70 @@ +--- src/clipper_progs/src/intensity_target.h.orig 2010-01-21 11:27:13.236795886 -0600 ++++ src/clipper_progs/src/intensity_target.h 2010-01-21 11:31:33.450686927 -0600 +@@ -70,9 +70,31 @@ + { + public: + //! constructor: takes the datalist against which to calc target +- TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ); ++ TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) ++ { ++ hkl_data1 = &hkl_data1_; ++ hkl_data2 = &hkl_data2_; ++ } + //! return the value and derivatives of the target function +- Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const; ++ Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const ++ { ++ Rderiv result; ++ result.r = result.dr = result.dr2 = 0.0; ++ const T1& it1 = (*hkl_data1)[ih]; ++ const T2& it2 = (*hkl_data2)[ih]; ++ if ( !it1.missing() && !it2.missing() ) ++ if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { ++ const ftype eps = ih.hkl_class().epsilon(); ++ const ftype i1 = it1.I() / eps; ++ const ftype i2 = it2.I() / eps; ++ const ftype w = sqrt( i1 * i2 ); ++ const ftype d = intensityh + log(i1) - log(i2); ++ result.r = w * d * d; ++ result.dr = 2.0 * w * d; ++ result.dr2 = 2.0 * w; ++ } ++ return result; ++ } + //! the type of the function: optionally used to improve convergence + FNtype type() const { return QUADRATIC; } + private: +@@ -109,33 +131,4 @@ + return result; + } + +- // Log I1-I2 scaling +- +- template<class T1, class T2> TargetFn_scaleLogI1I2<T1,T2>::TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) +- { +- hkl_data1 = &hkl_data1_; +- hkl_data2 = &hkl_data2_; +- } +- +- template<class T1, class T2> TargetFn_base::Rderiv TargetFn_scaleLogI1I2<T1,T2>::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const +- { +- Rderiv result; +- result.r = result.dr = result.dr2 = 0.0; +- const T1& it1 = (*hkl_data1)[ih]; +- const T2& it2 = (*hkl_data2)[ih]; +- if ( !it1.missing() && !it2.missing() ) +- if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { +- const ftype eps = ih.hkl_class().epsilon(); +- const ftype i1 = it1.I() / eps; +- const ftype i2 = it2.I() / eps; +- const ftype w = sqrt( i1 * i2 ); +- const ftype d = intensityh + log(i1) - log(i2); +- result.r = w * d * d; +- result.dr = 2.0 * w * d; +- result.dr2 = 2.0 * w; +- } +- return result; +- } +- +- + #endif diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch new file mode 100644 index 000000000000..f1df3e5e19f9 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch @@ -0,0 +1,14 @@ +diff --git a/share/Makefile.in b/share/Makefile.in +index 2d4f20b..4500993 100755 +--- a/share/Makefile.in ++++ b/share/Makefile.in +@@ -18,9 +18,6 @@ install : + for i in $(MRBUMP_TARGETS); do \ + test -s $(MRBUMP_BINDIR)/$$i && $(INSTALL_PROGRAM) $(MRBUMP_BINDIR)/$$i $(bindir)/$$i || true ;\ + done +- for i in $(BALBES_TARGETS); do \ +- test -s $(BALBES_BINDIR)/$$i && $(INSTALL_PROGRAM) $(BALBES_BINDIR)/$$i $(bindir)/$$i || true ;\ +- done + + clean : ; -rm -f core *.o *~ a.out + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch new file mode 100644 index 000000000000..e62ae12adfbe --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch @@ -0,0 +1,24 @@ +--- ccp4-6.1.1/x-windows/Makefile.in 2008-08-11 19:20:01.000000000 +0200 ++++ ccp4-6.1.1/x-windows/Makefile.in.new 2009-02-27 14:32:25.000000000 +0100 +@@ -35,7 +35,7 @@ + # + # all + # +-all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy rasmol2 ipmosflm ++all : rotgen_ hklview xjiffy + # + # xdl_view + # +@@ -157,11 +157,10 @@ + # + install_obj = hklview rotgen ipmosflm + install: all ++ mkdir -p $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) + cd $(srcdir)/XCCPJIFFY ; $(MAKE) bindir=$(bindir) libdir=$(libdir) install +- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install +- $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) + # + # clean + # diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch new file mode 100644 index 000000000000..f645643e1c67 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch @@ -0,0 +1,11 @@ +--- ccp4i/Makefile.in 2009-06-19 15:08:53.000000000 +0200 ++++ ccp4i/Makefile.in.new 2009-08-04 21:10:14.000000000 +0200 +@@ -9,7 +9,7 @@ + SHELL = /bin/sh + DESTDIR = $(prefix) + CCP4I_BINDIR = $(top_srcdir)/ccp4i/bin +-CCP4I_TARGETS = ccp4i imosflm loggraph crank mapslicer ++CCP4I_TARGETS = ccp4i loggraph crank mapslicer + + install : + for i in $(CCP4I_TARGETS); do \ diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch new file mode 100644 index 000000000000..1d1323005540 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch @@ -0,0 +1,35 @@ +--- Makefile.in 2009-06-19 15:13:29.000000000 +0200 ++++ Makefile.in.new 2009-08-02 23:06:41.000000000 +0200 +@@ -2,7 +2,7 @@ + # $Id$ + + SHELL = /bin/sh +-DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) ++DIRS = src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) + # this is for the benefit of makes that don't pass variable values in + # recursive invocations, so that you can override these values on the + # command line at the top level +@@ -69,19 +69,19 @@ + $(MAKE) -i $(MFLAGS) $(MVARS) install; else true; fi ; \ + $(MAKE) install + +-srcdir : FORCE libdir ++srcdir : FORCE + if test -d src; then cd src; $(MAKE) $(MFLAGS) $(MVARS); else true; fi + + supported : srcdir + +-unsupported : FORCE libdir ++unsupported : FORCE + if test -d unsupported/src; then cd unsupported/src; \ + $(MAKE) $(MFLAGS) $(MVARS); else true; fi + +-datadir : FORCE libdir ++datadir : FORCE + cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) + +-xwindir : FORCE libdir ++xwindir : FORCE + if test -f x-windows/Makefile; then cd x-windows; \ + $(MAKE) -i $(MFLAGS) ; else true; fi + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch new file mode 100644 index 000000000000..f16b0ecb938c --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch @@ -0,0 +1,19 @@ +--- src/pisa/Makefile.am 2007-07-10 10:56:05.000000000 +0200 ++++ src/pisa/Makefile.am.new 2009-06-11 21:16:51.000000000 +0200 +@@ -1,4 +1,4 @@ +-SUBDIRS = molref pisastore sbase ++SUBDIRS = pisastore sbase + + pkgdatadir = $(datadir)/pisa + +--- src/pisa/Makefile.in 2009-06-12 21:12:08.000000000 +0200 ++++ src/pisa/Makefile.in.new 2009-06-12 21:41:52.000000000 +0200 +@@ -82,7 +82,7 @@ + am__quote = @am__quote@ + install_sh = @install_sh@ + pisa_LDFLAGS = @pisa_LDFLAGS@ +-SUBDIRS = molref pisastore sbase ++SUBDIRS = pisastore sbase + + dist_pkgdata_DATA = pisa.cfg + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch new file mode 100644 index 000000000000..af4fd8219c4f --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch @@ -0,0 +1,42 @@ +--- ./src/Makefile.in 2009-03-20 15:06:41.000000000 +0100 ++++ ./src/Makefile.in.new 2009-07-31 23:46:13.000000000 +0200 +@@ -50,7 +50,7 @@ + + # these live in subdirectories and have more than one dependency: + OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ +- scala dm dmmulti stereo mapmask maprot ncsmask \ ++ dm dmmulti stereo mapmask maprot ncsmask \ + sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ + anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat + +@@ -637,7 +637,7 @@ + + ### scala, mapmask, maprot, ncsmask, combat + +-scala mapmask maprot ncsmask combat sc dyndom: # dependencies below ++mapmask maprot ncsmask combat sc dyndom: # dependencies below + @$(SETFLAGS) pwd=`pwd` ; rm -f $@; \ + cd $(srcdir)/$@_; \ + echo $(FC) $${$@_FLAGS-"$(FFLAGS)"} -c -o $$pwd/$@.o `pwd`/$@.f ;\ +@@ -1002,21 +1002,6 @@ + proclean: $(srcdir)/procheck/clean.f $(srcdir)/procheck/brkcln.par + rmsdev: $(srcdir)/procheck/rmsdev.f $(srcdir)/procheck/rmsdev.inc + +-scaladir = $(srcdir)/scala_ +-scala : $(scaladir)/scala.f $(scaladir)/column.fh $(scaladir)/orient.fh \ +- $(scaladir)/params.fh $(scaladir)/rfile.fh $(scaladir)/scales.fh \ +- $(scaladir)/nbtchc.fh $(scaladir)/parameter.fh $(scaladir)/refcon.fh \ +- $(scaladir)/rundef.fh $(scaladir)/sdfacc.fh $(scaladir)/flags.fh \ +- $(scaladir)/inout.fh $(scaladir)/dump.fh $(scaladir)/tie.fh \ +- $(scaladir)/outcon.fh $(scaladir)/version.fh $(scaladir)/anomtc.fh \ +- $(scaladir)/axes.fh $(scaladir)/bigarg.fh \ +- $(scaladir)/errors.fh $(scaladir)/flow.fh $(scaladir)/glocon.fh \ +- $(scaladir)/means.fh $(scaladir)/refflg.fh $(scaladir)/stats.fh \ +- $(scaladir)/symmty.fh $(scaladir)/sharvest.fh $(scaladir)/chtml.fh \ +- $(scaladir)/htmbuf.fh $(scaladir)/sphhrm.fh $(scaladir)/crlncf.fh \ +- $(scaladir)/datasets.fh $(scaladir)/dts_storage.fh \ +- $(scaladir)/sclinimeans.fh $(scaladir)/timecor.fh +- + freemask.o: $(dmdir)/freemask.f $(dmdir)/crystal.fh $(dmdir)/cycl.fh \ + $(dmdir)/dmheader.fh $(dmdir)/io.fh $(dmdir)/output.fh \ + $(dmdir)/params.fh $(dmdir)/uvwdata.fh diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch new file mode 100644 index 000000000000..3af4af503fa6 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch @@ -0,0 +1,14 @@ +--- src/Makefile.in 2009-07-05 16:50:25.000000000 +0200 ++++ src/Makefile.in.new 2009-07-05 19:38:06.000000000 +0200 +@@ -50,9 +50,9 @@ + + # these live in subdirectories and have more than one dependency: + OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ +- scala dm dmmulti stereo mapmask maprot ncsmask chef \ ++ scala dm dmmulti stereo mapmask maprot ncsmask \ + sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ +- anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat ++ anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf + + # targets built from .c sources: + CSIMPLE = pltdev binsort diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch new file mode 100644 index 000000000000..1e59578473ff --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch @@ -0,0 +1,111 @@ +--- configure 2009-08-07 12:11:28.000000000 +0200 ++++ configure.new.nolib 2009-08-17 22:30:39.000000000 +0200 +@@ -3113,41 +3113,6 @@ + RX_L="$configdir/lib/rxdispencer/rx" + export RX_H RX_L + fi +- echo +- echo "Running separate configure for CCIF library." +- echo +- cd lib/ccif +- echo "Updating modification times for configuration files" +- echo "Please wait..." +- for i in configure.in aclocal.m4 configure Makefile.in; do +- touch $i && sleep 1 +- done +- echo "...done." +- +- if [ "X$LIBFOPTIM" != "X" ]; then +- FOPTIM_save=$FOPTIM +- FOPTIM=$LIBFOPTIM +- FFLAGS="${FOPTIM} ${XFFLAGS}" +- fi +- if [ "X$LIBCOPTIM" != "X" ]; then +- COPTIM_save=$COPTIM +- COPTIM=$LIBCOPTIM +- CFLAGS="${COPTIM} ${XCFLAGS}" +- fi +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif +- rm -f /tmp/$$.cache_file +- if [ "X$LIBFOPTIM" != "X" ]; then +- FOPTIM=$FOPTIM_save +- FFLAGS="${FOPTIM} ${XFFLAGS}" +- fi +- if [ "X$LIBCOPTIM" != "X" ]; then +- COPTIM=$COPTIM_save +- CFLAGS="${COPTIM} ${XCFLAGS}" +- fi +- cd ../.. + echo + echo "Returning to main configure." + echo +@@ -5094,53 +5059,6 @@ + echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" + ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} + echo +- echo "CCP4 configure: Running separate configure for libjwc_c library." +- echo +- cd ${srcdir}/${xwindir}/libjwc/libjwc_c +- echo "Updating modification times for configuration files in libjwc_c" +- echo "Please wait..." +- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do +- touch $i && sleep 1 +- done +- echo "...done." +- echo +- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- rm -f /tmp/$$.cache_file +- echo +- echo "CCP4 configure: Running separate configure for libjwc_f library." +- echo +- cd ${srcdir}/${xwindir}/libjwc/libjwc_f +- # for g77 3.1 some builds do not have no-common for system libs, +- # so disable for now +- echo "Updating modification times for configuration files in libjwc_f" +- echo "Please wait..." +- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do +- touch $i && sleep 1 +- done +- echo "...done." +- echo +- # for g77 3.1 some builds do not have no-common for system libs, +- # so disable for now +- case $system in +- Darwin* ) +- echo "configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- ;; +- * ) +- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- esac +- rm -f /tmp/$$.cache_file + + if test "$non_shared" = yes; then + #this is a bit of a cheat/fudge but that's life! +@@ -5210,12 +5128,6 @@ + fi + + echo +- echo "CCP4 configure: Running separate configure for Mosflm" +- echo +- cd ${srcdir}/${mosflmdir} +- echo "configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ./configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- echo + cd ../.. + echo "Returning to main configure." + echo diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch new file mode 100644 index 000000000000..583697cea0a1 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-6.0.99e.orig/configure 2008-07-31 10:37:22.000000000 -0700 ++++ ccp4-6.0.99e/configure 2008-07-31 10:39:18.000000000 -0700 +@@ -643,45 +643,45 @@ + # echo "! Beware -- the $system installation isn't properly tested." ; } + syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' + +-if test -z "$onlylibs" ; then +- for i in CCP4_SCR BINSORT_SCR; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the value of $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir includedir; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the argument of --$i." +- badvar=1 +- fi +- done +- +- for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do +- if test -d $i || mkdir $i; then : +- else +- eval echo "! No directory $i and can\'t create it." +- badvar=1 +- fi +- done +-else +- # Kludge to fool the "Makefile" target in the top-level CCP4 +- # Makefile into not trying to remake src/Makefile.in +- for i in $srcdir/src $srcdir/lib/src ; do +- if test -d $i || mkdir $i; then +- if ! test -f $i/Makefile.in ; then +- echo +- echo "onlylibs: making dummy file $i/Makefile.in" +- touch $i/Makefile.in +- fi +- fi +- done +-fi ++#if test -z "$onlylibs" ; then ++# for i in CCP4_SCR BINSORT_SCR; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the value of $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir includedir; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the argument of --$i." ++# badvar=1 ++# fi ++# done ++# ++# for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do ++# if test -d $i || mkdir $i; then : ++# else ++# eval echo "! No directory $i and can\'t create it." ++# badvar=1 ++# fi ++# done ++#else ++# # Kludge to fool the "Makefile" target in the top-level CCP4 ++# # Makefile into not trying to remake src/Makefile.in ++# for i in $srcdir/src $srcdir/lib/src ; do ++# if test -d $i || mkdir $i; then ++# if ! test -f $i/Makefile.in ; then ++# echo ++# echo "onlylibs: making dummy file $i/Makefile.in" ++# touch $i/Makefile.in ++# fi ++# fi ++# done ++#fi + + ### sanity checks + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch new file mode 100644 index 000000000000..db8236063043 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch @@ -0,0 +1,152 @@ +diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c +index bfda882..f821e04 100755 +--- a/lib/DiffractionImage/Bruker/FRM_LIB.c ++++ b/lib/DiffractionImage/Bruker/FRM_LIB.c +@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files. + #include "sys/types.h" /* _open, etc. */ + #include "sys/stat.h" /* _open, etc. */ + ++#include <unistd.h> ++ + #ifndef _MSC_VER + int min(int a, int b) + { +diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c +index 1a933de..1c40c32 100755 +--- a/lib/DiffractionImage/MAR/mar300_header.c ++++ b/lib/DiffractionImage/MAR/mar300_header.c +@@ -23,6 +23,9 @@ + */ + #include "mar300_header.h" + ++#include <sys/types.h> ++#include <unistd.h> ++ + /* + * Local functions + */ +diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c +index a8351ea..16d0f7b 100755 +--- a/lib/DiffractionImage/MAR/mar345_header.c ++++ b/lib/DiffractionImage/MAR/mar345_header.c +@@ -32,6 +32,9 @@ + */ + #include "mar345_header.h" + ++#include <sys/types.h> ++#include <unistd.h> ++ + /* + * Definitions + */ +diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c +index 07f2741..6364ca4 100755 +--- a/lib/DiffractionImage/MAR/nb_header.c ++++ b/lib/DiffractionImage/MAR/nb_header.c +@@ -20,6 +20,8 @@ + #include <io.h> + #endif + ++#include <sys/types.h> ++#include <unistd.h> + /* + * mar software include files + */ +diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c +index 443bb8c..0d96b3f 100755 +--- a/lib/DiffractionImage/MAR/swap.c ++++ b/lib/DiffractionImage/MAR/swap.c +@@ -10,6 +10,9 @@ + * + **********************************************************************/ + ++#define _XOPEN_SOURCE ++#include <unistd.h> ++ + void swaplong(); + void swapshort(); + +diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c +index 0f6a6b7..a09dc48 100755 +--- a/lib/ccif/f_interface.c ++++ b/lib/ccif/f_interface.c +@@ -25,6 +25,7 @@ + ********************************************************************/ + + #include "stdpccts.h" ++#include <sys/mman.h> + + /* This file is terribly organised, and badly needs re-doing. There is probably + * scope for splitting this into three modules: +diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c +index 8b5d04f..74ee3f7 100755 +--- a/lib/src/ccp4_general_f.c ++++ b/lib/src/ccp4_general_f.c +@@ -26,6 +26,7 @@ + #include <string.h> + #include <stdlib.h> + #include <math.h> ++#include <time.h> + #include "ccp4_errno.h" + #include "ccp4_fortran.h" + #include "ccp4_parser.h" +diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c +index 3e83d4d..bb3e975 100755 +--- a/lib/src/ccp4_program.c ++++ b/lib/src/ccp4_program.c +@@ -25,6 +25,7 @@ + #include <stdio.h> + #include <stdlib.h> + #include <string.h> ++#include <time.h> + #include "ccp4_program.h" + #include "ccp4_parser.h" + #include "ccp4_utils.h" +diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c +index ee8af24..c6fb3cd 100755 +--- a/lib/src/fsplit.c ++++ b/lib/src/fsplit.c +@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c 5.5 (Berkeley) 3/12/91"; + #include <string.h> + #include <sys/types.h> + #include <sys/stat.h> ++#include <unistd.h> + + /* + * usage: fsplit [-e efile] ... [file] +diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c +index ea52e96..30dbd56 100755 +--- a/src/clipper_progs/src/pirate/compress42.c ++++ b/src/clipper_progs/src/pirate/compress42.c +@@ -142,6 +142,7 @@ + #include <sys/types.h> + #include <sys/stat.h> + #include <errno.h> ++#include <unistd.h> + + #ifdef DIRENT + # include <dirent.h> +diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c +index e224430..c7b82f4 100755 +--- a/src/mtz2cif_/mtz2cif.c ++++ b/src/mtz2cif_/mtz2cif.c +@@ -28,6 +28,7 @@ + #include "cmtzlib.h" + #include "ccp4_parser.h" + #include "ccp4_general.h" ++#include "ccp4_program.h" + #include "csymlib.h" + #include "mtz2cif_lib.h" + +diff --git a/x-windows/XCCPJIFFY/xplot84driver.c b/x-windows/XCCPJIFFY/xplot84driver.c +index 67e0bf1..76526ab 100755 +--- a/x-windows/XCCPJIFFY/xplot84driver.c ++++ b/x-windows/XCCPJIFFY/xplot84driver.c +@@ -11,6 +11,7 @@ + + #include <stdio.h> + #include <sys/types.h> ++#include <stdlib.h> + + #include <X11/StringDefs.h> + #include <X11/Intrinsic.h> diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch new file mode 100644 index 000000000000..62892db01147 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch @@ -0,0 +1,597 @@ +diff --git a/configure b/configure +index 833f483..bcfa62d 100755 +--- a/configure ++++ b/configure +@@ -3226,574 +3226,14 @@ else + echo + echo "Warning: this option has not been extensively tested!" + echo "Please report problems to ccp4@ccp4.ac.uk" +- # Search for vendor LAPACK/BLAS first +- if test ! "$with_netlib_lapack" ; then +- # Initialise variables to blank +- lapackdir= +- XLAPACK_LIB= +- # Possible directories to check for vendor or pre-existing LAPACK or +- # BLAS - add to these if you want to test others +- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib" +- # Possible library names +- # These are the names like xxxx where the library will be libxxxx.a +- # or libxxxx.so +- echo +- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries" +- echo "on this system" +- case $system in +- linux | linux64 | linux32 ) +- # linux users will usually have them in /usr/lib but don't call it +- trylapack="lapack" +- tryblas="blas" +- # if code is non_shared then this can lead to problems. both blas and lapack +- # need to be resolved even if they are not called! +- if test "$non_shared" = yes; then +- echo "You are compiling linux non_shared. This sometimes causes problems " +- echo " so checking for requirements." +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +- PROGRAM TESTLINK +-C A bit of scala code to test the linking +- real bf(3), bnorm +-c +- integer maxbmt +- parameter (maxbmt = 2) +- double precision B(maxbmt,maxbmt), eigval(maxbmt), +- $ eigvec(maxbmt,maxbmt), w(5*maxbmt) +- integer m, ia, ix, istat +-c +- B(1,1) = 1.00 +- B(1,2) = 1.00 +- B(2,1) = 1.00 +- B(2,2) = 1.00 +-c +- m = maxbmt +- ia = maxbmt +- ix = maxbmt +- call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat) +- end +-EOF +- #firstly test without -lblas +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" +- echo $test_compile +- if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... only -llapack needed" +- XLAPACK_LIB="-llapack" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="lapack" +- noblas=yes +- trylapack= +- tryblas= +- else +- echo "more than just -llapack needed...." +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "...-llapack and -lblas were needed" +- XLAPACK_LIB="-llapack -lblas" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="lapack blas" +- noblas=no +- trylapack= +- tryblas= +- else +- echo "....could not find either lapack or blas." +- fi +- fi +- fi +- # add 64 bit libs +- case $system in +- linux64 ) trydirs="/usr/lib64 ${trydirs}" ;; +- esac +- +- ;; +- osf1) +- # OSF1 has dxml (old version) and cxml +- # which should have both lapack and blas +- trylapack="dxml cxml" +- tryblas= +- trydirs="${trydirs} /usr/shlib" +- ;; +- irix) +- # Additional search paths for IRIX +- trydirs="${trydirs} /usr/lib32" +- # SCSL should have both LAPACK and BLAS +- trylapack="scs" +- tryblas="blas" +- ;; +- irix64) +- # Additional search paths for IRIX64 +- trydirs="${trydirs} /usr/lib64" +- # SCSL should have both LAPACK and BLAS +- trylapack="scs" +- tryblas="blas" +- # Extra compiler flags? +- #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON" +- ;; +- aix) +- # Additional search paths for AIX +- trydirs="${trydirs}" +- # AIX might have ESSL library - blas only I think +- trylapack= +- tryblas="essl" +- ;; +- hpux) +- # Additional search paths for HPUX +- trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0" +- # HPUX should have both LAPACK (part of mlib) and BLAS +- trylapack="lapack" +- tryblas="blas" +- # Extra compiler flags? +- # +U77 required for ETIME function - this is already in XFFLAGS +- #XLAPACKFLAGS="+U77" +- ;; +- +- sunos | sunos64) +- # Sun has libraries with BLAS and LAPACK invoked using +- # -xlic_lib=sunperf +- trylapack= +- tryblas= +- echo "SunOs can use the Sun Performance Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- echo "Looking for a valid library to use..." +- echo +- # Loop over the possible library names +- try_libs="sunperf" +- for testlib in $try_libs +- do +- if test ! "$XLAPACK_LIB" ; then +- # Try running a test compile to see if this a valid library +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -xlic_lib=$testlib is okay" +- XLAPACK_LIB="-dalign -xlic_lib=$testlib" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="$testlib" +- noblas=yes +- else +- # Compilation failed +- echo "... cannot use -xlic_lib=$testlib" +- fi +- # End of test for testlib +- fi +- # End of loop over possible lib names +- done +- # Report if no suitable library was found +- if test ! "$XLAPACK_LIB" ; then +- echo +- echo "No suitable LAPACK library was found." +- echo "This may be because the Sun Performance Library is not" +- echo "installed on your system" +- echo "Contact your system administrator or Sun vendor" +- fi +- ;; +- Darwin | Darwin32 | Darwin64 ) +- # Darwin has libraries with BLAS and LAPACK invoked using +- # -framework vecLib +- echo "Darwin can use the vecLib Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- # This is a special case so try running a test compile +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -framework vecLib is okay" +- XLAPACK_LIB="-framework vecLib" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="vecLib" +- noblas=yes +- else +-#alternative linking for vecLib libraries +- case `uname -sr` in +- *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;; +- * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;; +- esac +- +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -framework vecLib is okay" +- XLAPACK_LIB="-Wl,-framework -Wl,vecLib" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="-Wl,-framework -Wl,vecLib" +- noblas=yes +- else +- # Compilation failed +- echo "... cannot use -framework vecLib" +- echo +- fi +- fi +- trylapack= +- tryblas= +-# try the fink installation +- trydirs="${trydirs} /sw" +- ;; +- Darwin_ibm_compilers ) +- # Darwin has libraries with BLAS and LAPACK invoked using +- # -framework vecLib +- echo "Darwin can use the vecLib Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- # This is a special case so try running a test compile +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- case `uname -sr` in +- Darwin\ 8* ) +- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" +- ;; +- Darwin\ 7* ) +- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB" +- ;; +- *) +- XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib" +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" +- esac +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -framework vecLib is okay" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="vecLib" +- noblas=yes +- else +- # Compilation failed +- XLAPACK_LIB="" +- echo "... cannot use -framework vecLib" +- echo +- fi +- trylapack= +- tryblas= +-# try the fink installation +- trydirs="${trydirs} /sw" +- ;; +- +- Darwin_intel_compilers) +- # Darwin has libraries with BLAS and LAPACK invoked using +- # -F vecLib +- echo "Darwin can use the vecLib Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- # This is a special case so try running a test compile +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- # doesn't try to build netlib libraries +- XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib" +- LAPACKLIB="vecLib" +- noblas=yes +- else +- # Compilation failed +- echo "... cannot use -framework vecLib" +- echo +- fi +- trylapack= +- tryblas= +-# try the fink installation +- trydirs="${trydirs} /sw" +- ;; +- +-# linux_ia64_sgi_altix) +-# SGI Japan +- ia64_linux_intel) +- # Additional search paths for Linux/IA64 +- trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib" +- # SCSL and MKL should have both LAPACK and BLAS +- trylapack="mkl_lapack scs lapack" +- tryblas="mkl scs blas" +- ;; +- linux_ibm_compilers ) +- trylapack="lapack" +- tryblas="blas" +- ;; +- linux64_ibm_compilers ) +- trydirs="/usr/lib64 ${trydirs}" +- trylapack="lapack" +- tryblas="blas" +- ;; +- linux_intel_compilers ) +- trydirs="/usr/lib64 ${trydirs}" +- trylapack="mkl_lapack lapack" +- tryblas="mkl blas" +- ;; +- *) +- echo "The guesses for this system may not be correct - please" +- echo "e-mail ccp4@ccp4.ac.uk if you have any extra information" +- echo +- # Default guess is just libblas +- trylapack="lapack" +- tryblas="blas" +- ;; +- esac +- # +- # Search for LAPACK libraries +- # +- # Write out what the guesses are +- if test "$trylapack" ; then +- echo "Possible LAPACK library names for this system:" +- for libname in $trylapack +- do +- echo " lib$libname" +- done +- # Possible library name extensions +- tryexts="a so dylib" +- # Now loop over all the possibilities and see if anything +- # turns up +- echo +- echo "Searching for libraries with LAPACK and BLAS:" +- for testdir in $trydirs +- do +- for testlib in $trylapack +- do +- for ext in $tryexts +- do +- if test ! "$LAPACKLIB"; then +- if test -s "$testdir/lib$testlib.$ext" ; then +- echo "...found LAPACK library: $testdir/lib$testlib.$ext" +- # Now try and link to a test program +- # This is really for IRIX where libraries can be +- # o32 or n32 +- echo " Testing: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- have_lapack=yes +- else +-# cover clapack option +- echo $test_ccompile +- if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then +- have_lapack=yes +- fi +- fi +- if test x$have_lapack = xyes ; then +- # This one is okay +- LAPACKLIB="$testlib" +- LAPACKDIR="$testdir" +- echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" +- # +- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" +- # +- # Test to see if we need BLAS too +- # Do this by trying to compile a test program +- # Use the LSAME test for now +- echo +- echo " * Checking whether we need a separate BLAS library *" +- echo " Testing: try linking library against test program" +- cd lib/lapack/test +- if test -f testlsame ; then +- rm -f testsame testlsame.o +- fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" +- echo $test_compile +- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then +- have_blas=yes +- else +-#cblas route +- echo $test_ccompile +- if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then +- have_blas=yes +- fi +- fi +- if test x$have_blas = xyes ; then +- echo "Test program okay - additional separate BLAS not required" +- noblas=yes +- else +- echo "Test program failed - need a separate BLAS library" +- fi +- cd ../../.. +- else +- # Keep looking +- echo " link failed - cannot use lib$testlib" +- fi +- fi +- fi +- done +- done +- if test ! "$LAPACKLIB"; then +- echo "...nothing in $testdir" +- fi +- done +- fi +- +- # If LAPACKLIB hasn't been set at this point then no LAPACK library +- # was found +- if test ! "$LAPACKLIB" ; then +- echo +- echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead" +- make_lapack=lapacklib +- fi +- # Look for possible BLAS +- if test ! "$noblas" ; then +- if test "$tryblas" ; then +- echo +- echo "Possible BLAS library names for this system:" +- for libname in $tryblas +- do +- echo " lib$libname" +- done +- # Possible library name extensions +- tryexts="a so" +- # Now loop over all the possibilities and see if anything +- # turns up +- echo +- echo "Searching for libraries with BLAS:" +- for testdir in $trydirs +- do +- for testlib in $tryblas +- do +- for ext in $tryexts +- do +- if test ! "$BLASLIB"; then +- if test -s "$testdir/lib$testlib.$ext" ; then +- echo "...found BLAS library: $testdir/lib$testlib.$ext" +- # Now try and link to a test program +- # This is really for IRIX where libraries can be +- # o32 or n32 +- echo " Testing: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" +- echo $test_compile +- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then +- have_blas=yes +- else +- echo $test_ccompile +- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then +- have_blas=yes +- fi +- fi +- if test x$have_blas = xyes ; then +- # This one is okay +- BLASLIB="$testlib" +- BLASDIR="$testdir" +- BLASEXT="$ext" +- echo "Link ok - using lib$BLASLIB from $BLASDIR" +- XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB" +- else +- # Keep looking +- echo " link failed - cannot use lib$testlib" +- fi +- fi +- fi +- done +- done +- if test ! "$BLASLIB"; then +- echo "...nothing in $testdir" +- fi +- done +- fi +- # Do we need to build BLAS too? +- if test ! "$BLASLIB" ; then +- echo +- echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead" +- echo "This may result in poorer performance of the LAPACK routines" +- make_blas=blaslib +- BLASLIB=blas +- BLASDIR="$srcdir/lib/lapack" +- BLASEXT="a" +- fi +- fi ++ # gentoo is clever ++ make_blas= ++ make_lapack= ++ BLASLIB=$(${PKG_CONFIG} --libs blas) ++ LAPACKLIB=$(${PKG_CONFIG} --libs lapack) ++ XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}" ++ XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)" + # Otherwise force building of NetLib BLAS and LAPACK libs +- else +- echo +- echo "! Force building of NetLib BLAS and LAPACK..." +- make_blas=blaslib +- make_lapack=lapacklib +- BLASLIB=blas +- BLASDIR="$srcdir/lib/lapack" +- BLASEXT="a" +- fi + # need to know if we the lapack library was linked using the C or + # fortran linker + if test -f testlink.f || test -f testlink || test -f testlink.c ; then +@@ -3916,8 +3356,8 @@ RANLIB = ${RANLIB} + INSTALL_DATA = ${INSTALL_DATA} + libdir = $libdir + # +-BLASLIB = lib${BLASLIB}.${BLASEXT} +-LAPACKLIB = liblapack.a ++BLASLIB = ${BLASLIB} ++LAPACKLIB = ${LAPACKLIB} + # + # These variables define targets in the main Makefile + blaslib = ${make_blas} diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch new file mode 100644 index 000000000000..9d8fefe965e5 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch @@ -0,0 +1,23 @@ +diff --git a/src/pisa/sbase/Makefile.am b/src/pisa/sbase/Makefile.am +index 053e83a..4ff3394 100755 +--- a/src/pisa/sbase/Makefile.am ++++ b/src/pisa/sbase/Makefile.am +@@ -1,4 +1,4 @@ +-pkgdatadir = $(datadir)/sbase ++pkgdatadir = $(datadir)/pisa/sbase + dist_pkgdata_DATA = \ + graph.sbase index.sbase struct.sbase + +diff --git a/src/pisa/sbase/Makefile.in b/src/pisa/sbase/Makefile.in +index faa3f7f..8630bd7 100755 +--- a/src/pisa/sbase/Makefile.in ++++ b/src/pisa/sbase/Makefile.in +@@ -62,7 +62,7 @@ POST_UNINSTALL = : + EXEEXT = @EXEEXT@ + OBJEXT = @OBJEXT@ + PATH_SEPARATOR = @PATH_SEPARATOR@ +-pkgdatadir = $(datadir)/sbase ++pkgdatadir = $(datadir)/pisa/sbase + AMTAR = @AMTAR@ + AR_FLAGS = @AR_FLAGS@ + AWK = @AWK@ diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch new file mode 100644 index 000000000000..7a012be6ef02 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch @@ -0,0 +1,65 @@ +diff --git a/ccp4-6.1.2/include/ccp4.setup-bash b/ccp4-6.1.2/include/ccp4.setup-bash +index 9848101..cea8ae6 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-bash ++++ b/ccp4-6.1.2/include/ccp4.setup-bash +@@ -188,9 +188,9 @@ fi + #Python path for the subprocess fixed module + + if [ $ccp4_first_in_path -eq 1 ]; then +- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} ++ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python ++ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + fi + + ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### +diff --git a/ccp4-6.1.2/include/ccp4.setup-csh b/ccp4-6.1.2/include/ccp4.setup-csh +index 42f0820..93c2cf3 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-csh ++++ b/ccp4-6.1.2/include/ccp4.setup-csh +@@ -180,9 +180,9 @@ endif + #Python path for the subprocess fixed module + if (${?PYTHONPATH}) then + if ($ccp4_first_in_path) then +- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} ++ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python ++ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + endif + else + setenv PYTHONPATH ${CCP4}/share/python +diff --git a/ccp4-6.1.2/include/ccp4.setup-sh b/ccp4-6.1.2/include/ccp4.setup-sh +index 4396ebf..a0455bd 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-sh ++++ b/ccp4-6.1.2/include/ccp4.setup-sh +@@ -228,9 +228,9 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg + #Python path for the subprocess fixed module + + if test $ccp4_first_in_path -eq 1; then +- export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} ++ export PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python ++ export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + fi + + ################### THE REST SHOULDN'T NEED EDITING ##################### +diff --git a/ccp4-6.1.2/include/ccp4.setup-zsh b/ccp4-6.1.2/include/ccp4.setup-zsh +index 0e5c2ce..53523f3 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-zsh ++++ b/ccp4-6.1.2/include/ccp4.setup-zsh +@@ -157,10 +157,10 @@ export CLASSPATH + #Python path for the subprocess fixed module + + if ($ccp4_first_in_path) then +- PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} ++ PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + export PYTHONPATH + else +- PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python ++ PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + export PYTHONPATH + fi + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch new file mode 100644 index 000000000000..a5144cfa5d33 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch @@ -0,0 +1,60 @@ +diff --git a/src/Makefile.in b/src/Makefile.in +index 70781f3..b2dcc25 100755 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o + pdbcur : $(pdbcurobjs) + @$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS) + ncont : $(ncontobjs) +- @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) ++ @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb + coord_format : $(coord_formatobjs) + @$(SETFLAGS) xxx=1 ; \ + rm -f coord_format; \ +diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am +index 85f212e..2608c6d 100755 +--- a/src/rapper/LOOP/Makefile.am ++++ b/src/rapper/LOOP/Makefile.am +@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains. + hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \ + residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp + +-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la ++rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@ + + pkgdatadir = $(datadir)/rapper + dist_pkgdata_DATA = params.xml + +-INCLUDES = -I. -I../gc7.0/include -I../libxml2/include ++INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@ + #SUBDIRS = \ + #@PYTHON_USE_TRUE@ python + +diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am +index e78b10d..486b931 100755 +--- a/src/rapper/Makefile.am ++++ b/src/rapper/Makefile.am +@@ -1,3 +1,3 @@ +-SUBDIRS = libxml2 gc7.0 LOOP data ++SUBDIRS = LOOP data + + EXTRA_DIST = +diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac +index 5e4ef69..268a579 100755 +--- a/src/rapper/configure.ac ++++ b/src/rapper/configure.ac +@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) + + AC_SUBST(rapper_LDFLAGS) + +-AC_CONFIG_SUBDIRS([gc7.0 libxml2]) ++PKG_CHECK_MODULES([LIBXML],[libxml-2.0]) ++AC_SUBST([LIBXML_CFLAGS]) ++AC_SUBST([LIBXML_LIBS]) ++ ++PKG_CHECK_MODULES([GC],[bdw-gc]) ++AC_SUBST([GC_CFLAGS]) ++AC_SUBST([GC_LIBS]) ++ + #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) + AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch new file mode 100644 index 000000000000..107cfd740238 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch @@ -0,0 +1,131 @@ + src/Makefile.in | 14 +++++----- + src/pisa/configure.ac | 67 +++++++++---------------------------------------- + 2 files changed, 19 insertions(+), 62 deletions(-) + +diff --git a/src/Makefile.in b/src/Makefile.in +index 70781f3..b11db04 100755 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -778,8 +778,8 @@ chainsaw : $(chainsawobjs) + eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o chainsaw $(chainsawobjs) $(LDCXXFLAGS) + pdbcur.o pcur_funcs.o ncont.o coord_format.o pdb_merge.o chainsaw.o: # dependencies at end + @$(SETFLAGS) xxx=1 ; \ +- echo $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; +- eval $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ++ echo $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; ++ eval $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp + + ### bp3, afro, gcx + +@@ -813,8 +813,8 @@ gcx : libbp3 $(gcxobjs) + + $(libbp3objs) $(bp3objs) $(afroobjs) $(gcxobjs) : # dependencies at end + @$(SETFLAGS) xxx=1 ; \ +- echo $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ +- eval $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ++ echo $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ ++ eval $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C + + ### crunch2 pmf + +@@ -853,7 +853,7 @@ cif2xml : $(cif2xmlobjs) + cross_validate : $(cross_validateobjs) + @$(SETFLAGS); rm -f cross_validate; eval $(CXX) $${harvest_app_FLAGS-"$(CXXFLAGS)"} -o cross_validate $(cross_validateobjs) $(LDCXXFLAGS) + cif2xml.o cross_validate.o : # dependencies at end +- @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) -I$(incdir)/mmdb $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp ++ @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp + + pdb_extractdir = $(srcdir)/harvest_app_/pdb_extract + pdb_extract_suite : +@@ -873,8 +873,8 @@ $(dev_tools_ctargets) : + $(dev_tools_cxxtargets) : + @$(SETFLAGS) xxx=1; \ + rm -f $@; \ +- echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ;\ +- eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ++ echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) ;\ ++ eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) + + ### mlphare + mlphare: +diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac +index 81afdda..044b6f8 100755 +--- a/src/pisa/configure.ac ++++ b/src/pisa/configure.ac +@@ -31,64 +31,21 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) + # test for function in m + AC_CHECK_LIB([m], [sqrt]) + +-dnl Optional: Check for MMDB. +-AM_PATH_MMDB(, +- [ if test "x$mmdb_prefix" != x ; then +- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then +- case "$ac_MMDB_CXXFLAGS" in +- *src/mmdb ) +- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` +- ;; +- *include/mmdb ) +- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` +- ;; +- *) +- esac +- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" +- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` +- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) +- else +- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" +- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" +- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) +- fi +- else +- AC_MSG_ERROR([mmdb not found]) +- fi +- ] +-) ++PKG_CHECK_MODULES([MMDB],[mmdb]) ++PKG_CHECK_MODULES([SSM],[ssm]) ++ ++MMDB_CXXFLAGS=${MMDB_CFLAGS} ++ ++AC_SUBST([MMDB_CFLAGS]) ++AC_SUBST([MMDB_CXXFLAGS]) ++AC_SUBST([SSM_CFLAGS]) ++ ++AC_SUBST([MMDB_LIBS]) ++AC_SUBST([SSM_LIBS]) + +-ac_saved_CXXFLAGS=$CXXFLAGS +-ac_saved_LIBS=$LIBS + CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" + LIBS="$MMDB_LIBS $LIBS" +-AM_PATH_SSM(, +- [ if test "x$ssm_prefix" != x ; then +- if test "x$ac_SSM_CXXFLAGS" != x && test "x$ac_SSM_LDOPTS" = x ; then +- case "$ac_SSM_CXXFLAGS" in +- *lib/ssm ) +- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#lib/ssm#lib#g` +- ;; +- *include/ssm ) +- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#include/ssm#lib#g` +- ;; +- *) +- esac +- SSM_CXXFLAGS="$ac_SSM_CXXFLAGS" +- SSM_LIBS=`echo "$ac_SSM_LDOPTS -lssm" | sed s#-I#-L#` +- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) +- else +- SSM_CXXFLAGS="-I$ssm_prefix/include/ssm -I$ssm_prefix/lib/ssm" +- SSM_LIBS="-L$ssm_prefix/lib -L$ssm_prefix/lib/ssm -lssm" +- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) +- fi +- else +- AC_MSG_ERROR([ssm not found]) +- fi +- ] +-) +-CXXFLAGS=$ac_saved_CXXFLAGS +-LIBS=$ac_saved_LIBS ++ + + # Checks for typedefs, structures, and compiler characteristics. + # diff --git a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch new file mode 100644 index 000000000000..4b98545eec83 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch @@ -0,0 +1,130 @@ + src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c | 34 ++++++++++++++--------------- + 1 file changed, 17 insertions(+), 17 deletions(-) + +diff --git a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c +index 2c9f02f..98d814a 100755 +--- a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c ++++ b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c +@@ -297,7 +297,7 @@ int canvas_draw_line(char *canvas, int npts, float *x, float *y, char *tags, + puts("canvas_draw_line: about to evaluate the command..."); + } + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_draw_line: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_draw_line: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + return 0; + } + if (CCP4MAPWISH_CANVAS_DIAG) +@@ -432,7 +432,7 @@ int canvas_draw_rectangle(char *canvas, int npts, float *x, float *y, + puts("canvas_draw_rectangle: about to evaluate the command..."); + } + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_draw_rectangle: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_draw_rectangle: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + printf("canvas_draw_rectangle:\ncanvas = \"%s\"\ntags = \"%s\"\ncolor = \"%s\"\nunits = \"%c\"\n",canvas,tags,color,units); + return 0; + } +@@ -536,7 +536,7 @@ int canvas_draw_label(char *canvas, char *text, float x, float y, + /* Execute the command which draws the label */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_draw_label: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_draw_label: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_draw_label: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -617,7 +617,7 @@ int canvas_scale_canvas(char *canvas, char *tag, float scale) + /* Execute the command which scales the canvas */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_scale_canvas: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -706,7 +706,7 @@ int canvas_shift_canvas(char *canvas) + /* Execute the command which resizes the canvas */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -789,7 +789,7 @@ int canvas_shift_element(char *canvas, char *tag, int shiftx, int shifty) + /* Execute the command which resizes the canvas */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_shift_element: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_shift_element: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -861,7 +861,7 @@ int canvas_delete(char *canvas, char *tag) + /* Execute the command which deletes the tagged items */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_delete: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -892,15 +892,15 @@ int canvas_exists(char *canvas) + + sprintf(tmpstr,"winfo exists %s",canvas); + if (Tcl_Eval(interp,tmpstr) != TCL_OK) { +- printf("canvas_exists: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_exists: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + return 0; + } + /* Extract a long int using strtol + If no conversion takes place then "endptr" will be equal + to "result" */ +- istatus = (int) strtol(interp->result,&endptr,10); +- if (strcmp(interp->result,endptr) == 0) { +- printf("canvas_exists: bad return status from winfo command \"%s\"\n",interp->result); ++ istatus = (int) strtol(Tcl_GetStringResult(interp),&endptr,10); ++ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) { ++ printf("canvas_exists: bad return status from winfo command \"%s\"\n",Tcl_GetStringResult(interp)); + return 0; + } + if (!istatus) { +@@ -930,13 +930,13 @@ float canvas_get_tk_scaling(char *canvas, char units) + + /* Execute the tk scaling command */ + if (Tcl_Eval(interp,"tk scaling") != TCL_OK) { +- printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + return (float) 0.0; + } + + /* Extract a float from the result */ +- tkscale = ((float) strtod(interp->result,&endptr)); +- if (strcmp(interp->result,endptr) == 0) { ++ tkscale = ((float) strtod(Tcl_GetStringResult(interp),&endptr)); ++ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) { + printf("canvas_get_tk_scaling: couldn't extract scale factor\n"); + return (float) 0.0; + } +@@ -1021,19 +1021,19 @@ int canvas_get_limits(char *canvas, int limits[4]) + + /* Evaluate the command */ + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_get_limits: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_get_limits: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + + /* Process the result - it should consist of 4 integers */ + /* Use strtok which can split the string based on tokens + set by the programmer - in this case a space */ +- if (!interp->result) { ++ if (!Tcl_GetStringResult(interp)) { + puts("canvas_get_limits: failed to fetch canvas limits"); + return TCL_ERROR; + } + i = 0; +- p = strtok(interp->result," "); ++ p = strtok(Tcl_GetStringResult(interp)," "); + if (p == NULL) { + return 0; + } diff --git a/sci-chemistry/ccp4-apps/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/ccp4-apps/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild b/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild new file mode 100644 index 000000000000..eea4a408b472 --- /dev/null +++ b/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit fortran-2 + +DESCRIPTION="Protein X-ray crystallography toolkit -- meta package" +HOMEPAGE="http://www.ccp4.ac.uk/" +SRC_URI="" + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="X arpwarp +balbes" + +RDEPEND=" + ~sci-chemistry/ccp4-apps-${PV}[X?] + !<=sci-chemistry/ccp4-apps-${PV}-r2 + >=sci-chemistry/molrep-11.0.00-r1 + >=sci-chemistry/mosflm-7.0.6-r2 + sci-chemistry/mrbump[X?] + >=sci-chemistry/oasis-4.0-r1 + >=sci-chemistry/pdb-extract-3.004-r2 + >=sci-chemistry/refmac-5.5.0110-r1 + >=sci-chemistry/scala-3.3.18-r1 + >=sci-chemistry/sfcheck-7.03.18-r1 + sci-chemistry/xia2 + arpwarp? ( sci-chemistry/arp-warp-bin ) + balbes? ( sci-chemistry/balbes ) + X? ( + ~sci-chemistry/ccp4i-${PV} + sci-chemistry/imosflm + sci-chemistry/pymol + sci-chemistry/rasmol + )" +DEPEND="" diff --git a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch new file mode 100644 index 000000000000..1420419ffab0 --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-6.0.1.orig/configure 2006-06-10 17:30:02.000000000 -0700 ++++ ccp4-6.0.1/configure 2006-06-10 17:45:43.000000000 -0700 +@@ -623,45 +623,45 @@ + # echo "! Beware -- the $system installation isn't properly tested." ; } + syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' + +-if test -z "$onlylibs" ; then +- for i in CCP4_SCR BINSORT_SCR; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the value of $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the argument of --$i." +- badvar=1 +- fi +- done +- +- for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do +- if test -d $i || mkdir $i; then : +- else +- eval echo "! No directory $i and can\'t create it." +- badvar=1 +- fi +- done +-else +- # Kludge to fool the "Makefile" target in the top-level CCP4 +- # Makefile into not trying to remake src/Makefile.in +- for i in $srcdir/src $srcdir/lib/src ; do +- if test -d $i || mkdir $i; then +- if ! test -f $i/Makefile.in ; then +- echo +- echo "onlylibs: making dummy file $i/Makefile.in" +- touch $i/Makefile.in +- fi +- fi +- done +-fi ++#if test -z "$onlylibs" ; then ++# for i in CCP4_SCR BINSORT_SCR; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the value of $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the argument of --$i." ++# badvar=1 ++# fi ++# done ++# ++# for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do ++# if test -d $i || mkdir $i; then : ++# else ++# eval echo "! No directory $i and can\'t create it." ++# badvar=1 ++# fi ++# done ++#else ++# # Kludge to fool the "Makefile" target in the top-level CCP4 ++# # Makefile into not trying to remake src/Makefile.in ++# for i in $srcdir/src $srcdir/lib/src ; do ++# if test -d $i || mkdir $i; then ++# if ! test -f $i/Makefile.in ; then ++# echo ++# echo "onlylibs: making dummy file $i/Makefile.in" ++# touch $i/Makefile.in ++# fi ++# fi ++# done ++#fi + + ### sanity checks + diff --git a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch new file mode 100644 index 000000000000..a77d9494a05c --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch @@ -0,0 +1,11 @@ +--- ccp4-6.0.1.orig/lib/src/library_f.c 2006-06-12 07:06:22.000000000 -0700 ++++ ccp4-6.0.1/lib/src/library_f.c 2006-06-12 07:21:56.000000000 -0700 +@@ -716,7 +716,7 @@ + + #endif /* end of apple xlf support */ + +-#if ( defined (__linux__) && defined (_CALL_SYSV) ) ++#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) ) + /* linuxppc xlf support */ + void gerror_ (str, Lstr) + char *str; diff --git a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch new file mode 100644 index 000000000000..1420419ffab0 --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-6.0.1.orig/configure 2006-06-10 17:30:02.000000000 -0700 ++++ ccp4-6.0.1/configure 2006-06-10 17:45:43.000000000 -0700 +@@ -623,45 +623,45 @@ + # echo "! Beware -- the $system installation isn't properly tested." ; } + syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' + +-if test -z "$onlylibs" ; then +- for i in CCP4_SCR BINSORT_SCR; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the value of $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the argument of --$i." +- badvar=1 +- fi +- done +- +- for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do +- if test -d $i || mkdir $i; then : +- else +- eval echo "! No directory $i and can\'t create it." +- badvar=1 +- fi +- done +-else +- # Kludge to fool the "Makefile" target in the top-level CCP4 +- # Makefile into not trying to remake src/Makefile.in +- for i in $srcdir/src $srcdir/lib/src ; do +- if test -d $i || mkdir $i; then +- if ! test -f $i/Makefile.in ; then +- echo +- echo "onlylibs: making dummy file $i/Makefile.in" +- touch $i/Makefile.in +- fi +- fi +- done +-fi ++#if test -z "$onlylibs" ; then ++# for i in CCP4_SCR BINSORT_SCR; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the value of $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the argument of --$i." ++# badvar=1 ++# fi ++# done ++# ++# for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do ++# if test -d $i || mkdir $i; then : ++# else ++# eval echo "! No directory $i and can\'t create it." ++# badvar=1 ++# fi ++# done ++#else ++# # Kludge to fool the "Makefile" target in the top-level CCP4 ++# # Makefile into not trying to remake src/Makefile.in ++# for i in $srcdir/src $srcdir/lib/src ; do ++# if test -d $i || mkdir $i; then ++# if ! test -f $i/Makefile.in ; then ++# echo ++# echo "onlylibs: making dummy file $i/Makefile.in" ++# touch $i/Makefile.in ++# fi ++# fi ++# done ++#fi + + ### sanity checks + diff --git a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch b/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch new file mode 100644 index 000000000000..c118cc53baff --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch @@ -0,0 +1,14 @@ +https://bugs.gentoo.org/show_bug.cgi?id=175630 +JTRiley + +--- ccp4-6.0.2.orig/src/refmac5_/make_unix_ccp4.f 2005-09-06 07:29:56.000000000 -0400 ++++ ccp4-6.0.2.new/src/refmac5_/make_unix_ccp4.f 2007-05-02 20:03:46.000000000 -0400 +@@ -97,7 +97,7 @@ + + READ(CID,'(I2,1X,I2,1X,I2,2X)') IH(4),IH(3),IH(2) + +- CALL IDATE(IMON,IDAY,IYR) ++ CALL UIDATE(IMON,IDAY,IYR) + IF(IYR.GE.99) THEN + IYR=IYR+1900 + ELSE diff --git a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch new file mode 100644 index 000000000000..a77d9494a05c --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch @@ -0,0 +1,11 @@ +--- ccp4-6.0.1.orig/lib/src/library_f.c 2006-06-12 07:06:22.000000000 -0700 ++++ ccp4-6.0.1/lib/src/library_f.c 2006-06-12 07:21:56.000000000 -0700 +@@ -716,7 +716,7 @@ + + #endif /* end of apple xlf support */ + +-#if ( defined (__linux__) && defined (_CALL_SYSV) ) ++#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) ) + /* linuxppc xlf support */ + void gerror_ (str, Lstr) + char *str; diff --git a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch new file mode 100644 index 000000000000..106db895b775 --- /dev/null +++ b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch @@ -0,0 +1,13 @@ +--- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist 2006-01-06 17:54:17.000000000 -0800 ++++ ccp4-5.99.5/ccp4i/etc/configure.def.dist 2006-01-06 17:54:47.000000000 -0800 +@@ -54,8 +54,8 @@ + MESSAGE _text "" + BLT_LIBRARY _text "" + MENU_LENGTH _positiveint 25 +-HYPERTEXT_VIEWER _text netscape +-START_NETSCAPE _text netscape ++HYPERTEXT_VIEWER _text firefox ++START_NETSCAPE _text firefox + O_MAPMAN _text mapman + MAPMAN_MAXSIZE _positiveint 4194304 + QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch new file mode 100644 index 000000000000..02a2aa6d8877 --- /dev/null +++ b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch @@ -0,0 +1,103 @@ +--- ccp4-5.99.5.orig/configure 2006-01-17 00:35:36.000000000 -0800 ++++ ccp4-5.99.5/configure 2006-01-17 10:44:39.000000000 -0800 +@@ -2410,12 +2410,12 @@ + end + EOF + #firslty test without -lblas +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread" + echo $test_compile + if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then + # Compilation was okay +- echo "... only -llapack needed" +- XLAPACK_LIB="-llapack" ++ echo "... only -llapack -lpthread needed" ++ XLAPACK_LIB="-llapack -lpthread" + # Set the next two variables so that configure + # doesn't try to build netlib libraries + LAPACKLIB="lapack" +@@ -2424,12 +2424,12 @@ + tryblas= + else + echo "more than just -llapack needed...." +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread" + echo $test_compile + if { (eval $test_compile ) 2>&1; } && test -s testlink ; then + # Compilation was okay +- echo "...-llapack and -lblas were needed" +- XLAPACK_LIB="-llapack -lblas" ++ echo "...-llapack, -lpthread and -lblas were needed" ++ XLAPACK_LIB="-llapack -lpthread -lblas" + # Set the next two variables so that configure + # doesn't try to build netlib libraries + LAPACKLIB="lapack blas" +@@ -2720,8 +2720,8 @@ + STOP + END + EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" + echo $test_compile + if { (eval $test_compile ) 2>&1; } && test -s testlink ; then + have_lapack=yes +@@ -2738,7 +2738,7 @@ + LAPACKDIR="$testdir" + echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" + # +- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" ++ XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread" + # + # Test to see if we need BLAS too + # Do this by trying to compile a test program +@@ -2750,8 +2750,8 @@ + if test -f testlsame ; then + rm -f testsame testlsame.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then + have_blas=yes +@@ -2830,8 +2830,8 @@ + STOP + END + EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlink ; then + have_blas=yes +@@ -3033,7 +3033,7 @@ + if test -f testlsame ; then + rm -f testsame testlsame.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then + echo "Found LSAME in lib$BLASLIB" +@@ -3046,7 +3046,7 @@ + if test -f testxerbla ; then + rm -f testxerbla testxerbla.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then + # Found lsame +@@ -3080,7 +3080,7 @@ + cd ../.. + # + lapackdir=lib/lapack +- XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB" ++ XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread" + # netlib lapack is in fortran, so we may need the fortran libraries when + # we are linking using the C or C++ compilers + case $system in diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch new file mode 100644 index 000000000000..3bf5a0652247 --- /dev/null +++ b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5/lib/clipper/configure.orig 2006-01-07 16:54:13.000000000 -0800 ++++ ccp4-5.99.5/lib/clipper/configure 2006-01-07 16:54:31.000000000 -0800 +@@ -21751,7 +21751,7 @@ + + if test "x$mccp4_prefix" != x; then + # ie. mccp4=thing was given (thing is what we're checking for) +- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include" ++ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4" + ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4" + else + # treat as standard lib/include diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch new file mode 100644 index 000000000000..34d6197572fc --- /dev/null +++ b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2006-01-06 12:31:02.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Makefile.in 2006-01-06 12:31:30.000000000 -0800 +@@ -158,6 +158,7 @@ + install_obj = ipdisp.exe hklview xdldataman xdlmapman \ + rotgen ipmosflm + install: all ++ mkdir -p $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch new file mode 100644 index 000000000000..8da54fd26de8 --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-build-rasmol.patch @@ -0,0 +1,19 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 03:06:57.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Makefile.in 2005-12-05 03:07:23.000000000 -0800 +@@ -35,7 +35,7 @@ + # + # all + # +-all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm ++all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm + # + # xdl_view + # +@@ -161,7 +161,6 @@ + $(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir) + cd $(srcdir)/XCCPJIFFY ; $(MAKE) install +- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install + $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) + cd $(xdlview_dir); $(MAKE) install diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch new file mode 100644 index 000000000000..7813141b2ec2 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:12.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:41.000000000 -0800 +@@ -37,6 +37,7 @@ + ${F77} ${FFLAGS} -o $@ $< + + ipmosflm: ${OBJS} ++ mkdir -p ${DPSBIN} + ${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \ + -o ${DPSBIN}/ipmosflm ${LDFLAGS} + diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch new file mode 100644 index 000000000000..ae4b7633b105 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:42:19.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:43:35.000000000 -0800 +@@ -132,7 +132,7 @@ + # + # CBF library + # +-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) ++$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB) + $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) + $(AR) cr $@ *.o + $(RANLIB) $@ diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch new file mode 100644 index 000000000000..97607b689672 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:09.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:30.000000000 -0800 +@@ -76,6 +76,7 @@ + + # local version of libdps_index.a + ${LIB}/dps_index.a: ${IOBJS} ${HOBJS} ++ mkdir -p ${LIB} + ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS} + + ${LIB}/libpeak.a: diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch new file mode 100644 index 000000000000..eac1b9f1721e --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:48:47.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:49:02.000000000 -0800 +@@ -42,6 +42,7 @@ + $(LOCALLIBS) $(LIBS) + + index: $(IOBJS) ++ mkdir -p $(LIBDIR) + ${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS) + chmod 644 $(LIBDIR)/libdps_index.a + diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch new file mode 100644 index 000000000000..3e1a8b0e6be8 --- /dev/null +++ b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5.orig/configure 2006-01-06 11:45:43.000000000 -0800 ++++ ccp4-5.99.5/configure 2006-01-06 11:46:53.000000000 -0800 +@@ -3210,7 +3210,7 @@ + #ccp4 setup + xopts="${xopts} --with-ccp4=${srcdir}" + #interface setup +- xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol" ++ xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr" + echo + echo "********* CLIPPER CONFIGURATION ***********" + echo diff --git a/sci-chemistry/ccp4/metadata.xml b/sci-chemistry/ccp4/metadata.xml new file mode 100644 index 000000000000..d37774eb9ada --- /dev/null +++ b/sci-chemistry/ccp4/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <use> + <flag name="balbes">Install sci-chemistry/balbes</flag> + <flag name="arpwarp">Add binary arp-warp for molecular replacement</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest new file mode 100644 index 000000000000..e082cb44f7fb --- /dev/null +++ b/sci-chemistry/ccp4i/Manifest @@ -0,0 +1,3 @@ +DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820 +DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c +DIST ccp4i-6.1.3-arpwarp.patch.bz2 58498 SHA256 297e6f75354f3a1932302f7039bf449484c95eb41b8634ae96d93c754b47c687 SHA512 0bf18d9768b722c553e79eed04de316f6b0b4695f7678e1d850d5e22735ecc79cdb961ea76b6482457fff232892b81ce191cd48fa588ded8058184a871dffb65 WHIRLPOOL f24625941e31e951f13c94cf31e2ca061840b016aa3fd038d29710d9ca400d364467dc3fa1e42a55944d63ac7e42a0a6baa39a596c55b18610eeb552d232d1b8 diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild new file mode 100644 index 000000000000..f5ac55ef17fa --- /dev/null +++ b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild @@ -0,0 +1,99 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-single-r1 virtualx + +MY_PN="${PN%i}" +MY_P="${MY_PN}-${PV}" + +#UPDATE="04_03_09" +#PATCHDATE="090511" + +SRC="ftp://ftp.ccp4.ac.uk/ccp4" + +DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface" +HOMEPAGE="http://www.ccp4.ac.uk/" +SRC_URI=" + ${SRC}/${PV}/${MY_P}-core-src.tar.gz + mirror://gentoo/${P}-arpwarp.patch.bz2 + http://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" +[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" +[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" + +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +LICENSE="ccp4" +IUSE="" + +RDEPEND=" + app-shells/tcsh + media-gfx/graphviz + >=dev-lang/tk-8.3:0 + >=dev-tcltk/blt-2.4 + sci-libs/ccp4-libs" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}"/${PV}-fix-baubles.patch + "${WORKDIR}"/${P}-arpwarp.patch + ) + +src_prepare() { + epatch ${PATCHES[@]} + + [[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch + + epatch "${WORKDIR}"/${PV}-oasis4.0.patch + python_fix_shebang ccp4i/ share/dbccp4i/ +} + +src_configure() { + : +} + +src_compile() { + : +} + +src_install() { + # rm imosflm stuff + rm -rf "${S}"/ccp4i/{bin/imosflm,imosflm} || die + + rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS || die + + # This is installed by mrbump + rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} || die + + # CCP4Interface - GUI + insinto /usr/$(get_libdir)/ccp4 + doins -r "${S}"/ccp4i + exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin + doexe "${S}"/ccp4i/bin/* + dosym ../$(get_libdir)/ccp4/ccp4i/bin/ccp4i /usr/bin/ccp4i + + dodir /usr/$(get_libdir)/ccp4/ccp4i/unix + + # dbccp4i + insinto /usr/share/ccp4 + doins -r "${S}"/share/dbccp4i +} + +pkg_postinst() { + _ccp4-setup() { + source "${EPREFIX}/etc/profile" + export USER=root + bash "${EPREFIX}"/usr/$(get_libdir)/ccp4/ccp4i/bin/ccp4i -h > /dev/null + } + VIRTUALX_COMMAND="_ccp4-setup" virtualmake + echo "" + elog "ccp4i needs some enviromental settings. So please" + elog "\t source ${EPREFIX}/etc/profile" + echo "" +} diff --git a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch new file mode 100644 index 000000000000..2c5f659b8018 --- /dev/null +++ b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch @@ -0,0 +1,22 @@ +--- ccp4i/etc/configure.def.dist 2009-01-09 16:45:08.000000000 +0100 ++++ ccp4i/etc/configure.def.dist.new 2009-07-07 23:17:26.000000000 +0200 +@@ -53,8 +53,8 @@ + RUN_IMOSFLM _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]" + RUN_CCP4MG _text "ccp4mg" + RUN_COOT _text "coot" +-RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share smartie baubles.py]" +-RUN_DBVIEWER _text "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]" ++RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]" ++RUN_DBVIEWER _text "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]" + ENABLE_BUBBLE_HELP _logical 1 + DISABLE_TASKS _logical 1 + CCP4_SETUP_COMMAND _text setup_ccp4 +@@ -62,7 +62,7 @@ + BLT_LIBRARY _text "" + MENU_LENGTH _positiveint 25 + HYPERTEXT_VIEWER _text firefox +-START_NETSCAPE _text netscape ++START_NETSCAPE _text firefox + O_MAPMAN _text mapman + MAPMAN_MAXSIZE _positiveint 4194304 + QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch new file mode 100644 index 000000000000..9f5cfb4b635f --- /dev/null +++ b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch @@ -0,0 +1,61 @@ +diff --git a/ccp4i/scripts/check.script b/ccp4i/scripts/check.script +index def44bc..dd4bb7e 100755 +--- a/ccp4i/scripts/check.script ++++ b/ccp4i/scripts/check.script +@@ -24,7 +24,7 @@ + if $RUN_RAMPAGE { + + # Generate command line +- set cmd "[BinPath rapper]" ++ set cmd "[BinPath rappermc]" + + set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] + set paramsfile [FileJoin $rapperdatadir params.xml] +diff --git a/ccp4i/scripts/rapper.script b/ccp4i/scripts/rapper.script +index cdae1e2..faae226 100755 +--- a/ccp4i/scripts/rapper.script ++++ b/ccp4i/scripts/rapper.script +@@ -17,7 +17,7 @@ + + #set up command line + +-set cmd "[BinPath rapper]" ++set cmd "[BinPath rappermc]" + + set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] + set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml] +@@ -180,7 +180,7 @@ append outfiles " $XYZOUT PROJECT" + + # Run RAPPER to join loop back to framework and out put to defined pdb file + # Also need to sort out multimodel files join - FIX ME +-set cmd2 "[BinPath rapper]" ++set cmd2 "[BinPath rappermc]" + append cmd2 " $paramsfile joinpdb " + append cmd2 " --pdb2 \"$root\-loop.pdb\" " + append cmd2 " --pdb \"$root\-framework.pdb\" " +diff --git a/ccp4i/tasks/check.tcl b/ccp4i/tasks/check.tcl +index ae88ff2..ee3307b 100755 +--- a/ccp4i/tasks/check.tcl ++++ b/ccp4i/tasks/check.tcl +@@ -46,7 +46,7 @@ proc check_run { arrayname } { + # Check for Rampage program. If it is not found, we switch off the option. + # If it was the only option, script will fail with next check. + if { $array(RUN_RAMPAGE) == 1 } { +- if { [FindExecutable "rapper"] == "" } { ++ if { [FindExecutable "rappermc"] == "" } { + WarningMessage "Input Error: Rapper_Rampage program not found in system path." + set array(RUN_RAMPAGE) 0 + } +diff --git a/ccp4i/tasks/rapper.tcl b/ccp4i/tasks/rapper.tcl +index e299057..8843a3f 100755 +--- a/ccp4i/tasks/rapper.tcl ++++ b/ccp4i/tasks/rapper.tcl +@@ -28,7 +28,7 @@ proc rapper_run { arrayname } { + # Check for RAPPER program. If it is not found, we switch off the option. + # If it was the only option, script will fail with next check. + if { [regexp MODEL $build_type ] && $prog_type == "RAPPER"} { +- if { [FindExecutable "rapper"] == "" } { ++ if { [FindExecutable "rappermc"] == "" } { + WarningMessage "Input Error: RAPPER program not found in system path." + set build_type 0 + } diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch new file mode 100644 index 000000000000..74cd2b946601 --- /dev/null +++ b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch @@ -0,0 +1,26 @@ +diff --git a/ccp4i/scripts/superpose.script b/ccp4i/scripts/superpose.script +index 3483c97..5027536 100755 +--- a/ccp4i/scripts/superpose.script ++++ b/ccp4i/scripts/superpose.script +@@ -21,7 +21,7 @@ + + if { [regexp SSM $SUPERPOSE_MODE ] } { + +- set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" ++ set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" + set status [Execute $cmd "" program_status report ] + + } elseif { [regexp TOP $SUPERPOSE_MODE ] } { +diff --git a/ccp4i/tasks/superpose.tcl b/ccp4i/tasks/superpose.tcl +index 748bf6e..c92122a 100755 +--- a/ccp4i/tasks/superpose.tcl ++++ b/ccp4i/tasks/superpose.tcl +@@ -100,7 +100,7 @@ proc superpose_run { arrayname } { + # If user is match equivalent named residues/atoms then fit in the match fields + switch [GetValue $arrayname SUPERPOSE_MODE] \ + SSM { +- if { ![file exists [FindExecutable superpose]] } { ++ if { ![file exists [FindExecutable superpose-ccp4]] } { + WarningMessage "The program \"superpose\" is not on your path. + Check your installation for \"superpose\" program and \"ssm\" library." + return 0 diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch new file mode 100644 index 000000000000..9af60b7c5152 --- /dev/null +++ b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch @@ -0,0 +1,91 @@ +diff --git a/ccp4i/crank/plugins/prep/crank_prep.tcl b/ccp4i/crank/plugins/prep/crank_prep.tcl +index 7d05905..d01f1dc 100755 +--- a/ccp4i/crank/plugins/prep/crank_prep.tcl ++++ b/ccp4i/crank/plugins/prep/crank_prep.tcl +@@ -226,7 +226,7 @@ proc run_truncate { i j } { + set script "$script\n$labout" + set script "$script\nEND\n" + +- set run_command "truncate $command << \"$script\"" ++ set run_command "ftruncate $command << \"$script\"" + puts $run_command + catch {eval exec $run_command } output + puts $output +diff --git a/ccp4i/scripts/dtrek2mtz.script b/ccp4i/scripts/dtrek2mtz.script +index e74aa0d..a2a1adb 100755 +--- a/ccp4i/scripts/dtrek2mtz.script ++++ b/ccp4i/scripts/dtrek2mtz.script +@@ -36,7 +36,7 @@ + set HKL_TRUNCATE [GetTmpFileName -ext mtz] + + CreateComScript truncate truncate_script +- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" + set status [Execute $cmd $truncate_script program_status report] + + HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate +diff --git a/ccp4i/scripts/import.script b/ccp4i/scripts/import.script +index 90cba83..1c90c33 100755 +--- a/ccp4i/scripts/import.script ++++ b/ccp4i/scripts/import.script +@@ -144,7 +144,7 @@ if { $FORMAT == "MTZ" } { + + set truncatemtz [GetTmpFileName -ext mtz ] + CreateComScript truncate truncate_script +- set cmd "[BinPath truncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\"" + set status [Execute $cmd $truncate_script program_status report] + + +diff --git a/ccp4i/scripts/import_scaled.script b/ccp4i/scripts/import_scaled.script +index dcc619b..7250513 100755 +--- a/ccp4i/scripts/import_scaled.script ++++ b/ccp4i/scripts/import_scaled.script +@@ -62,7 +62,7 @@ + + } else { + CreateComScript truncate truncate_script +- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" + set status [Execute $cmd $truncate_script program_status report] + + HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate +diff --git a/ccp4i/scripts/scala.script b/ccp4i/scripts/scala.script +index 6940ccd..bde10d6 100755 +--- a/ccp4i/scripts/scala.script ++++ b/ccp4i/scripts/scala.script +@@ -275,7 +275,7 @@ END" + + } else { + CreateComScript truncate truncate_script +- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" + set status [Execute $cmd $truncate_script $LOG_FILE program_status report ] + } + +diff --git a/ccp4i/scripts/scalepack2mtz.script b/ccp4i/scripts/scalepack2mtz.script +index 986e06c..a1947a6 100755 +--- a/ccp4i/scripts/scalepack2mtz.script ++++ b/ccp4i/scripts/scalepack2mtz.script +@@ -35,7 +35,7 @@ + + set HKL_TRUNCATE [GetTmpFileName -ext mtz] + CreateComScript truncate truncate_script +- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" + set status [Execute $cmd $truncate_script program_status report] + + HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate +diff --git a/ccp4i/scripts/truncate.script b/ccp4i/scripts/truncate.script +index e0e09ce..2d448a2 100755 +--- a/ccp4i/scripts/truncate.script ++++ b/ccp4i/scripts/truncate.script +@@ -45,7 +45,7 @@ + + CreateComScript truncate truncate_script + +- set cmd "[BinPath truncate] HKLIN \"$HKLIN\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\"" + if { ![StringSame $INPUT_DATA AMPLITUDES] } { + append cmd " HKLOUT \"$HKL_TRUNCATE\"" + } diff --git a/sci-chemistry/ccp4i/metadata.xml b/sci-chemistry/ccp4i/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/ccp4i/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest new file mode 100644 index 000000000000..73f83f19c7b2 --- /dev/null +++ b/sci-chemistry/ccpn/Manifest @@ -0,0 +1,6 @@ +DIST analysis2.4.1.tar.gz 36088236 SHA256 1cb089dcc739e8536d938a68536f556094f5d728907b251fe337758ba5bef106 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1 WHIRLPOOL b53fc0438a878a8f8ce0244f5c1ce9edb616665149a699364e3bcd38c5db548c22b80ef67b4183ad5321b71b69a3b85aecc7d912893bba947700003a411651ac +DIST analysis2.4.2.tar.gz 36390919 SHA256 14941131033cbd4b0b13d6d4fe3f9253360a7c2ace8ece9194be00c1fe4b2903 SHA512 694faefd3c085b559b6bb4729141a9ab885334f578bfbb0ebf260366dbca38c31738d5f5af50b5c7ea16b304b27adf80411082859796a5afeec630c36d56bd8b WHIRLPOOL 4499dcb074d445bfc972f9dea43e6f3e3c28722d513dce0fec4e1b2b5dab8be098f53f82565d86a4e7935f0595ef303465668230aa61021cf88e13cce8606214 +DIST ccpn-update-2.4.1-150226.patch.xz 10732 SHA256 74e8723d310d336cd4215ed4e9a1a1c0b2c0efdb4c03aaacba7ecd0575b38287 SHA512 60eb4acf6179f80207a72076ff5d5d733d3c3e804c1ce0a48701dd6e923146af49cd6759a529c8125f4b26eb3f8f83b35acc0c48b88a3e3034b25b5438a04feb WHIRLPOOL 3a2357d4fcb086206d45edd5b9cc807313b5f62be2f2a70e8f011f5521cf8729371b8c7149837c4ea1f6f059e26a49c1d20492f338a844e15f38ccf543faf6e1 +DIST ccpn-update-2.4.2-150325.patch.xz 2096 SHA256 d33676fd93aaa5814aa43179f221df69f4bae9b8ec98ce5b6cc57ce6aacab732 SHA512 c544e0a4a93d0e3275a22d07d21bf3bb5ed90cf041f40bf08fbc687b431640ad5c56180eadd4b43e4023b08ef42afe5a874423becc6f9313a0b1f642a4b97873 WHIRLPOOL f2e9780eb3216185cc6b89ca490e14c2de1130393eda4308fc71e6a2eb0460fc97f83ab3c92fb6a488a1926ba2f3099c7ae5f0a4bd216f8ffa24bfd87e360838 +DIST ccpn-update-2.4.2-150413.patch.xz 3132 SHA256 c0796e1f739f799003304c8b8d23ea0ee42b2e0a6dd59b292cb2a1167b5725f5 SHA512 99893ca009ff76b015017b29cfd97e0ae935ed2d62aa5a99d52dd9a5f22cf0d369e5019273fe3c3811c28b32568721fb64f71c5927eb57d0cc91dcea44b0288d WHIRLPOOL 48a355ef4824d41517d618178be4cd4efc42a6f5e190bac88348041504da0807aa1b34bafbc3937d7f6fc3b5b52fe469431fb6ce9df40bb1c56d7faad88cfe51 +DIST ccpn-update-2.4.2-150421.patch.xz 3788 SHA256 df8f7dd81281f3f7ddd266b8bd90a089f61a9e8f0cda3bcba8b495a6f4be6238 SHA512 0e8a10b6d9721b52574cd2fe0413dca0fac32a948eb31d3db6e2c4d4f7d85c341e8d53d70954341792ea598a37ec87e4392a615e1c2f6f8bbfc0e42a750be648 WHIRLPOOL 2673ac33b2eca1a3fb873567784f1d77937e7ec6aec3ab7eef6065f9322513326993786bd3865a50c50c58e05bf874ba25df02d15083f50aef9acb404ca4e1ef diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild new file mode 100644 index 000000000000..6768d790f140 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild new file mode 100644 index 000000000000..b97807a88f38 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +#PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild new file mode 100644 index 000000000000..6768d790f140 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild new file mode 100644 index 000000000000..6768d790f140 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild new file mode 100644 index 000000000000..6768d790f140 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/files/2.3.1-parallel.patch b/sci-chemistry/ccpn/files/2.3.1-parallel.patch new file mode 100644 index 000000000000..fcf44707e082 --- /dev/null +++ b/sci-chemistry/ccpn/files/2.3.1-parallel.patch @@ -0,0 +1,38 @@ +diff --git a/ccpnmr2.3/c/Makefile b/ccpnmr2.3/c/Makefile +index 01fb25a..8e8e1fe 100644 +--- a/ccpnmr2.3/c/Makefile ++++ b/ccpnmr2.3/c/Makefile +@@ -5,22 +5,22 @@ all: compile + compile: global structure analysis clouds dynamics bayes + + global: +- cd memops/global && $(MAKE) ++ $(MAKE) -C memops/global + +-structure: +- cd ccp/structure && $(MAKE) ++structure: global ++ $(MAKE) -C ccp/structure + +-analysis: +- cd ccpnmr/analysis && $(MAKE) ++analysis: global ++ $(MAKE) -C ccpnmr/analysis + +-clouds: +- cd ccpnmr/clouds && $(MAKE) ++clouds: global ++ $(MAKE) -C ccpnmr/clouds + +-dynamics: +- cd ccpnmr/dynamics && $(MAKE) ++dynamics: global ++ $(MAKE) -C ccpnmr/dynamics + +-bayes: +- cd other/cambridge/bayes && $(MAKE) ++bayes: global ++ $(MAKE) -C other/cambridge/bayes + + clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean + diff --git a/sci-chemistry/ccpn/files/analysis b/sci-chemistry/ccpn/files/analysis new file mode 100644 index 000000000000..828ed4e64ae9 --- /dev/null +++ b/sci-chemistry/ccpn/files/analysis @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -i -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/analysis/AnalysisGui.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/dangle b/sci-chemistry/ccpn/files/dangle new file mode 100644 index 000000000000..6d8a42e615de --- /dev/null +++ b/sci-chemistry/ccpn/files/dangle @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/cambridge/dangle/DangleGui.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/dataShifter b/sci-chemistry/ccpn/files/dataShifter new file mode 100644 index 000000000000..c083960f2f60 --- /dev/null +++ b/sci-chemistry/ccpn/files/dataShifter @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/DataShifter.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/depositionFileImporter b/sci-chemistry/ccpn/files/depositionFileImporter new file mode 100644 index 000000000000..09505ccc4925 --- /dev/null +++ b/sci-chemistry/ccpn/files/depositionFileImporter @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/pdbe/deposition/dataFileImport/dataFileImportGui.py $@ diff --git a/sci-chemistry/ccpn/files/eci b/sci-chemistry/ccpn/files/eci new file mode 100644 index 000000000000..54d913348718 --- /dev/null +++ b/sci-chemistry/ccpn/files/eci @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/eci/EntryCompletionGui.py $* diff --git a/sci-chemistry/ccpn/files/extendNmr b/sci-chemistry/ccpn/files/extendNmr new file mode 100644 index 000000000000..a2fe4c997c7c --- /dev/null +++ b/sci-chemistry/ccpn/files/extendNmr @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O -i -O ${CCPNMR_TOP_DIR}/ccpn/python/extendNmr/ExtendNmrGui.py $@ diff --git a/sci-chemistry/ccpn/files/formatConverter b/sci-chemistry/ccpn/files/formatConverter new file mode 100644 index 000000000000..6cb273612352 --- /dev/null +++ b/sci-chemistry/ccpn/files/formatConverter @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/FormatConverter.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/pipe2azara b/sci-chemistry/ccpn/files/pipe2azara new file mode 100644 index 000000000000..5a3710a134a7 --- /dev/null +++ b/sci-chemistry/ccpn/files/pipe2azara @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/NmrPipeData.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/talosn.patch b/sci-chemistry/ccpn/files/talosn.patch new file mode 100644 index 000000000000..e19a0ab19783 --- /dev/null +++ b/sci-chemistry/ccpn/files/talosn.patch @@ -0,0 +1,16 @@ + ccpnmr2.3/python/ccpnmr/format/general/Constants.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/ccpnmr2.3/python/ccpnmr/format/general/Constants.py b/ccpnmr2.3/python/ccpnmr/format/general/Constants.py +index d10553e..fb732db 100644 +--- a/ccpnmr2.3/python/ccpnmr/format/general/Constants.py ++++ b/ccpnmr2.3/python/ccpnmr/format/general/Constants.py +@@ -865,7 +865,7 @@ IoSetupList = [ + 'cyana': ['dihedrals.aco',1,1, [['SelectionList','version','Cyana version:',['2.0','2.1'],None]], + [['SelectionList','version','Cyana version:',['2.0','2.1'],None]]], + 'nmrStar': ['nmrStar.str',1,0, [],[]], +- 'talos': ['dihedral.tab',1,0, [['MultiSelectionList','validClasses','Classes for valid constraint:',['Good','New','Warn','None'],None], ++ 'talos': ['dihedral.tab',1,0, [['MultiSelectionList','validClasses','Classes for valid constraint:',['Good','New','Warn','Dyn', 'Strong', 'Generous', 'None'],None], + ['IntEntry','validCount','Count variable lower limit for valid constraint:',0,None], + ['FloatEntry','multiplyDeviation','Multiplication factor to convert deviation in constraint range:',2.0,None]], + []]}, diff --git a/sci-chemistry/ccpn/files/xeasy2azara b/sci-chemistry/ccpn/files/xeasy2azara new file mode 100644 index 000000000000..7b73714c2fa5 --- /dev/null +++ b/sci-chemistry/ccpn/files/xeasy2azara @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/XeasyData.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/metadata.xml b/sci-chemistry/ccpn/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/ccpn/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest new file mode 100644 index 000000000000..d8db80c30926 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/Manifest @@ -0,0 +1 @@ +DIST chemical-mime-data-0.1.94.tar.bz2 146077 SHA256 4907cdf60e9edca0a453f6f24e9179ae9da085b67168e932ba44a4280316bff1 SHA512 7f3d967149f27ab1de53c948dc055959e661e1be9d778e3d56d06bea95769da7770ab5fb66afab6607747ef91ffb1dbbcf921e5f06e3303351781968594b5f00 WHIRLPOOL 2e601b37ca22cc1d2b77b5d82713e756dea380fcb0a01c517513be0271162df6e19e7cc7dbc0af8f25e579bb809e0768cc2ee394124c91c296ed0d4c38cfa213 diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r1.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r1.ebuild new file mode 100644 index 000000000000..c63c806baa7c --- /dev/null +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils fdo-mime + +DESCRIPTION="A collection of data files to add support for chemical MIME types" +HOMEPAGE="http://chemical-mime.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="virtual/pkgconfig + x11-misc/shared-mime-info + dev-util/intltool + dev-util/desktop-file-utils + dev-libs/libxslt + media-gfx/imagemagick[xml] + gnome-base/gnome-mime-data" + +RDEPEND="" + +src_configure() { + econf --disable-update-database --htmldir=/usr/share/doc/${PF}/html +} + +src_install() { + emake DESTDIR="${D}" install || die "emake install failed" +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + ewarn "You can ignore any 'Unknown media type in type' warnings." +} diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild new file mode 100644 index 000000000000..851bd6b2bec4 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils fdo-mime + +DESCRIPTION="A collection of data files to add support for chemical MIME types" +HOMEPAGE="http://chemical-mime.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + gnome-base/gnome-mime-data + x11-misc/shared-mime-info" +DEPEND="${RDEPEND} + dev-util/intltool + dev-util/desktop-file-utils + dev-libs/libxslt + media-gfx/imagemagick[xml] + media-gfx/inkscape + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}"/${P}-turbomole.patch + "${FILESDIR}"/${P}-pigz.patch + "${FILESDIR}"/${P}-namespace-svg.patch + ) + +src_prepare() { + # needed for convert/inkscape #464782 + export XDG_CONFIG_HOME=$HOME/.config + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-update-database + --htmldir=/usr/share/doc/${PF}/html + ) + autotools-utils_src_configure +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + ewarn "You can ignore any 'Unknown media type in type' warnings." +} + +pkg_postrm() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + ewarn "You can ignore any 'Unknown media type in type' warnings." +} diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94.ebuild new file mode 100644 index 000000000000..c965d2f88027 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils fdo-mime + +DESCRIPTION="A collection of data files to add support for chemical MIME types" +HOMEPAGE="http://chemical-mime.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND="virtual/pkgconfig + x11-misc/shared-mime-info + dev-util/intltool + dev-util/desktop-file-utils + dev-libs/libxslt + media-gfx/imagemagick[xml] + gnome-base/gnome-mime-data" + +RDEPEND="" + +src_configure() { + econf --disable-update-database --htmldir=/usr/share/doc/${PN}/html +} + +src_install() { + emake DESTDIR="${D}" install || die "emake install failed" +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + ewarn "You can ignore any 'Unknown media type in type' warnings." +} diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch new file mode 100644 index 000000000000..9860261af403 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch @@ -0,0 +1,16 @@ + icons/hicolor/gnome-mime-chemical.svg | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/icons/hicolor/gnome-mime-chemical.svg b/icons/hicolor/gnome-mime-chemical.svg +index 1a8d428..804514c 100644 +--- a/icons/hicolor/gnome-mime-chemical.svg ++++ b/icons/hicolor/gnome-mime-chemical.svg +@@ -5,7 +5,7 @@ + <!ENTITY ns_svg "http://www.w3.org/2000/svg"> + <!ENTITY ns_xlink "http://www.w3.org/1999/xlink"> + ]> +-<svg xmlns="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/" ++<svg xmlns:svg="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/" + width="128" height="128" viewBox="0 0 128 128" overflow="visible" enable-background="new 0 0 128 128" xml:space="preserve"> + <g id="Layer_1"> + <g> diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch new file mode 100644 index 000000000000..8b5ccfbc3fd9 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch @@ -0,0 +1,16 @@ + Makefile.am | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Makefile.am b/Makefile.am +index 96e03ab..ba0847a 100644 +--- a/icons/hicolor/Makefile.am ++++ b/icons/hicolor/Makefile.am +@@ -21,7 +21,7 @@ icon_sizes = 16 22 24 32 36 48 64 72 96 128 192 + if BOOL_HICOLOR_THEME + + .svg.svgz: +- gzip $< -c > $@ ++ gzip -c $< > $@ + for size in $(icon_sizes) ; do \ + if test "x$(RSVG)" != "x" ; then \ + $(RSVG) -w $${size} -h $${size} -f png $< $*_$${size}.png ; \ diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch new file mode 100644 index 000000000000..852d6b0605be --- /dev/null +++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch @@ -0,0 +1,57 @@ +diff -up chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in +--- chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole 2009-08-10 09:37:06.000000000 +0200 ++++ chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in 2009-08-10 09:40:57.000000000 +0200 +@@ -1290,7 +1290,7 @@ + <specification url="http://ca.expasy.org/sprot/userman.html"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-basis" support="no"> ++ <mime-type type="chemical/x-turbomole-basis" support="yes"> + <_comment>Turbomole Basis Set File</_comment> + <glob pattern="basis"/> + <sub-class-of type="text/plain"/> +@@ -1304,7 +1304,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-control" support="no"> ++ <mime-type type="chemical/x-turbomole-control" support="yes"> + <_comment>Turbomole Control File</_comment> + <glob pattern="control"/> + <sub-class-of type="text/plain"/> +@@ -1320,7 +1320,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/node230.html"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-coord" support="no"> ++ <mime-type type="chemical/x-turbomole-coord" support="yes"> + <_comment>Turbomole Coordinate File</_comment> + <glob pattern="coord"/> + <glob pattern="*.tmol"/> +@@ -1335,7 +1335,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-grad" support="no"> ++ <mime-type type="chemical/x-turbomole-grad" support="yes"> + <_comment>Turbomole Gradient File</_comment> + <glob pattern="gradient"/> + <sub-class-of type="text/plain"/> +@@ -1383,7 +1383,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-scfmo" support="no"> ++ <mime-type type="chemical/x-turbomole-scfmo" support="yes"> + <_comment>Turbomole SCF Molecular Orbital File</_comment> + <acronym>MO</acronym> + <expanded-acronym>Molecular Orbital</expanded-acronym> +@@ -1401,7 +1401,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-vibrational" support="no"> ++ <mime-type type="chemical/x-turbomole-vibrational" support="yes"> + <_comment>Turbomole Vibrational Data File</_comment> + <glob pattern="???"/> + <sub-class-of type="text/plain"/> diff --git a/sci-chemistry/chemical-mime-data/metadata.xml b/sci-chemistry/chemical-mime-data/metadata.xml new file mode 100644 index 000000000000..941ce487e86e --- /dev/null +++ b/sci-chemistry/chemical-mime-data/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <longdescription lang="en"> +A collection of data files to add support for chemical MIME types. +</longdescription> + <upstream> + <remote-id type="sourceforge">chemical-mime</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/chemtool/Manifest b/sci-chemistry/chemtool/Manifest new file mode 100644 index 000000000000..a364d0afdaea --- /dev/null +++ b/sci-chemistry/chemtool/Manifest @@ -0,0 +1,2 @@ +DIST chemtool-1.6.13.tar.gz 838868 SHA256 31a07683f55305c3e0c4d7af3bc3d1d3a9a2eff4d836455fe1e382962f0aa0c8 SHA512 6c248321f73b6eab4ad21e810639a1f0b14cc30db9c9fdc8fe66ee218bd88ead5e74f1f047f5badcb91b515827c2eddc64b28ead380d9b14ab5b76777e7134dd WHIRLPOOL c7158a75480e9b98eb2ed5c16d73c4d5e5fa05375009ac1778b7e9bf0e9a2ef9092032557d46ea506a6503c0799676998a6fcb80063ed56a7ae8d360c1f273bc +DIST chemtool-1.6.14.tar.gz 817735 SHA256 86161a0461386b334a5ffb17cdf094a491941884678272f45749813514ddafcb SHA512 066c83c61aced3134b081767e788143a047889a2fee4b6535c2b0a3166bccc73d75981e1cf35b7bcaa5b8fe2e0227b28693b659decd82f7783cb4082ac6ed2bd WHIRLPOOL 41a2bd4662c06307a94281e6a54d4e129b407bc597c7d08c8a9f976332cb727f3e195d1d85429716ac22a34ea1dae03b724167bbb5444c03dcb24131cc20ae1d diff --git a/sci-chemistry/chemtool/chemtool-1.6.13.ebuild b/sci-chemistry/chemtool/chemtool-1.6.13.ebuild new file mode 100644 index 000000000000..2ab2dc197a0b --- /dev/null +++ b/sci-chemistry/chemtool/chemtool-1.6.13.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils eutils + +DESCRIPTION="A GTK program for drawing organic molecules" +HOMEPAGE="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/" +SRC_URI="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="emf gnome nls" + +RDEPEND=" + dev-libs/glib:2 + media-gfx/transfig + x11-libs/gtk+:2 + x11-libs/libX11 + x11-libs/pango + emf? ( media-libs/libemf )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +PATCHES=( + "${FILESDIR}"/${PV}-no-underlinking.patch + ) + +src_configure() { + local myeconfargs=( + --without-kdedir + $(use_with gnome gnomedir /usr) + $(use_enable emf) + --enable-undo + --enable-menu + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + + insinto /usr/share/${PN}/examples + doins "${S}"/examples/* + if ! use nls; then rm -rf "${ED}"/usr/share/locale || die; fi + + insinto /usr/share/pixmaps + doins chemtool.xpm + make_desktop_entry ${PN} Chemtool ${PN} "Education;Science;Chemistry" +} diff --git a/sci-chemistry/chemtool/chemtool-1.6.14.ebuild b/sci-chemistry/chemtool/chemtool-1.6.14.ebuild new file mode 100644 index 000000000000..b77cb79569e4 --- /dev/null +++ b/sci-chemistry/chemtool/chemtool-1.6.14.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils eutils + +DESCRIPTION="A GTK program for drawing organic molecules" +HOMEPAGE="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/" +SRC_URI="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="emf gnome nls" + +RDEPEND=" + dev-libs/glib:2 + media-gfx/transfig + x11-libs/gtk+:2 + x11-libs/libX11 + x11-libs/pango + emf? ( media-libs/libemf )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +PATCHES=( + "${FILESDIR}"/1.6.13-no-underlinking.patch +) + +src_configure() { + local myeconfargs=( + --without-kdedir + $(use_with gnome gnomedir /usr) + $(use_enable emf) + --enable-undo + --enable-menu + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + + insinto /usr/share/${PN}/examples + doins "${S}"/examples/* + if ! use nls; then rm -rf "${ED}"/usr/share/locale || die; fi + + insinto /usr/share/pixmaps + doins chemtool.xpm + make_desktop_entry ${PN} Chemtool ${PN} "Education;Science;Chemistry" +} diff --git a/sci-chemistry/chemtool/files/1.6.13-no-underlinking.patch b/sci-chemistry/chemtool/files/1.6.13-no-underlinking.patch new file mode 100644 index 000000000000..5d2fe36d6bf1 --- /dev/null +++ b/sci-chemistry/chemtool/files/1.6.13-no-underlinking.patch @@ -0,0 +1,78 @@ + Makefile.am | 6 ++++-- + configure.ac | 24 ++++-------------------- + 2 files changed, 8 insertions(+), 22 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 99dbf8c..931ba16 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -22,10 +22,12 @@ localedir = $(datadir)/locale + DEFS = -DLOCALEDIR=\"$(localedir)\" @DEFS@ + + # Make sure the gettext.h include file is found. +-AM_CPPFLAGS = -I. -I$(srcdir) @GTK_CFLAGS@ ++AM_CPPFLAGS = -I. -I$(srcdir) @GTK_CFLAGS@ @EMFINCL@ + + # Link time dependencies. +-LDADD = @LIBINTL@ @GTK_LIBS@ @EMFLIBS@ ++LDADD = @LIBINTL@ @GTK_LIBS@ @EMFLIBS@ -lX11 ++ ++AM_CFLAGS = -DGTK2 + + # Additional files to be distributed. + EXTRA_DIST = autogen.sh autoclean.sh +diff --git a/configure.ac b/configure.ac +index 6d8c45a..c5fab42 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -32,32 +32,14 @@ AC_PATH_PROG(PKG_CONFIG, pkg-config, no) + + AC_MSG_CHECKING([for GTK version and compile options ]) + +-if test x$PKG_CONFIG = xno -o x$enable_gtk1 = xyes ; then +-AM_PATH_GTK(1.0.2, , exit 1) +-else +-if $PKG_CONFIG gtk+-2.0 --cflags ; then +- GTK_CFLAGS="-DGTK2 `$PKG_CONFIG gtk+-2.0 --cflags` " +- GTK_LIBS=`$PKG_CONFIG gtk+-2.0 --libs` +-dnl use_gtk2=yes +- AC_DEFINE([GTK2], [1], [the GTK2 library]) +- enable_stockgtk=yes +-else +-if $PKG_CONFIG --cflags gtk+ ; then +- GTK_CFLAGS=`$PKG_CONFIG gtk+ --cflags` +- GTK_LIBS=`$PKG_CONFIG gtk+ --libs` +-dnl use_gtk2=no +-fi +-fi +-fi +- +-dnl AC_MSG_RESULT using GTK2 : $use_gtk2 ++PKG_CHECK_MODULES([GTK],[gtk+-2.0]) + + dnl Checks for header files. + AC_PATH_XTRA + AC_HEADER_DIRENT + AC_HEADER_STDC + +-LDFLAGS="$X_LIBS" ++LDFLAGS+="$X_LIBS" + AC_CHECK_LIB([X11],[XOpenDisplay]) + dnl just an ugly hack to work around the more aggressive header checks + dnl in recent autoconf. Not sure if we should really rely on include +@@ -184,6 +166,7 @@ if test x$enable_emf = xyes; then + AC_MSG_RESULT(yes) + AC_DEFINE([EMF], [1], [use optional libEMF instead of fig2dev for EMF output]) + EMFLIBS="-lEMF -lstdc++" ++ EMFINCL="-I${includedir}libEMF" + else + AC_MSG_RESULT(no) + EMFLIBS="" +@@ -221,6 +204,7 @@ AC_SUBST(localedir) + AC_SUBST(kdemimedir) + AC_SUBST(gnomemimedir) + AC_SUBST(EMFLIBS) ++AC_SUBST(EMFINCL) + AC_SUBST(MYGTKSRCS) + AC_SUBST(MYGTKOBJS) + AC_SUBST(GTK_CFLAGS) diff --git a/sci-chemistry/chemtool/metadata.xml b/sci-chemistry/chemtool/metadata.xml new file mode 100644 index 000000000000..26c258873424 --- /dev/null +++ b/sci-chemistry/chemtool/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <use> + <flag name="emf">EMF export support</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/clashlist/Manifest b/sci-chemistry/clashlist/Manifest new file mode 100644 index 000000000000..3c71b7792037 --- /dev/null +++ b/sci-chemistry/clashlist/Manifest @@ -0,0 +1 @@ +DIST molprobity-3.17.tgz 26429898 SHA256 2e70814efb4f566a522762a626f69669c09285cbb6fc26444eb947fde9b30f25 SHA512 a6e986f285ff7e8d167e2d1c935a55b080446c9809d352c95e2ffa32265892b59cd1611730e75ca88aa28387495d3ebd84226e1a9cdd33f0b27b1a8a1b6a469f WHIRLPOOL 3981522eeacaa589530e7d268cda786bebeaf676f7fa5c26508798022126bd1a1c8ea193f65e3c5c739fb3b516b26c3cf24ac0e7898e764a9cffab6637dcd5a9 diff --git a/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild b/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild new file mode 100644 index 000000000000..7aedd7743f6b --- /dev/null +++ b/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +DESCRIPTION="Build lists of van der Waals clashes from an input PDB file" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" +SRC_URI="mirror://gentoo/molprobity-${PV}.tgz" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="~amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/cluster-1.3.081231-r1 + sci-chemistry/probe" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +src_prepare() { + sed \ + -e 's: cluster : molprobity-cluster :g' \ + -i molprobity3/bin/clashlist || die +} + +src_install() { + dobin molprobity3/bin/clashlist +} diff --git a/sci-chemistry/clashlist/clashlist-3.17.ebuild b/sci-chemistry/clashlist/clashlist-3.17.ebuild new file mode 100644 index 000000000000..513a1e024746 --- /dev/null +++ b/sci-chemistry/clashlist/clashlist-3.17.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +DESCRIPTION="Build lists of van der Waals clashes from an input PDB file" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" +SRC_URI="mirror://gentoo/molprobity-${PV}.tgz" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + <=sci-chemistry/cluster-1.3.081231 + sci-chemistry/probe" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +src_install() { + dobin molprobity3/bin/clashlist +} diff --git a/sci-chemistry/clashlist/metadata.xml b/sci-chemistry/clashlist/metadata.xml new file mode 100644 index 000000000000..c96b852229d5 --- /dev/null +++ b/sci-chemistry/clashlist/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +Clashlist is a simple UNIX script which uses the awk facility along with +the programs Probe and Cluster to build lists of van der Waals clashes +from an input PDB-format molecular data file (with H atoms). These lists +are organized such that collections of interacting residues are grouped +together, sorted by the worst clash. For the purposes of this analysis, +a clash is defined as a van der Waals overlap >= 0.4 A. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/cluster/Manifest b/sci-chemistry/cluster/Manifest new file mode 100644 index 000000000000..1a7bcd779934 --- /dev/null +++ b/sci-chemistry/cluster/Manifest @@ -0,0 +1 @@ +DIST cluster.1.3.081231.src.tgz 8860 SHA256 4e0986d5ff124936b5fff4b6f8989dd04be11180d6552fddc34b2c10dfcc870f SHA512 af5851ef467458d45ee5f2309c6344ae16145ac371a1b9d0a3d8b5769a18b98877cf7cb65b85f71108d927b0e6c363e06b85a67e7cb2e5e0b41af375cb2db7ac WHIRLPOOL 2f02de20b323792360b28d5a42d233d06be529414e29796a39a439651fee9e8ba73bdd05033907ac7434890bfa2a31aaf57ab98bbe59964d06a2d63646833f5f diff --git a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild new file mode 100644 index 000000000000..801d4209627a --- /dev/null +++ b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Build lists of collections of interacting items" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}"/${PN}1.3src + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-ldflags.patch \ + "${FILESDIR}"/${PV}-includes.patch + tc-export CXX +} + +src_install() { + newbin ${PN} molprobity-${PN} + dodoc README.cluster +} diff --git a/sci-chemistry/cluster/cluster-1.3.081231.ebuild b/sci-chemistry/cluster/cluster-1.3.081231.ebuild new file mode 100644 index 000000000000..abb875d7f2d0 --- /dev/null +++ b/sci-chemistry/cluster/cluster-1.3.081231.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Build lists of collections of interacting items" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}"/${PN}1.3src + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-ldflags.patch \ + "${FILESDIR}"/${PV}-includes.patch + tc-export CXX +} + +src_install() { + dobin ${PN} + dodoc README.cluster +} diff --git a/sci-chemistry/cluster/files/1.3.081231-includes.patch b/sci-chemistry/cluster/files/1.3.081231-includes.patch new file mode 100644 index 000000000000..a5586a540a4f --- /dev/null +++ b/sci-chemistry/cluster/files/1.3.081231-includes.patch @@ -0,0 +1,12 @@ +diff --git a/cluster.cpp b/cluster.cpp +index 0a8c3c1..1384949 100644 +--- a/cluster.cpp ++++ b/cluster.cpp +@@ -24,6 +24,7 @@ + #include <iostream> + #include <vector> + #include <string> ++#include <cstring> + + #include <iostream> + #include <fstream> diff --git a/sci-chemistry/cluster/files/1.3.081231-ldflags.patch b/sci-chemistry/cluster/files/1.3.081231-ldflags.patch new file mode 100644 index 000000000000..1b99f6d662f2 --- /dev/null +++ b/sci-chemistry/cluster/files/1.3.081231-ldflags.patch @@ -0,0 +1,41 @@ + Makefile | 12 ++++++------ + 1 files changed, 6 insertions(+), 6 deletions(-) + +diff --git a/Makefile b/Makefile +index 7892054..929564b 100644 +--- a/Makefile ++++ b/Makefile +@@ -3,27 +3,27 @@ PROG_FLGS = -D BOOLPREDEFINED + + SRCS = cluster.cpp DisjointSets.cpp utility.cpp + +-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) ++CXXFLAGS += $(OPT) $(DEBUG) $(PROG_FLGS) + + LFLAGS = + + OBJLIST = cluster.o DisjointSets.o utility.o + +-CXX = g++ ++CXX ?= g++ + + .cpp.o: +- $(CXX) -c $*.cpp $(CFLAGS) ++ $(CXX) $(CXXFLAGS) -c $*.cpp + +-OPT = -O3 ++OPT = + DEBUG = $(CXXDEBUGFLAGS) + + all: cluster + + cluster: $(OBJLIST) +- $(CXX) -o $@ $(OBJLIST) $(LFLAGS) ++ $(CXX) $(LDFLAGS) -o $@ $(OBJLIST) + + depend: +- makedepend -- $(CFLAGS) -- $(SRCS) ++ makedepend -- $(CXXFLAGS) -- $(SRCS) + + clean: + @rm -rf *.o *.ckp ii_files diff --git a/sci-chemistry/cluster/metadata.xml b/sci-chemistry/cluster/metadata.xml new file mode 100644 index 000000000000..76f6a5d9e463 --- /dev/null +++ b/sci-chemistry/cluster/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +Cluster is a simple UNIX C++ program to build lists of collections +of interacting items from records containing interacting pairs +and larger fragments. + +It reads in lines consisting of two or more names and output +connected clusters of names. Each line of output is +prefixed with a cluster number, the size of the cluster +and an optional name string. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest new file mode 100644 index 000000000000..d0d2b7b0dc55 --- /dev/null +++ b/sci-chemistry/cns/Manifest @@ -0,0 +1,4 @@ +DIST aria2.3.1.tar.gz 1833973 SHA256 cc45ed2d66182cf0ee197a7cf3bc7edd8d5043d95cdcd19e1cec9aeb82c2fdbc SHA512 79a2cd89e2120acecb04f286a153dbf52c16500e8956c9dad49b1e1ed94a7b2449c7b044bae6f87e0d2b452a1467a2c02de74f0fa85b0eae66042386e2f5e2d5 WHIRLPOOL 2ff003322601b42bec0d2431e2f1f85819b3982f8da612ff778bb404e51f0fcbca3faa6998e9c0635f9e73899609bb1e273420cac182952aa744364c20299723 +DIST aria2.3.2.tar.gz 1836270 SHA256 30727ea8bdc2e3b44e5970545008fcfa07fa59aa28b76824956a2aa71daa9615 SHA512 009a1d0079f5cc162dc732749ddd2b33297268f0d988b2f37bda4ed50c7764ceef7ae5b56b322c7ac79427a4a2a92d1239199891445cb5e2b3d0908ed670e2aa WHIRLPOOL f18af5b751e79c92e04f4dc12b6b806a1c505b269559a2342bdd6280b790f9f0df9bb4afe366af03beaf09af0128c6b68c39bc66603d51ad24914c78b2579cf3 +DIST cns_solve_1.21_all-mp.tar.gz 32748040 SHA256 7ab464e20932eb024ba6378738da77a4a03642d63b0ca9772b612a7cf27baec1 SHA512 383324d771570b501e388fba9bf20789f483a3a4044eb3334c7a7e7835e0c345b784e0d344b22d20a10fe1c33ed21c9013adb1af5912808af480b96abe275857 WHIRLPOOL fecd0b2dfba43e5525a9fcc8543a55867602b376744848ddafd4c132bcdfc32225780f543742fa225b5e0f0ce658c1029a9ca8b80d5ee3f2491b6d63e8ad91b0 +DIST cns_solve_1.3_all.tar.gz 64167735 SHA256 2ee368022c5ecabf66ce7d32059d93cd7d885ad2d684a094b87c64f6b3dfea0d SHA512 4fe73820e96999bb33a59ff6da979794628552f49bc03cdebcb9439b57e6042b92190e04bb7e4079157adf06a6facc5c16b8ae91621bd24a4b35ee382e53ae37 WHIRLPOOL b3cd14ab7a8a29a44f6e6c3cbc22ee2c665eb8c8565969337b24deffb2a1fd007fae11c5eb73ac38ddf9a38e850948e3b2df2548931722a2a383d5e8c72607a1 diff --git a/sci-chemistry/cns/cns-1.2.1-r8.ebuild b/sci-chemistry/cns/cns-1.2.1-r8.ebuild new file mode 100644 index 000000000000..d9cc723f98b3 --- /dev/null +++ b/sci-chemistry/cns/cns-1.2.1-r8.ebuild @@ -0,0 +1,233 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic + +MY_PN="${PN}_solve" +MY_PV="$(delete_version_separator 2)" +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Crystallography and NMR System" +HOMEPAGE="http://cns.csb.yale.edu/" +SRC_URI=" + ${MY_P}_all-mp.tar.gz + aria? ( aria2.3.2.tar.gz )" + +SLOT="0" +LICENSE="cns" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="aria openmp" + +RDEPEND="app-shells/tcsh" +DEPEND="${RDEPEND}" + +FORTRAN_NEED_OPENMP=1 + +S="${WORKDIR}/${MY_P}" + +RESTRICT="fetch test" + +pkg_nofetch() { + elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" + use aria && elog "and http://aria.pasteur.fr/" + elog "and place these files:" + elog ${A} + elog "in ${DISTDIR}." +} + +get_fcomp() { + case $(tc-getFC) in + *gfortran* ) + FCOMP="gfortran" ;; + ifort ) + FCOMP="ifc" ;; + * ) + FCOMP=$(tc-getFC) ;; + esac +} + +pkg_setup() { + fortran-2_pkg_setup + get_fcomp +} + +get_bitness() { + echo > "${T}"/test.c + $(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o + case $(file "${T}"/test.o) in + *64-bit*|*ppc64*|*x86_64*) export _bitness="64";; + *32-bit*|*ppc*|*i386*) export _bitness="32";; + *) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";; + esac +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-gentoo.patch \ + "${FILESDIR}"/${PV}-parallel.patch + + get_bitness + + if use aria; then + pushd "${WORKDIR}"/aria* >& /dev/null + # Update the cns sources in aria for version 1.2.1 + epatch "${FILESDIR}"/1.2.1-aria2.3.patch + + # Update the code with aria specific things + cp -rf cns/src/* "${S}"/source/ || die + popd >& /dev/null + fi + + # the code uses Intel-compiler-specific directives + if [[ $(tc-getFC) =~ gfortran ]]; then + epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch + use openmp && \ + append-flags -fopenmp && append-ldflags -fopenmp + COMP="gfortran" + [[ ${_bitness} == 64 ]] && \ + append-fflags -fdefault-integer-8 + elif [[ $(tc-getFC) == if* ]]; then + epatch "${FILESDIR}"/${PV}-ifort.patch + use openmp && \ + append-flags -openmp && append-ldflags -openmp + COMP="ifort" + [[ ${_bitness} == 64 ]] && append-fflags -i8 + fi + + [[ ${_bitness} == 64 ]] && \ + append-cflags "-DINTEGER='long long int'" + + # Set up location for the build directory + # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION + cp "${FILESDIR}"/cns_solve_env_sh "${T}"/ || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ + -i "${S}"/cns_solve_env || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ + -i "${T}"/cns_solve_env_sh || die + + einfo "Fixing shebangs..." + find "${S}" -type f \ + -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die +} + +src_compile() { + local GLOBALS + local MALIGN + if [[ $(tc-getFC) =~ g77 ]]; then + GLOBALS="-fno-globals" + MALIGN='\$(CNS_MALIGN_I86)' + fi + + # Set up the compiler to use + ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die + + # make install really means build, since it's expected to be used in-place + # -j1 doesn't mean we do no respect MAKEOPTS! + emake -j1 \ + CC="$(tc-getCC)" \ + F77=$(tc-getFC) \ + LD=$(tc-getFC) \ + CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + LDFLAGS="${LDFLAGS}" \ + F77OPT="${FCFLAGS} ${MALIGN}" \ + F77STD="${GLOBALS}" \ + OMPLIB="${OMPLIB}" \ + compiler="${COMP}" \ + install +} + +src_test() { + # We need to force on g77 manually, because we can't get aliases working + # when we source in a -c + einfo "Running tests ..." + csh -c \ + "export CNS_G77=ON; source ${S}/cns_solve_env; make run_tests" \ + || die "tests failed" + einfo "Displaying test results ..." + cat "${S}"/*_g77/test/*.diff-test +} + +src_install() { + # Install to locations resembling FHS + sed \ + -e "s:${S}:usr:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \ + -e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \ + -e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \ + -e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \ + -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ + -e "/^g77on/d" \ + -i "${S}"/cns_solve_env || die + # I don't entirely understand why the sh version requires a leading / + # for CNS_SOLVE and CNS_ROOT, but it does + sed \ + -e "s:${S}:/usr:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \ + -e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \ + -e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \ + -e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \ + -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ + -e "/^g77on/d" \ + -e "/^g77off/d" \ + -i "${T}"/cns_solve_env_sh || die + + # Get rid of setup stuff we don't need in the installed script + sed \ + -e "83,$ d" \ + -e "37,46 d" \ + -i "${S}"/cns_solve_env || die + sed \ + -e "84,$ d" \ + -e "39,50 d" \ + -i "${T}"/cns_solve_env_sh || die + + newbin "${S}"/*linux*/bin/cns_solve* cns_solve + + # Can be run by either cns_solve or cns + dosym cns_solve /usr/bin/cns + + # Don't want to install this + rm -f "${S}"/*linux*/utils/Makefile || die + + dobin "${S}"/*linux*/utils/* + + sed \ + -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ + -i "${S}"/bin/cns_web || die + + dobin "${S}"/bin/cns_{edit,header,transfer,web} + + insinto /usr/share/cns + doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib + doins "${S}"/bin/cns_info + + insinto /etc/profile.d + newins "${S}"/cns_solve_env cns_solve_env.csh + newins "${T}"/cns_solve_env_sh cns_solve_env.sh + + dohtml \ + -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ + -f all_cns_info_template,omac,def \ + -r doc/html/* + # Conflits with app-text/dos2unix + rm -f "${D}"/usr/bin/dos2unix || die +} + +pkg_postinst() { + if use openmp; then + elog "Set OMP_NUM_THREADS to the number of threads you want." + elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" + elog "variable if using gcc (16384 should be good)." + fi +} diff --git a/sci-chemistry/cns/cns-1.3_p7-r1.ebuild b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild new file mode 100644 index 000000000000..724c62f7e98c --- /dev/null +++ b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild @@ -0,0 +1,216 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic + +MY_PN="${PN}_solve" +MY_PV="$(delete_version_separator 2)" +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Crystallography and NMR System" +HOMEPAGE="http://cns.csb.yale.edu/" +SRC_URI=" + ${MY_P/p7}_all.tar.gz + aria? ( aria2.3.1.tar.gz )" + +SLOT="0" +LICENSE="cns" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="aria openmp" + +RDEPEND="app-shells/tcsh" +DEPEND="${RDEPEND}" + +FORTRAN_NEED_OPENMP=1 + +S="${WORKDIR}/${MY_P/p7}" + +RESTRICT="fetch" + +pkg_nofetch() { + elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" + use aria && elog "and http://aria.pasteur.fr/" + elog "and place these files:" + elog ${A} + elog "in ${DISTDIR}." +} + +get_fcomp() { + case $(tc-getFC) in + *gfortran* ) + FCOMP="gfortran" ;; + ifort ) + FCOMP="ifc" ;; + * ) + FCOMP=$(tc-getFC) ;; + esac +} + +pkg_setup() { + fortran-2_pkg_setup + get_fcomp +} + +get_bitness() { + echo > "${T}"/test.c + $(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o + case $(file "${T}"/test.o) in + *64-bit*|*ppc64*|*x86_64*) export _bitness="64";; + *32-bit*|*ppc*|*i386*) export _bitness="32";; + *) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";; + esac +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-gentoo.patch \ + "${FILESDIR}"/${PV}-delete.patch + + get_bitness + + if use aria; then + pushd "${WORKDIR}"/aria* >& /dev/null + # Update the cns sources in aria for version 1.2.1 + epatch "${FILESDIR}"/1.2.1-aria2.3.patch + + # Update the code with aria specific things + cp -rf cns/src/* "${S}"/source/ || die + popd >& /dev/null + fi + + # the code uses Intel-compiler-specific directives + if [[ $(tc-getFC) =~ gfortran ]]; then + use openmp && \ + append-flags -fopenmp && append-ldflags -fopenmp + COMP="gfortran" + [[ ${_bitness} == 64 ]] && \ + append-fflags -fdefault-integer-8 + elif [[ $(tc-getFC) == if* ]]; then + use openmp && \ + append-flags -openmp && append-ldflags -openmp + COMP="ifort" + [[ ${_bitness} == 64 ]] && append-fflags -i8 + fi + + [[ ${_bitness} == 64 ]] && \ + append-cflags "-DINTEGER='long long int'" + + # Set up location for the build directory + # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION + cp "${FILESDIR}"/cns_solve_env_sh-${PV} "${T}"/cns_solve_env_sh || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ + -i "${S}"/cns_solve_env || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ + -e "s:setenv OMP_STACKSIZE 256m:export OMP_STACKSIZE=256m:g" \ + -e "s:^limit:^ulimit:g" \ + -i "${T}"/cns_solve_env_sh || die + + ebegin "Fixing shebangs..." + find "${S}" -type f \ + -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die + find . -name "Makefile*" \ + -exec \ + sed \ + -e "s:^SHELL=/bin/sh:SHELL=${EPREFIX}/bin/sh:g" \ + -e "s:/bin/ls:ls:g" \ + -e "s:/bin/rm:rm:g" \ + -i '{}' + || die + eend +} + +src_compile() { + local GLOBALS + local MALIGN + + # Set up the compiler to use + ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die + + # make install really means build, since it's expected to be used in-place + # -j1 doesn't mean we do no respect MAKEOPTS! + emake -j1 \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + F77=$(tc-getFC) \ + LD=$(tc-getFC) \ + CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + CXXFLAGS="${CXXFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + LDFLAGS="${LDFLAGS}" \ + F77OPT="${FCFLAGS} ${MALIGN}" \ + F77STD="${GLOBALS}" \ + OMPLIB="${OMPLIB}" \ + compiler="${COMP}" \ + install +} + +src_test() { + # We need to force on g77 manually, because we can't get aliases working + # when we source in a -c + einfo "Running tests ..." + sh -c \ + "export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \ + || die "tests failed" + einfo "Displaying test results ..." + cat "${S}"/*_g77/test/*.diff-test +} + +src_install() { + cat >> "${T}"/66cns <<- EOF + CNS_SOLVE="${EPREFIX}/usr" + CNS_ROOT="${EPREFIX}/usr" + CNS_DATA="${EPREFIX}/usr/share/cns" + CNS_DOC="${EPREFIX}/usr/share/doc/cns-1.3" + CNS_LIB="${EPREFIX}/usr/share/cns/libraries" + CNS_MODULE="${EPREFIX}/usr/share/cns/modules" + CNS_TOPPAR="${EPREFIX}/usr/share/cns/libraries/toppar" + CNS_CONFDB="${EPREFIX}/usr/share/cns/libraries/confdb" + CNS_XTALLIB="${EPREFIX}/usr/share/cns/libraries/xtal" + CNS_NMRLIB="${EPREFIX}/usr/share/cns/libraries/nmr" + CNS_XRAYLIB="${EPREFIX}/usr/share/cns/libraries/xray" + CNS_XTALMODULE="${EPREFIX}/usr/share/cns/modules/xtal" + CNS_NMRMODULE="${EPREFIX}/usr/share/cns/modules/nmr" + CNS_HELPLIB="${EPREFIX}/usr/share/cns/helplib" + EOF + + doenvd "${T}"/66cns || die + + # Don't want to install this + rm -f "${S}"/*linux*/utils/Makefile || die + + sed \ + -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ + -i "${S}"/bin/cns_web || die + + newbin "${S}"/*linux*/bin/cns_solve* cns_solve + + # Can be run by either cns_solve or cns + dosym cns_solve /usr/bin/cns + + dobin \ + "${S}"/*linux*/utils/* \ + "${S}"/bin/cns_{edit,header,import_cif,transfer,web} + + insinto /usr/share/cns + doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib "${S}"/bin/cns_info + + dohtml \ + -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ + -f all_cns_info_template,omac,def \ + -r doc/html/* + # Conflits with app-text/dos2unix + rm -f "${D}"/usr/bin/dos2unix || die +} + +pkg_postinst() { + if use openmp; then + elog "Set OMP_NUM_THREADS to the number of threads you want." + elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" + elog "variable if using gcc (16384 should be good)." + fi +} diff --git a/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch new file mode 100644 index 000000000000..42b9b0572231 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch @@ -0,0 +1,20 @@ +--- source/xfft.f.orig 2008-08-03 00:36:52.000000000 -0700 ++++ source/xfft.f 2008-08-03 00:37:06.000000000 -0700 +@@ -514,7 +514,7 @@ + LOGICAL QHERM + DOUBLE PRECISION XRCELL(9), MAPR + C local +-!$ integer omp_get_max_threads, kmp_get_stacksize ++!$ integer omp_get_max_threads + LOGICAL DONE + DOUBLE PRECISION ZERO + PARAMETER (ZERO=0.0D0) +@@ -537,7 +537,7 @@ + NBPP=1 + ! The following command is only relevant for the ifort compiler (if -openmp option is used). + ! If your compiler is not ifort, and gives an error, just comment the next line out: +-!$ if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23) ++! if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23) + ! Explanation: the default KMP_STACKSIZE of ifort is 2**21 bytes (2Mb) for 32bit, + ! and 2**22 bytes (4Mb) for 64bit. + ! This may be low for big structures, which leads to segmentation faults! diff --git a/sci-chemistry/cns/files/1.2.1-aria2.3.patch b/sci-chemistry/cns/files/1.2.1-aria2.3.patch new file mode 100644 index 000000000000..8c6939d8eb92 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-aria2.3.patch @@ -0,0 +1,22 @@ +diff --git a/cns/src/cns.f b/cns/src/cns.f +index a3c2cbe..51a34f8 100644 +--- a/cns/src/cns.f ++++ b/cns/src/cns.f +@@ -470,6 +470,7 @@ C local + INTEGER HNLEN, TMP, PTRSZ, STLEN + CHARACTER*(1) CNSPTMP + CHARACTER*(4) ST ++!$ integer omp_get_max_threads + C + C write header + WRITE(6,'(10X,A)') +@@ -526,6 +527,9 @@ C + WRITE(6,'(10X,7A)') + & ' Running on machine: ',HOSTNM(1:HNLEN), + & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)' ++!$ write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(), ++!$ & ' threads' ++!$C (to change use setenv OMP_NUM_THREADS x) + C + CALL GETNAM(USERNM,12,TMP) + WRITE(6,'(10X,2A)') diff --git a/sci-chemistry/cns/files/1.2.1-gentoo.patch b/sci-chemistry/cns/files/1.2.1-gentoo.patch new file mode 100644 index 000000000000..2b47bfcc7d86 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-gentoo.patch @@ -0,0 +1,63 @@ +--- cns_solve_1.21/instlib/source/Makefile.proto 2000-09-07 20:35:33.000000000 +0200 ++++ cns_solve_1.21/instlib/source/Makefile.proto.new 2009-07-14 09:18:37.000000000 +0200 +@@ -11,6 +11,8 @@ + + SHELL=/bin/sh + ++cns_string=`date "+%y%m%d%H%M"` ++ + # commands + RM = /bin/rm + +@@ -25,26 +27,20 @@ + + # rule for the fortran routines + $(OBJS): +- @ echo "compiling: $(@:.o=.f)"; \ +- $(F77) -c $(F77FLAGS) $(@:.o=.f) ++ $(F77) -c $(F77FLAGS) $(@:.o=.f) + + # rule for the dynamic memory allocation C routines + dmemory.o: dmemory.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the machine specific C routines + machine_c.o: machine_c.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the executable itself + ../bin/cns_solve: $(DEPENDS) +- @ echo ; echo "linking: cns_solve"; echo +- @ cns_string=`date "+%y%m%d%H%M"`; \ +- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ +- $(LDFLAGS) \ +- $(CNS_FFTDIR) $(CNS_FFTLIB); \ ++ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ ++ $(CNS_FFTDIR) $(CNS_FFTLIB); \ + if [ -x cns_solve-$$cns_string.exe ]; \ + then echo "created executable file cns_solve-$$cns_string.exe"; \ + echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ +--- cns_solve_1.21/instlib/utils/Makefile 2004-08-30 00:40:35.000000000 +0200 ++++ cns_solve_1.21/instlib/utils/Makefile.new 2009-07-14 09:50:27.000000000 +0200 +@@ -22,14 +22,14 @@ + make clean + + .f: +- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) ++ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) + + .c: +- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) ++ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) + + .l: + lex $(@).l +- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) ++ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) + + relink: + @ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` diff --git a/sci-chemistry/cns/files/1.2.1-ifort.patch b/sci-chemistry/cns/files/1.2.1-ifort.patch new file mode 100644 index 000000000000..ba44bebd1b68 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-ifort.patch @@ -0,0 +1,126 @@ +diff --git a/source/angledb.f b/source/angledb.f +index 28ad657..eaa847d 100644 +--- a/source/angledb.f ++++ b/source/angledb.f +@@ -1416,10 +1416,10 @@ C include files + C local variables + INTEGER COUNT, SPTR, OLDCLASS, OLDMAXANGLEDBS + INTEGER THETYPE, CURPSIS, CURPHIS +- INTEGER CLASSINDEX ++ INTEGER CLASINDEX + DOUBLE PRECISION K1, CUTOFF + CHARACTER*4 THENAME +- CHARACTER*20 CLASSNAME ++ CHARACTER*20 CLASNAME + C begin + C + IF (ANGLEDBFLAG) THEN +@@ -1450,10 +1450,10 @@ C + ELSE IF (WD(1:4).EQ.'CLAS') THEN + OLDCLASS = CURANGLEDBCLASS + CALL NEXTWD('class name =') +- CLASSNAME = WD(1:20) ++ CLASNAME = WD(1:20) + ANGLEDBMODE = NEW + DO COUNT = 1, NANGLEDBCLASSES +- IF (ANGDBCLASSNAMES(COUNT).EQ.CLASSNAME) THEN ++ IF (ANGDBCLASSNAMES(COUNT).EQ.CLASNAME) THEN + ANGLEDBMODE = UPDATE + CURANGLEDBCLASS = COUNT + END IF +@@ -1472,7 +1472,7 @@ C + END IF + NANGLEDBCLASSES = NANGLEDBCLASSES + 1 + CURANGLEDBCLASS = NANGLEDBCLASSES +- ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASSNAME ++ ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASNAME + ANGLEDBASSNDX(CURANGLEDBCLASS) = NANGLEDBS + END IF + C +@@ -1733,16 +1733,16 @@ C + & HEAP(ANGLEDBTPTR)) + ELSE IF (WD(1:4).EQ.'CLAS') THEN + CALL NEXTWD('Class name>') +- CLASSNAME = WD(1:20) +- CLASSINDEX = 0 ++ CLASNAME = WD(1:20) ++ CLASINDEX = 0 + DO COUNT = 1, NANGLEDBCLASSES + IF (ANGDBCLASSNAMES(COUNT).EQ. +- & CLASSNAME) THEN ++ & CLASNAME) THEN + PRINTTHISCLASS(COUNT) = .TRUE. +- CLASSINDEX = COUNT ++ CLASINDEX = COUNT + END IF + END DO +- IF (CLASSINDEX.EQ.0) THEN ++ IF (CLASINDEX.EQ.0) THEN + CALL DSPERR('ANGLEDB', + & 'unknown class. Using first.') + PRINTTHISCLASS(1) = .TRUE. +diff --git a/source/rama.f b/source/rama.f +index c5d14f2..3063e7b 100644 +--- a/source/rama.f ++++ b/source/rama.f +@@ -1468,11 +1468,11 @@ C include files + C local variables + INTEGER COUNT, SPTR, OLDCLASS, OLDMAXRAMAS, + & THETYPE, CURPSIS, CURPHIS, +- & CURCHIS, CURTHTS, CLASSINDEX ++ & CURCHIS, CURTHTS, CLASINDEX + INTEGER CLEN + DOUBLE PRECISION K1, CUTOFF + CHARACTER*4 THENAME +- CHARACTER*50 CLASSNAME ++ CHARACTER*50 CLASNAME + C begin + C + C this is used by READRAMA2 to hold the selection +@@ -1503,10 +1503,10 @@ C + ELSE IF (WD(1:4).EQ.'CLAS') THEN + OLDCLASS = CURRAMACLASS + CALL NEXTWD('class name =') +- CLASSNAME = WD(1:50) ++ CLASNAME = WD(1:50) + RAMAMODE = NEW + DO COUNT = 1, NRAMACLASSES +- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) THEN ++ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) THEN + RAMAMODE = UPDATE + CURRAMACLASS = COUNT + END IF +@@ -1525,7 +1525,7 @@ C + END IF + NRAMACLASSES = NRAMACLASSES + 1 + CURRAMACLASS = NRAMACLASSES +- RAMACLASSNAMES(CURRAMACLASS) = CLASSNAME ++ RAMACLASSNAMES(CURRAMACLASS) = CLASNAME + END IF + C + C set force constant for current class, +@@ -1954,18 +1954,18 @@ C + & HEAP(RAMAATOMPTR), 0) + ELSE IF (WD(1:4).EQ.'CLAS') THEN + CALL NEXTWD('Class name>') +- CLASSINDEX = 0 ++ CLASINDEX = 0 + DO COUNT = 1, NRAMACLASSES +- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) +- & CLASSINDEX = COUNT ++ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) ++ & CLASINDEX = COUNT + END DO +- IF (CLASSINDEX.EQ.0) THEN ++ IF (CLASINDEX.EQ.0) THEN + CALL DSPERR('RAMA', + & 'unknown class. Using first.') +- CLASSINDEX = 1 ++ CLASINDEX = 1 + END IF + CALL PRINTRAMAS(CUTOFF, HEAP(CALCRAMAPTR), +- & HEAP(RAMAATOMPTR), CLASSINDEX) ++ & HEAP(RAMAATOMPTR), CLASINDEX) + ELSE + CALL DSPERR('RAMA', + & 'Expected ALL or CLASs.') diff --git a/sci-chemistry/cns/files/1.2.1-parallel.patch b/sci-chemistry/cns/files/1.2.1-parallel.patch new file mode 100644 index 000000000000..dfaa40021d66 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-parallel.patch @@ -0,0 +1,17 @@ +diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto +index 0d0dd3e..ae9e422 100644 +--- a/instlib/source/Makefile.proto ++++ b/instlib/source/Makefile.proto +@@ -19,9 +19,9 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o + + # the default is to make the cns executable + cns_solve: +- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k exepurge ++ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make exepurge + + # rule for the fortran routines + $(OBJS): diff --git a/sci-chemistry/cns/files/1.3_p7-delete.patch b/sci-chemistry/cns/files/1.3_p7-delete.patch new file mode 100644 index 000000000000..cbddf4289158 --- /dev/null +++ b/sci-chemistry/cns/files/1.3_p7-delete.patch @@ -0,0 +1,13 @@ +diff --git a/utils/cluster_struc.cpp b/utils/cluster_struc.cpp +index b64467a..5f727db 100644 +--- a/utils/cluster_struc.cpp ++++ b/utils/cluster_struc.cpp +@@ -173,7 +173,7 @@ int main(int argc, char *argv[]) { + for (int i = 0; i < nrstruc; i++) { + delete[] neighbor[i]; + } +- delete[] neighbor, neighborcount; ++ delete[] neighbor, delete[] neighborcount; + return 5; + } + if (rmsd < cutoff) { diff --git a/sci-chemistry/cns/files/1.3_p7-gentoo.patch b/sci-chemistry/cns/files/1.3_p7-gentoo.patch new file mode 100644 index 000000000000..7942c55abfb9 --- /dev/null +++ b/sci-chemistry/cns/files/1.3_p7-gentoo.patch @@ -0,0 +1,80 @@ +diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto +index 0d0dd3e..dd4b680 100644 +--- a/instlib/source/Makefile.proto ++++ b/instlib/source/Makefile.proto +@@ -11,6 +11,8 @@ + + SHELL=/bin/sh + ++cns_string=`date "+%y%m%d%H%M"` ++ + # commands + RM = /bin/rm + +@@ -19,32 +21,26 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o + + # the default is to make the cns executable + cns_solve: +- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k exepurge ++ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make exepurge + + # rule for the fortran routines + $(OBJS): +- @ echo "compiling: $(@:.o=.f)"; \ +- $(F77) -c $(F77FLAGS) $(@:.o=.f) ++ $(F77) -c $(F77FLAGS) $(@:.o=.f) + + # rule for the dynamic memory allocation C routines + dmemory.o: dmemory.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the machine specific C routines + machine_c.o: machine_c.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the executable itself + ../bin/cns_solve: $(DEPENDS) +- @ echo ; echo "linking: cns_solve"; echo +- @ cns_string=`date "+%y%m%d%H%M"`; \ +- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ +- $(LDFLAGS) \ +- $(CNS_FFTDIR) $(CNS_FFTLIB); \ ++ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ ++ $(CNS_FFTDIR) $(CNS_FFTLIB); \ + if [ -x cns_solve-$$cns_string.exe ]; \ + then echo "created executable file cns_solve-$$cns_string.exe"; \ + echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ +diff --git a/instlib/utils/Makefile b/instlib/utils/Makefile +index 98de84f..4f32b34 100644 +--- a/instlib/utils/Makefile ++++ b/instlib/utils/Makefile +@@ -22,17 +22,17 @@ utils: + make clean + + .f: +- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) ++ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) + + .c: +- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) ++ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) + + .cpp: +- $(CPP) -o $@ $(CCFLAGS) $(@).cpp $(CCLINK) ++ $(CXX) $(LDFLAGS) -o $@ $(CXXFLAGS) $(@).cpp $(CCLINK) + + .l: + lex $(@).l +- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) ++ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) + + relink: + @ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` diff --git a/sci-chemistry/cns/files/cns_solve_env_sh b/sci-chemistry/cns/files/cns_solve_env_sh new file mode 100644 index 000000000000..34e1a2b635cf --- /dev/null +++ b/sci-chemistry/cns/files/cns_solve_env_sh @@ -0,0 +1,221 @@ +#!/bin/sh +# +# This file sets up the appropriate environmental variables and paths +# for CNSsolve. In the case of the same machines with different versions +# of the OS, backward compatibility is assumed - ie. a later version will +# be setup for a previous version of the OS if nothing else is available. +# +# written by: Paul Adams +# +# copyright Yale University +# +# ========================================================================== +# +# >>>>>> Important: define the location of the CNSsolve directory <<<<<< +# +# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY + + CNS_SOLVE=_CNSsolve_location_ + +# +# ========================================================================== +# +# full expansion of the CNS_SOLVE variable prior to use. +# +export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE +# +# ========================================================================== +# +# set the number of threads for SGI multiprocessors +# if this causes a problem on other systems it can be commented out +# +export MP_SET_NUMTHREADS; MP_SET_NUMTHREADS=1 +# +# ========================================================================== +# +# get the machine architecture +# +if [ -d $CNS_SOLVE ]; then + if [ ! "$CNS_ARCH" ]; then + export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch` + fi +else + export CNS_ARCH; CNS_ARCH='unknown' +fi +# +# system variables (this is needed for openmp) +# +ulimit -s unlimited +# ========================================================================== +# +# general environmental variables +# +export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries +export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules +export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar +export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb +export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal +export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr +export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray +export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal +export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr +export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib +# +# general user aliases +# +cns_web () { $CNS_SOLVE/bin/cns_web; } +cns_header () { $CNS_SOLVE/bin/cns_header; } +cns_info () { cat $CNS_SOLVE/bin/cns_info; } +cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } +if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then + cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } +else + cns_edit () { $CNS_SOLVE/bin/cns_edit; } +fi +run_tutorial () { "csh -f tutorial.csh"; } +# +# g77 compilation and use +# +g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; } +g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; } +# +# developer aliases +# +run_tests () { $CNS_SOLVE/bin/run_tests; } +run_diffs () { $CNS_SOLVE/bin/run_diffs; } +maketar () { $CNS_SOLVE/bin/maketar; } +create_patch () { $CNS_SOLVE/bin/create_patch; } +# +# +# ========================================================================== +# +# to do expansions - unset noglob just in case user has it otherwise +# +set +f +# +# try to set up appropriate path +# +# first strip off any trailing information (eg. _g77) +# +CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'` +# +cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'` +cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'` +cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'` +cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'` +cns_minor=`echo $cns_major | sed -e 's/\./ /g'` +# +# if we are looking for a specific type of setup then limit search +# +cns_dirs="" +if [ ! "$CNS_G77" ]; then + if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then + cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" + fi +else + CNS_ARCH="${CNS_ARCH}_g77" + if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then + cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" + fi +fi +# +# first look for an exact match (with os version) +# +# +cns_found=0 +if [ -n "$cns_dirs" ]; then + for cns_dir in $cns_dirs ; do + cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \ + $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + done +# +# +# now look for an exact match (without os version) +# + if [ $cns_found -eq 0 ]; then + for cns_dir in $cns_dirs ; do + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \ + $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + done + fi +# +# now look for a backwards compatible match (with os version major/minor) +# + if [ $cns_found -eq 0 ]; then + for cns_dir in $cns_dirs ; do + if [ $cns_found -eq 0 ]; then + cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then + osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'` + if [ $osv_test -eq 1 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + fi + fi + done + fi +# +# now look for a wildcard match on cpu +# + if [ $cns_found -eq 0 ]; then + cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'` + cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'` + for cns_dir in $cns_dirs ; do + if [ $cns_found -eq 0 ]; then + cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'` + cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \ + $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then + cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'` + if [ $cpu_test -eq 1 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + fi + fi + done + fi +fi +# +# if found set environment +# +if [ $cns_found -eq 1 ]; then + # + # set installation and source directory + # + export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv + export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source + # + # path for CNSsolve utility programs + # + if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then + export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils` + fi + # + # path for CNSsolve executable if installed + # + if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then + export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin` + fi +fi +# +unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor +unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same +unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test +# diff --git a/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 b/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 new file mode 100644 index 000000000000..12368f87b596 --- /dev/null +++ b/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 @@ -0,0 +1,229 @@ +#!/bin/sh +# +# This file sets up the appropriate environmental variables and paths +# for CNSsolve. In the case of the same machines with different versions +# of the OS, backward compatibility is assumed - ie. a later version will +# be setup for a previous version of the OS if nothing else is available. +# +# written by: Paul Adams +# +# copyright Yale University +# +# ========================================================================== +# +# >>>>>> Important: define the location of the CNSsolve directory <<<<<< +# +# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY + + CNS_SOLVE=_CNSsolve_location_ + +# +# ========================================================================== +# +# full expansion of the CNS_SOLVE variable prior to use. +# +export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE +# +# ========================================================================== +# +# get the machine architecture +# +if [ -d $CNS_SOLVE ]; then + if [ ! "$CNS_ARCH" ]; then + export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch` + fi +else + export CNS_ARCH; CNS_ARCH='unknown' +fi +# +# ========================================================================== +# +# system variables for OpenMP +# +# The default stack sizes are usually insufficient, especially when +# CNS is compiled using OpenMP. If the stack sizes are too +# small segfaults may occur. Recommended setting for "stacksize": +limit stacksize unlimited +# +# KMP_STACKSIZE is specific for Intel ifort, icc: +##setenv KMP_STACKSIZE 256m +# +# OMP_STACKSIZE is used by all compilers: +setenv OMP_STACKSIZE 256m +# +# Uncomment the following line and change as appropriate to set the number +# of processors (threads) to use. +###setenv OMP_NUM_THREADS 4 +# +# ========================================================================== +# +# general environmental variables +# +export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries +export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules +export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar +export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb +export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal +export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr +export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray +export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal +export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr +export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib +# +# general user aliases +# +cns_web () { $CNS_SOLVE/bin/cns_web; } +cns_header () { $CNS_SOLVE/bin/cns_header; } +cns_info () { cat $CNS_SOLVE/bin/cns_info; } +cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } +if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then + cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } +else + cns_edit () { $CNS_SOLVE/bin/cns_edit; } +fi +# +# g77 compilation and use +# +g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; } +g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; } +# +# developer aliases +# +run_tests () { $CNS_SOLVE/bin/run_tests; } +run_diffs () { $CNS_SOLVE/bin/run_diffs; } +maketar () { $CNS_SOLVE/bin/maketar; } +create_patch () { $CNS_SOLVE/bin/create_patch; } +# +# +# ========================================================================== +# +# to do expansions - unset noglob just in case user has it otherwise +# +set +f +# +# try to set up appropriate path +# +# first strip off any trailing information (eg. _g77) +# +CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'` +# +cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'` +cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'` +cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'` +cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'` +cns_minor=`echo $cns_major | sed -e 's/\./ /g'` +# +# if we are looking for a specific type of setup then limit search +# +cns_dirs="" +if [ ! "$CNS_G77" ]; then + if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then + cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" + fi +else + CNS_ARCH="${CNS_ARCH}_g77" + if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then + cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" + fi +fi +# +# first look for an exact match (with os version) +# +# +cns_found=0 +if [ -n "$cns_dirs" ]; then + for cns_dir in $cns_dirs ; do + cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \ + $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + done +# +# +# now look for an exact match (without os version) +# + if [ $cns_found -eq 0 ]; then + for cns_dir in $cns_dirs ; do + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \ + $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + done + fi +# +# now look for a backwards compatible match (with os version major/minor) +# + if [ $cns_found -eq 0 ]; then + for cns_dir in $cns_dirs ; do + if [ $cns_found -eq 0 ]; then + cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then + osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'` + if [ $osv_test -eq 1 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + fi + fi + done + fi +# +# now look for a wildcard match on cpu +# + if [ $cns_found -eq 0 ]; then + cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'` + cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'` + for cns_dir in $cns_dirs ; do + if [ $cns_found -eq 0 ]; then + cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'` + cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \ + $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then + cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'` + if [ $cpu_test -eq 1 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + fi + fi + done + fi +fi +# +# if found set environment +# +if [ $cns_found -eq 1 ]; then + # + # set installation and source directory + # + export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv + export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source + # + # path for CNSsolve utility programs + # + if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then + export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils` + fi + # + # path for CNSsolve executable if installed + # + if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then + export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin` + fi +fi +# +unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor +unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same +unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test +# diff --git a/sci-chemistry/cns/metadata.xml b/sci-chemistry/cns/metadata.xml new file mode 100644 index 000000000000..a9cb92ec3f79 --- /dev/null +++ b/sci-chemistry/cns/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <use> + <flag name="aria"> Support patch for sci-chemistry/aria</flag> + </use> + <longdescription> +Crystallography and NMR System (CNS) is the result of an international +collaborative effort among several research groups. The program has +been designed to provide a flexible multi-level hierachical approach for the +most commonly used algorithms in macromolecular structure determination. +Highlights include heavy atom searching, experimental phasing (including +MAD and MIR), density modification, crystallographic refinement with maximum +likelihood targets, and NMR structure calculation using NOEs, J-coupling, +chemical shift, and dipolar coupling data. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest new file mode 100644 index 000000000000..3b897f1a8159 --- /dev/null +++ b/sci-chemistry/coot/Manifest @@ -0,0 +1,6 @@ +DIST coot-0.7.1.tar.gz 16663581 SHA256 2310d48f7581283ee20eeb355d5fcef90e8d36bc032684b7b47f7c61e89ea0a9 SHA512 dad758b227231543cacd9b34ca00a0bff18bdc208c10529bbf2e504db9f17a3f1bbf610a52c21fe6046e443222667a3703dc962241debff87058ac041bbcec2e WHIRLPOOL 7c57f1161016a74449a9fee1202ada82044d17d957002c67c59f2eb9776f676eb525b605a1973b9bc479e15b40df5478e3b3fad9594433fee73bfc544d5d6b52 +DIST coot-0.7.2.tar.gz 16859099 SHA256 67fbb702559be850f3198c11038fa2c25c692ef8a284e88bbf6a0e941cf3dadd SHA512 84ced967ab661a36ae61a529c1e7fdef121283795fe2300946277c8ba0724724a0190806434257cae01302542efd628cb57d0f35f24968b061cb04faf43daefa WHIRLPOOL ef379156fdfafc275fa953c01b81a06bf75dbf51cc84d6669fa92aef4449e507f45429ad599b455ca3b6b53f9944116adfe42e7ef50e2c56396624f3b5ea5f79 +DIST coot-0.7.tar.gz 16172237 SHA256 e3d61d326ee906eb77081a6f646024cc6c5c92281f9508da3086fb937fb05aa2 SHA512 27fe0485240adcb7f370cf2daf116d8ea1c8e80e297c0975f1b2d2f78d4a5cd9314e06537e680993d465ef551ceba46a2b402c63acfabcbf599cca6bdb8f843f WHIRLPOOL cc919a7ec3731cfd482bb906c7fd9dc98d9ce2ba2f6bbaa91facf5e5195e27b3fe3f0e03e93668a1524bc2b2306ec23951e1db5033315ed1f26456768a5ac2a7 +DIST greg-data-0.7.1.tar.gz 8142259 SHA256 6f3e1c1bc540c8355583ce2e1807cc9f6a2f7b466384382a843942f96b1d31a1 SHA512 6ce97b72f3f984c0d2dc1eb4a259412761736bfaec23867eba46919b6c6444698dc0b0e717c1a095aa713b2a4726d4229aed5964d89a74f7c1f2aa058f4891bf WHIRLPOOL 65db8c976f481a765e1301526cc7af6939ceb4c1cc26f3c1d5e628512a9c34bc4a10e8380d10ab4773976def9b3e07cf84b2cdc1da821750118c405b2f8b34d4 +DIST greg-data-0.7.2.tar.gz 8142259 SHA256 6f3e1c1bc540c8355583ce2e1807cc9f6a2f7b466384382a843942f96b1d31a1 SHA512 6ce97b72f3f984c0d2dc1eb4a259412761736bfaec23867eba46919b6c6444698dc0b0e717c1a095aa713b2a4726d4229aed5964d89a74f7c1f2aa058f4891bf WHIRLPOOL 65db8c976f481a765e1301526cc7af6939ceb4c1cc26f3c1d5e628512a9c34bc4a10e8380d10ab4773976def9b3e07cf84b2cdc1da821750118c405b2f8b34d4 +DIST greg-data-0.7.tar.gz 8202091 SHA256 b82743b1d3c2d3acaa4adb4901368d46e0638733364963ad62044f79111f21f7 SHA512 71ab00869df074660103b824130776ceeaad398b1df8bbc30c9fc41660cc08a66998a406c5cfc93f4605cc5052aae414bd79b6e6de2ae46acd9c6997dbd5361b WHIRLPOOL 87deff25e864f55b316f432b9a9b595e23352720d08257e2b69bbe7946bf8ab5d1fcc9d13205354a0edd3fbea89422952df5f6fa0c05f9707167b544494b2c14 diff --git a/sci-chemistry/coot/coot-0.7.1-r1.ebuild b/sci-chemistry/coot/coot-0.7.1-r1.ebuild new file mode 100644 index 000000000000..c55da6705209 --- /dev/null +++ b/sci-chemistry/coot/coot-0.7.1-r1.ebuild @@ -0,0 +1,167 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +AUTOTOOLS_AUTORECONF="true" + +inherit autotools-utils python-single-r1 toolchain-funcs versionator + +MY_S2_PV=$(replace_version_separator 2 - ${PV}) +MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} +MY_S_P=${MY_S2_P}-${PR/r/revision-} +MY_PV=${PV} +MY_P=${PN}-${MY_PV} + +DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" +HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/" +SRC_URI=" + http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz + test? ( http://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+openmp static-libs test" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +SCIDEPS=" + >=sci-libs/ccp4-libs-6.1 + sci-libs/clipper + >=sci-libs/coot-data-2 + >=sci-libs/gsl-1.3 + >=sci-libs/mmdb-1.23:0 + sci-libs/ssm + sci-libs/monomer-db + sci-chemistry/reduce + sci-chemistry/refmac + sci-chemistry/probe" + +XDEPS=" + gnome-base/libgnomecanvas + gnome-base/librsvg:2 + media-libs/libpng + media-libs/freeglut + x11-libs/gtk+:2 + x11-libs/goocanvas:0 + x11-libs/gtkglext" + +SCHEMEDEPS=" + dev-scheme/net-http + dev-scheme/guile-gui + >=dev-scheme/guile-lib-0.1.6 + dev-scheme/guile-www + >=x11-libs/guile-gtk-2.1" + +RDEPEND=" + ${SCIDEPS} + ${XDEPS} + ${SCHEMEDEPS} + ${PYTHON_DEPS} + dev-python/pygtk:2[${PYTHON_USEDEP}] + >=dev-libs/gmp-4.2.2-r2 + >=net-misc/curl-7.19.6 + net-dns/libidn" +DEPEND="${RDEPEND} + >=sys-devel/libtool-2.4-r2 + dev-lang/swig + sys-devel/bc + test? ( dev-scheme/greg )" + +S="${WORKDIR}/${MY_P}" + +pkg_setup() { + if use openmp; then + tc-has-openmp || die "Please use an OPENMP capable compiler" + fi + python-single-r1_pkg_setup +} + +PATCHES=( + "${FILESDIR}"/${PN}-0.7-clipper-config.patch + "${FILESDIR}"/${PN}-0.7-goocanvas.patch + "${FILESDIR}"/${PN}-0.7-mmdb-config.patch + "${FILESDIR}"/${PN}-0.7-ssm.patch + ) + +src_prepare() { + sed \ + -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ + -i configure.in || die + + autotools-utils_src_prepare +} + +src_configure() { + # All the --with's are used to activate various parts. + # Yes, this is broken behavior. + local myeconfargs=( + --includedir='${prefix}/include/coot' + --with-goocanvas-prefix="${EPREFIX}/usr" + --with-guile + --with-python="${EPREFIX}/usr" + --with-guile-gtk + --with-gtk2 + --with-pygtk + $(use_enable openmp) + ) + autotools-utils_src_configure +} + +src_test() { + source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" + mkdir "${T}"/coot_test + + export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" + export COOT_SCHEME_DIR="${S}/scheme/" + export COOT_RESOURCES_FILE="${S}/cootrc" + export COOT_PIXMAPS_DIR="${S}/pixmaps/" + export COOT_DATA_DIR="${S}/" + export COOT_PYTHON_DIR="${S}/python/" + export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" + export PYTHONHOME="${EPREFIX}"/usr/ + export CCP4_SCR="${T}"/coot_test/ + export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" + export SYMINFO="${S}/syminfo.lib" + + export COOT_TEST_DATA_DIR="${WORKDIR}"/greg-data + + cat > command-line-greg.scm <<- EOF + (use-modules (ice-9 greg)) + (set! greg-tools (list "greg-tests")) + (set! greg-debug #t) + (set! greg-verbose 5) + (let ((r (greg-test-run))) + (if r + (coot-real-exit 0) + (coot-real-exit 1))) + EOF + + einfo "Running test with following paths ..." + einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" + einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" + einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" + einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" + einfo "COOT_DATA_DIR $COOT_DATA_DIR" + einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" + einfo "PYTHONPATH $PYTHONPATH" + einfo "PYTHONHOME $PYTHONHOME" + einfo "CCP4_SCR ${CCP4_SCR}" + einfo "CLIBD_MON ${CLIBD_MON}" + einfo "SYMINFO ${SYMINFO}" + + "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die + "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die +} + +src_install() { + autotools-utils_src_install + insinto /usr/share/${PN} + doins syminfo.lib +} diff --git a/sci-chemistry/coot/coot-0.7.2.ebuild b/sci-chemistry/coot/coot-0.7.2.ebuild new file mode 100644 index 000000000000..54e430017fc2 --- /dev/null +++ b/sci-chemistry/coot/coot-0.7.2.ebuild @@ -0,0 +1,165 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +AUTOTOOLS_AUTORECONF="true" + +inherit autotools-utils python-single-r1 toolchain-funcs versionator + +MY_S2_PV=$(replace_version_separator 2 - ${PV}) +MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} +MY_S_P=${MY_S2_P}-${PR/r/revision-} +MY_PV=${PV} +MY_P=${PN}-${MY_PV} + +DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" +HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/" +SRC_URI=" + http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz + test? ( http://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+openmp static-libs test" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +SCIDEPS=" + >=sci-libs/ccp4-libs-6.1 + sci-libs/clipper + >=sci-libs/coot-data-2 + >=sci-libs/gsl-1.3 + >=sci-libs/mmdb-1.23:0 + sci-libs/ssm + sci-libs/monomer-db + sci-chemistry/reduce + sci-chemistry/refmac + sci-chemistry/probe" + +XDEPS=" + gnome-base/libgnomecanvas + gnome-base/librsvg:2 + media-libs/libpng + media-libs/freeglut + x11-libs/gtk+:2 + x11-libs/goocanvas:0 + x11-libs/gtkglext" + +SCHEMEDEPS=" + dev-scheme/net-http + dev-scheme/guile-gui + >=dev-scheme/guile-lib-0.1.6 + dev-scheme/guile-www + >=x11-libs/guile-gtk-2.1" + +RDEPEND=" + ${SCIDEPS} + ${XDEPS} + ${SCHEMEDEPS} + ${PYTHON_DEPS} + dev-python/pygtk:2[${PYTHON_USEDEP}] + >=dev-libs/gmp-4.2.2-r2 + >=net-misc/curl-7.19.6 + net-dns/libidn" +DEPEND="${RDEPEND} + >=sys-devel/libtool-2.4-r2 + dev-lang/swig + sys-devel/bc + test? ( dev-scheme/greg )" + +S="${WORKDIR}/${MY_P}" + +pkg_setup() { + if use openmp; then + tc-has-openmp || die "Please use an OPENMP capable compiler" + fi + python-single-r1_pkg_setup +} + +PATCHES=( + "${FILESDIR}"/${PN}-0.7-clipper-config.patch + "${FILESDIR}"/${PN}-0.7-goocanvas.patch + "${FILESDIR}"/${PN}-0.7-mmdb-config.patch + ) + +src_prepare() { + sed \ + -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ + -i configure.in || die + + autotools-utils_src_prepare +} + +src_configure() { + # All the --with's are used to activate various parts. + # Yes, this is broken behavior. + local myeconfargs=( + --includedir='${prefix}/include/coot' + --with-goocanvas-prefix="${EPREFIX}/usr" + --with-guile + --with-python="${EPREFIX}/usr" + --with-guile-gtk + --with-gtk2 + --with-pygtk + $(use_enable openmp) + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + cp "${S}"/src/coot_gtk2.py python/coot.py || die +} + +src_test() { + source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" + mkdir "${T}"/coot_test + + export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" + export COOT_SCHEME_DIR="${S}/scheme/" + export COOT_RESOURCES_FILE="${S}/cootrc" + export COOT_PIXMAPS_DIR="${S}/pixmaps/" + export COOT_DATA_DIR="${S}/" + export COOT_PYTHON_DIR="${S}/python/" + export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" + export PYTHONHOME="${EPREFIX}"/usr/ + export CCP4_SCR="${T}"/coot_test/ + export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" + export SYMINFO="${S}/syminfo.lib" + + export COOT_TEST_DATA_DIR="${WORKDIR}"/greg-data + + cat > command-line-greg.scm <<- EOF + (use-modules (ice-9 greg)) + (set! greg-tools (list "greg-tests")) + (set! greg-debug #t) + (set! greg-verbose 5) + (let ((r (greg-test-run))) + (if r + (coot-real-exit 0) + (coot-real-exit 1))) + EOF + + einfo "Running test with following paths ..." + einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" + einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" + einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" + einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" + einfo "COOT_DATA_DIR $COOT_DATA_DIR" + einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" + einfo "PYTHONPATH $PYTHONPATH" + einfo "PYTHONHOME $PYTHONHOME" + einfo "CCP4_SCR ${CCP4_SCR}" + einfo "CLIBD_MON ${CLIBD_MON}" + einfo "SYMINFO ${SYMINFO}" + + "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die + "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die +} diff --git a/sci-chemistry/coot/coot-0.7.ebuild b/sci-chemistry/coot/coot-0.7.ebuild new file mode 100644 index 000000000000..2922f57bfe37 --- /dev/null +++ b/sci-chemistry/coot/coot-0.7.ebuild @@ -0,0 +1,159 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +PYTHON_DEPEND="2" + +AUTOTOOLS_AUTORECONF="true" + +inherit autotools-utils python toolchain-funcs versionator + +MY_S2_PV=$(replace_version_separator 2 - ${PV}) +MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} +MY_S_P=${MY_S2_P}-${PR/r/revision-} +MY_PV=${PV} +MY_P=${PN}-${MY_PV} + +DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" +HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/" +SRC_URI=" + http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz + test? ( http://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="+openmp static-libs test" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +SCIDEPS=" + >=sci-libs/ccp4-libs-6.1 + sci-libs/clipper + >=sci-libs/coot-data-2 + >=sci-libs/gsl-1.3 + >=sci-libs/mmdb-1.23:0 + sci-libs/ssm + <sci-libs/monomer-db-1 + sci-chemistry/reduce + <sci-chemistry/refmac-5.6 + sci-chemistry/probe" + +XDEPS=" + gnome-base/libgnomecanvas + gnome-base/librsvg:2 + media-libs/libpng + media-libs/freeglut + x11-libs/gtk+:2 + x11-libs/goocanvas:0 + x11-libs/gtkglext" + +SCHEMEDEPS=" + dev-scheme/net-http + dev-scheme/guile-gui + >=dev-scheme/guile-lib-0.1.6 + dev-scheme/guile-www + >=x11-libs/guile-gtk-2.1" + +RDEPEND=" + ${SCIDEPS} + ${XDEPS} + ${SCHEMEDEPS} + dev-python/pygtk:2 + >=dev-libs/gmp-4.2.2-r2 + >=net-misc/curl-7.19.6 + net-dns/libidn" +DEPEND="${RDEPEND} + >=sys-devel/libtool-2.4-r2 + dev-lang/swig + sys-devel/bc + test? ( dev-scheme/greg )" + +S="${WORKDIR}/${MY_P}" + +pkg_setup() { + if use openmp; then + tc-has-openmp || die "Please use an OPENMP capable compiler" + fi + python_set_active_version 2 + python_pkg_setup +} + +PATCHES=( + "${FILESDIR}"/${P}-clipper-config.patch + "${FILESDIR}"/${P}-goocanvas.patch + "${FILESDIR}"/${P}-mmdb-config.patch + "${FILESDIR}"/${P}-ssm.patch + ) + +src_prepare() { + sed \ + -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-$(PYTHON)-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ + -i configure.in || die + + autotools-utils_src_prepare +} + +src_configure() { + # All the --with's are used to activate various parts. + # Yes, this is broken behavior. + local myeconfargs=( + --includedir='${prefix}/include/coot' + --with-goocanvas-prefix="${EPREFIX}/usr" + --with-guile + --with-python="${EPREFIX}/usr" + --with-guile-gtk + --with-gtk2 + --with-pygtk + $(use_enable openmp) + ) + autotools-utils_src_configure +} + +src_test() { + source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" + mkdir "${T}"/coot_test + + export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" + export COOT_SCHEME_DIR="${S}/scheme/" + export COOT_RESOURCES_FILE="${S}/cootrc" + export COOT_PIXMAPS_DIR="${S}/pixmaps/" + export COOT_DATA_DIR="${S}/" + export COOT_PYTHON_DIR="${S}/python/" + export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" + export PYTHONHOME="${EPREFIX}"/usr/ + export CCP4_SCR="${T}"/coot_test/ + export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" + export SYMINFO="${S}/syminfo.lib" + + export COOT_TEST_DATA_DIR="${WORKDIR}"/data/greg-data + + cat > command-line-greg.scm <<- EOF + (use-modules (ice-9 greg)) + (set! greg-tools (list "greg-tests")) + (set! greg-debug #t) + (set! greg-verbose 5) + (let ((r (greg-test-run))) + (if r + (coot-real-exit 0) + (coot-real-exit 1))) + EOF + + einfo "Running test with following paths ..." + einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" + einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" + einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" + einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" + einfo "COOT_DATA_DIR $COOT_DATA_DIR" + einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" + einfo "PYTHONPATH $PYTHONPATH" + einfo "PYTHONHOME $PYTHONHOME" + einfo "CCP4_SCR ${CCP4_SCR}" + einfo "CLIBD_MON ${CLIBD_MON}" + einfo "SYMINFO ${SYMINFO}" + + "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die + "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die +} diff --git a/sci-chemistry/coot/files/0.6.2-clipper-config.patch b/sci-chemistry/coot/files/0.6.2-clipper-config.patch new file mode 100644 index 000000000000..311b5e88d84e --- /dev/null +++ b/sci-chemistry/coot/files/0.6.2-clipper-config.patch @@ -0,0 +1,17 @@ + macros/clipper.m4 | 3 +++ + 1 files changed, 3 insertions(+), 0 deletions(-) + +diff --git a/macros/clipper.m4 b/macros/clipper.m4 +index 0bf087a..d0e8b6b 100644 +--- a/macros/clipper.m4 ++++ b/macros/clipper.m4 +@@ -98,6 +98,9 @@ case $ac_cv_build_alias in + ;; + esac + ++CLIPPER_CXXFLAGS=`clipper-config --cflags` ++CLIPPER_LDOPTS=`clipper-config --libs` ++ + AC_MSG_CHECKING([for Clipper]) + + LIBS="$save_LIBS $CLIPPER_LDOPTS" diff --git a/sci-chemistry/coot/files/0.6.2-gl.patch b/sci-chemistry/coot/files/0.6.2-gl.patch new file mode 100644 index 000000000000..bbd858c646df --- /dev/null +++ b/sci-chemistry/coot/files/0.6.2-gl.patch @@ -0,0 +1,10 @@ +Index: coot-surface/Makefile.am +=================================================================== +--- coot-surface/Makefile.am (revision 3478) ++++ coot-surface/Makefile.am (working copy) +@@ -29,4 +29,4 @@ + + libcoot_surface_la_LIBADD = \ + $(top_builddir)/surface/libccp4mg-surface.la \ +- $(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) ++ $(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) -lGL diff --git a/sci-chemistry/coot/files/0.6.2-libpng15.patch b/sci-chemistry/coot/files/0.6.2-libpng15.patch new file mode 100644 index 000000000000..bddd251698de --- /dev/null +++ b/sci-chemistry/coot/files/0.6.2-libpng15.patch @@ -0,0 +1,29 @@ +--- ccp4mg-utils/ppmutil.cc ++++ ccp4mg-utils/ppmutil.cc +@@ -2494,15 +2494,21 @@ + + pixels = new unsigned char[width*height*colourspace]; + ++ png_colorp palette; ++ int num_trans; ++#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4 ++ png_bytep trans_alpha; ++#endif ++ + for (int i=0; i<height; i++){ + if(color_type==PNG_COLOR_TYPE_PALETTE){ + for (int j=0; j<width; j++){ +- pixels[i*width*colourspace+j*colourspace] = png_ptr->palette[row_pointers[i][j]].red; +- pixels[i*width*colourspace+j*colourspace+1] = png_ptr->palette[row_pointers[i][j]].green; +- pixels[i*width*colourspace+j*colourspace+2] = png_ptr->palette[row_pointers[i][j]].blue; +- if(row_pointers[i][j]<png_ptr->num_trans){ ++ pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red; ++ pixels[i*width*colourspace+j*colourspace+1] = palette[row_pointers[i][j]].green; ++ pixels[i*width*colourspace+j*colourspace+2] = palette[row_pointers[i][j]].blue; ++ if(row_pointers[i][j]<num_trans){ + #if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4 +- pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans_alpha[row_pointers[i][j]]; ++ pixels[i*width*colourspace+j*colourspace+3] = trans_alpha[row_pointers[i][j]]; + #else + pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]]; + #endif diff --git a/sci-chemistry/coot/files/0.6.2-mmdb-config.patch b/sci-chemistry/coot/files/0.6.2-mmdb-config.patch new file mode 100644 index 000000000000..1d7cbd452f7b --- /dev/null +++ b/sci-chemistry/coot/files/0.6.2-mmdb-config.patch @@ -0,0 +1,18 @@ + macros/mmdb.m4 | 4 ++++ + 1 files changed, 4 insertions(+), 0 deletions(-) + +diff --git a/macros/mmdb.m4 b/macros/mmdb.m4 +index b477597..d05cf66 100644 +--- a/macros/mmdb.m4 ++++ b/macros/mmdb.m4 +@@ -86,6 +86,10 @@ else + ac_MMDB_LDOPTS="-lmmdb -lm" + fi + ++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2]) ++ac_MMDB_LDOPTS="${MMDB_LIBS}" ++ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}" ++ + AC_MSG_CHECKING([for MMDB]) + + LIBS="$save_LIBS $ac_MMDB_LDOPTS" diff --git a/sci-chemistry/coot/files/0.6.2-ssm.patch b/sci-chemistry/coot/files/0.6.2-ssm.patch new file mode 100644 index 000000000000..c801da72410a --- /dev/null +++ b/sci-chemistry/coot/files/0.6.2-ssm.patch @@ -0,0 +1,56 @@ + macros/mmdb-ssm.m4 | 42 +----------------------------------------- + 1 files changed, 1 insertions(+), 41 deletions(-) + +diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4 +index 1937a16..6ef547c 100644 +--- a/macros/mmdb-ssm.m4 ++++ b/macros/mmdb-ssm.m4 +@@ -22,47 +22,7 @@ + AC_DEFUN([AM_WITH_MMDBSSM], + [AC_PROVIDE([AM_USE_MMDBSSM]) + +- +-AC_ARG_WITH(ssmlib-prefix, +- AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ), +- [ with_ssmlib_prefix="$withval" ], +- with_ssmlib_prefix="") +- +-AC_MSG_CHECKING([for SSMLib]) +- +-if test x$with_ssmlib_prefix != x; then +- +- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB" +- MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm" +- +-ac_mmdb_dirs=' +-. +-include +-include/ssm +-include/mmdb +-lib +-src +-lib/src +-lib/src/mmdb' +- +- for ac_dir in $ac_mmdb_dirs; do +- if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then +- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir" +- break +- fi +- done +- +- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS" +- +-else +- +- MMDBSSM_CXXFLAGS="" +- MMDBSSM_LIBS="" +- with_ssmlib_prefix=no +- +-fi +- +-AC_MSG_RESULT([$with_ssmlib_prefix]) ++PKG_CHECK_MODULES([MMDBSSM],[ssm]) + + AC_SUBST(MMDBSSM_CXXFLAGS) + AC_SUBST(MMDBSSM_LIBS) diff --git a/sci-chemistry/coot/files/0.6.2-test.patch b/sci-chemistry/coot/files/0.6.2-test.patch new file mode 100644 index 000000000000..8cb79e65d767 --- /dev/null +++ b/sci-chemistry/coot/files/0.6.2-test.patch @@ -0,0 +1,16 @@ + src/testing.cc | 4 +++- + 1 files changed, 3 insertions(+), 1 deletions(-) + +diff --git a/src/testing.cc b/src/testing.cc +index f767bf6..097b9b9 100644 +--- a/src/testing.cc ++++ b/src/testing.cc +@@ -86,6 +86,8 @@ std::string greg_test(const std::string &file_name) { + const char *c = getenv("COOT_TEST_DATA_DIR"); + if (c) { + dd = c; ++ dd += "/"; ++ dd += file_name; + } else { + const char *d = getenv("HOME"); + if (d) { diff --git a/sci-chemistry/coot/files/coot-0.7-clipper-config.patch b/sci-chemistry/coot/files/coot-0.7-clipper-config.patch new file mode 100644 index 000000000000..311b5e88d84e --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.7-clipper-config.patch @@ -0,0 +1,17 @@ + macros/clipper.m4 | 3 +++ + 1 files changed, 3 insertions(+), 0 deletions(-) + +diff --git a/macros/clipper.m4 b/macros/clipper.m4 +index 0bf087a..d0e8b6b 100644 +--- a/macros/clipper.m4 ++++ b/macros/clipper.m4 +@@ -98,6 +98,9 @@ case $ac_cv_build_alias in + ;; + esac + ++CLIPPER_CXXFLAGS=`clipper-config --cflags` ++CLIPPER_LDOPTS=`clipper-config --libs` ++ + AC_MSG_CHECKING([for Clipper]) + + LIBS="$save_LIBS $CLIPPER_LDOPTS" diff --git a/sci-chemistry/coot/files/coot-0.7-goocanvas.patch b/sci-chemistry/coot/files/coot-0.7-goocanvas.patch new file mode 100644 index 000000000000..ce0d4a00abba --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.7-goocanvas.patch @@ -0,0 +1,25 @@ +Index: macros/goo-canvas.m4 +=================================================================== +--- macros/goo-canvas.m4 (revision 3307) ++++ macros/goo-canvas.m4 (working copy) +@@ -56,9 +56,9 @@ + fi + fi + +-AC_MSG_CHECKING([for Goocanvas]) ++PKG_CHECK_MODULES(GOOCANVAS, goocanvas) + +-LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS" ++LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS" + CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS" + # + # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will +@@ -76,7 +76,7 @@ + if test x$have_goocanvas = xyes; then + + GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS" +- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS" ++ GOOCANVAS_LIBS="$GOOCANVAS_LIBS" + + ifelse([$1], , :, [$1]) + diff --git a/sci-chemistry/coot/files/coot-0.7-mmdb-config.patch b/sci-chemistry/coot/files/coot-0.7-mmdb-config.patch new file mode 100644 index 000000000000..b3b66ab65786 --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.7-mmdb-config.patch @@ -0,0 +1,18 @@ +Index: macros/mmdb.m4 +=================================================================== +--- macros/mmdb.m4 (revision 3579) ++++ macros/mmdb.m4 (working copy) +@@ -86,8 +86,12 @@ + ac_MMDB_LDOPTS="-lmmdb -lm" + fi + +-AC_MSG_CHECKING([for MMDB]) ++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2]) ++ac_MMDB_LDOPTS="${MMDB_LIBS}" ++ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}" + ++AC_MSG_CHECKING([for CISPEP in MMDB]) ++ + LIBS="$save_LIBS $ac_MMDB_LDOPTS" + CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS" + # diff --git a/sci-chemistry/coot/files/coot-0.7-ssm.patch b/sci-chemistry/coot/files/coot-0.7-ssm.patch new file mode 100644 index 000000000000..c801da72410a --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.7-ssm.patch @@ -0,0 +1,56 @@ + macros/mmdb-ssm.m4 | 42 +----------------------------------------- + 1 files changed, 1 insertions(+), 41 deletions(-) + +diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4 +index 1937a16..6ef547c 100644 +--- a/macros/mmdb-ssm.m4 ++++ b/macros/mmdb-ssm.m4 +@@ -22,47 +22,7 @@ + AC_DEFUN([AM_WITH_MMDBSSM], + [AC_PROVIDE([AM_USE_MMDBSSM]) + +- +-AC_ARG_WITH(ssmlib-prefix, +- AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ), +- [ with_ssmlib_prefix="$withval" ], +- with_ssmlib_prefix="") +- +-AC_MSG_CHECKING([for SSMLib]) +- +-if test x$with_ssmlib_prefix != x; then +- +- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB" +- MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm" +- +-ac_mmdb_dirs=' +-. +-include +-include/ssm +-include/mmdb +-lib +-src +-lib/src +-lib/src/mmdb' +- +- for ac_dir in $ac_mmdb_dirs; do +- if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then +- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir" +- break +- fi +- done +- +- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS" +- +-else +- +- MMDBSSM_CXXFLAGS="" +- MMDBSSM_LIBS="" +- with_ssmlib_prefix=no +- +-fi +- +-AC_MSG_RESULT([$with_ssmlib_prefix]) ++PKG_CHECK_MODULES([MMDBSSM],[ssm]) + + AC_SUBST(MMDBSSM_CXXFLAGS) + AC_SUBST(MMDBSSM_LIBS) diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/coot/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/cyana/Manifest b/sci-chemistry/cyana/Manifest new file mode 100644 index 000000000000..de99a95f8e55 --- /dev/null +++ b/sci-chemistry/cyana/Manifest @@ -0,0 +1 @@ +DIST cyana-2.1.tar.gz 2203650 SHA256 4b49d23eda3a327074fa337c7ee13262e93fb2b92cc6feb9139dfb7695bdeded SHA512 20f5369e47198000927ee9a60beda34d265fddcd6be59f0d5d81ac23691b7e870ca674bdd7215a13bc849586411a007ebb1ff46072b55f255a6d796359067be8 WHIRLPOOL dfc60a456c166d98bbdb60227a2dae63d12ea9fb7375dede3d372a6dbf0785bfd0c8b1069d985a6ee775ab136405b553ff9336a2603d139d81d853f0681f5167 diff --git a/sci-chemistry/cyana/cyana-2.1.ebuild b/sci-chemistry/cyana/cyana-2.1.ebuild new file mode 100644 index 000000000000..6d042584dbc1 --- /dev/null +++ b/sci-chemistry/cyana/cyana-2.1.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="Combined assignment and dynamics algorithm for NMR applications" +HOMEPAGE="http://www.las.jp/english/products/cyana.html" +SRC_URI="${P}.tar.gz" + +LICENSE="CYANA" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RESTRICT="fetch" + +# we need libg2c for gfortran # 136988 +DEPEND="dev-lang/ifc" +RDEPEND="${DEPEND}" + +pkg_nofetch() { + elog "Please visit" + elog "http://www.las.jp/english/products/cyana.html" + elog "and get a copy of ${A}." + elog "Place it in ${DISTDIR}." +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-typo.patch \ + "${FILESDIR}"/${PV}-exec.patch \ + "${FILESDIR}"/${PV}-expire.patch \ + "${FILESDIR}"/${PV}-xiar.patch + + cat >> etc/config <<- EOF + VERSION=${PV} + SHELL=${EPREFIX}/bin/sh + FC=ifort + FFLAGS=${FFLAGS} -openmp -threads + FFLAGS2=${FFLAGS} -openmp -threads + CC=$(tc-getCC) + AR=xiar + RANLIB=ranlib + FORK=g77fork.o + LDFLAGS=${LDFLAGS} -reentrancy threaded -openmp + LIBS= + DEFS=-Dintel + SYSTEM=intel + EOF +} + +src_compile() { + cd src || die + emake +} + +src_install() { + dobin cyana{job,table,filter,clean} + newbin src/${PN}/${PN}exe.* ${PN} + insinto /usr/share/${PN} + doins -r lib macro help + use examples && doins -r demo + + cat >> "${T}"/20cyana <<- EOF + CYANALIB="${EPREFIX}/usr/share/${PN}" + EOF + + doenvd "${T}"/20cyana +} diff --git a/sci-chemistry/cyana/files/2.1-exec.patch b/sci-chemistry/cyana/files/2.1-exec.patch new file mode 100644 index 000000000000..28cd88d3eee6 --- /dev/null +++ b/sci-chemistry/cyana/files/2.1-exec.patch @@ -0,0 +1,77 @@ +diff --git a/cyana b/cyana +index 4f746cf..a7ff060 100755 +--- a/cyana ++++ b/cyana +@@ -45,16 +45,13 @@ shift `expr $optind - 1` + + if [ "$h" ]; then usage=1; fi + if [ "$usage" ]; then +- echo "Usage: $prog -hctx parameters ..." ++ echo "Usage: $prog -hS parameters ..." + echo + echo " -h help" + echo " -c command command to start program (must contain \$exefile)" + echo " -S run in safe mode, i.e. within one directory" +- echo " -t system explicit system type" +- echo " -x display name of executable without executing it" + exit 2 + fi +-if [ "$c" ]; then cmd="$c"; fi + sys=$t + mode=$x + safe=$S +@@ -65,23 +62,6 @@ safe=$S + eval ${PROG}ARG='$*' + export ${PROG}ARG + +- +-# ------ Set library name ------ +- +-f=$0 +-if [ `echo $f | sed 's,^/.*,+,'` != "+" ]; then f=`which $0`; fi +-odir=`pwd` +-while [ "`ls -l $f | awk '{ print substr($1,1,1) }'`" = "l" ]; do +- l=`ls -l $f | awk '{ i = NF; print $i }'` +- cd `dirname $f`; cd `dirname $l`; l=`pwd`/`basename $l` +- f=$l +-done +-cd `dirname $f` +-libdir=`pwd | sed 's,/src/'${prog}'$,,'` +-cd $odir +-eval ${PROG}LIB=$libdir +-export ${PROG}LIB +- + if [ "$safe" ]; then + CYANAINIT=initsafe; export CYANAINIT + fi +@@ -89,29 +69,4 @@ fi + + # ------ Start the program ------ + +-if [ -d $libdir/src/$prog ]; then +- exe=$libdir/src/$prog/$exe +-else +- exe=$libdir/$exe +-fi +-if [ "$sys" = "" ]; then +- sys=`$libdir/etc/identify` +- files="$exe.$sys* $exe.gnu $exe.*" +-else +- files=$exe.$sys +-fi +-for exefile in $files; do +- if [ -x $exefile ]; then +- if [ "$mode" ]; then +- echo $exefile; exit 0 +- else +- if [ "`echo $cmd | grep -c '\$exefile'`" -gt 0 ]; then +- eval exec $cmd +- else +- eval exec $cmd $exefile +- fi +- fi +- fi +-done +-echo "No executable found in \"`dirname $exe`\"." +-exit 1 ++exec cyana diff --git a/sci-chemistry/cyana/files/2.1-expire.patch b/sci-chemistry/cyana/files/2.1-expire.patch new file mode 100644 index 000000000000..e18008286f68 --- /dev/null +++ b/sci-chemistry/cyana/files/2.1-expire.patch @@ -0,0 +1,15 @@ +--- src/inclan/unix.for.orig 2011-01-05 14:56:46.572193759 +0100 ++++ src/inclan/unix.for 2011-01-05 14:57:27.833627375 +0100 +@@ -206,11 +206,8 @@ + end if + if (iwbeg.lt.0) then + iwbeg=igttim +- iexpir=(julday(12,31,2010)-julday(1,1,1970))*24*3600 +- if (iwbeg.gt.iexpir) call fatmsg ('License expired.') ++ iexpir=iwbeg+100 + j=(iexpir-iwbeg)/(24*3600) +- if (j.lt.1000) +- * call wrnmsg ('License expires in '//plural(j,'day')//'.') + end if + iwall=igttim-iwbeg + c print *,'iwall = ',iwall,iwbeg,idat,itim
\ No newline at end of file diff --git a/sci-chemistry/cyana/files/2.1-typo.patch b/sci-chemistry/cyana/files/2.1-typo.patch new file mode 100644 index 000000000000..3f011a9b2c28 --- /dev/null +++ b/sci-chemistry/cyana/files/2.1-typo.patch @@ -0,0 +1,13 @@ +diff --git a/src/cyana/putpro.f b/src/cyana/putpro.f +index d4080f9..4490225 100644 +--- a/src/cyana/putpro.f ++++ b/src/cyana/putpro.f +@@ -66,7 +66,7 @@ c ------------------------------------------------------ BMRB header + * ' _Mol_residue_sequence', + * ';' + do i=1,nr,20 +- write (iunit,'(20A1))') (rcode(rnam(j)),j=i,min(nr,i+19)) ++ write (iunit,'(20A1)') (rcode(rnam(j)),j=i,min(nr,i+19)) + end do + + write (iunit,'(A)') diff --git a/sci-chemistry/cyana/files/2.1-xiar.patch b/sci-chemistry/cyana/files/2.1-xiar.patch new file mode 100644 index 000000000000..e8393253d7f6 --- /dev/null +++ b/sci-chemistry/cyana/files/2.1-xiar.patch @@ -0,0 +1,16 @@ + src/inclan/Makefile | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/src/inclan/Makefile b/src/inclan/Makefile +index fc5a8bf..482d48f 100644 +--- a/src/inclan/Makefile ++++ b/src/inclan/Makefile +@@ -35,7 +35,7 @@ clean: + + inclan.a: $(OBJS) + rm -f $@ +- ar rc $@ $(OBJS) ++ $(AR) rc $@ $(OBJS) + if [ "$(RANLIB)" ]; then $(RANLIB) $@; fi + + inclan.o: inclan.for diff --git a/sci-chemistry/cyana/metadata.xml b/sci-chemistry/cyana/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/cyana/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest new file mode 100644 index 000000000000..a5bba878b984 --- /dev/null +++ b/sci-chemistry/dssp/Manifest @@ -0,0 +1 @@ +DIST dssp-2.2.1.tgz 47141 SHA256 5fb5e7c085de16c05981e3a72869c8b082911a0b46e6dcc6dbd669c9f267e8e1 SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811 WHIRLPOOL abdb6777ccc06b062e3f20226c555348cd221d9c3e14d2adb9aeb85f14f84db8841c2fbbc4a487f5fa021da6616cddf2e96fde787d7670c419926d24d24944bd diff --git a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild new file mode 100644 index 000000000000..5e8b800f9488 --- /dev/null +++ b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="The protein secondary structure standard" +HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/" +SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz" + +LICENSE="Boost-1.0" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="dev-libs/boost:=" +DEPEND="${RDEPEND}" + +src_prepare() { + tc-export CXX + + cat >> make.config <<- EOF + BOOST_LIB_SUFFIX = -mt + BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)" + BOOST_INC_DIR = "${EPREFIX}/usr/include" + EOF + + epatch \ + "${FILESDIR}"/${PN}-2.1.0-gentoo.patch +} + +src_install() { + dobin mkdssp + dosym mkdssp /usr/bin/dssp + doman doc/mkdssp.1 + dodoc README.txt changelog + + cat >> "${T}"/30-${PN} <<- EOF + DSSP="${EPREFIX}"/usr/bin/${PN} + EOF + doenvd "${T}"/30-${PN} +} diff --git a/sci-chemistry/dssp/files/Makefile b/sci-chemistry/dssp/files/Makefile new file mode 100644 index 000000000000..575202ebbe2d --- /dev/null +++ b/sci-chemistry/dssp/files/Makefile @@ -0,0 +1,7 @@ +#OBJ = AccSurf.o CalcAccSurf.o Contacts.o Date.o Dssp.o DsspCMBI.o p2clib.o Vector.o +OBJ = AccSurf.o CalcAccSurf.o Contacts.o Date.o DsspCMBI.o p2clib.o Vector.o + +LIBS = -lm + +dssp: $(OBJ) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJ) $(LIBS) diff --git a/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch b/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch new file mode 100644 index 000000000000..5db1437beb1f --- /dev/null +++ b/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch @@ -0,0 +1,46 @@ + src/matrix.h | 5 +++-- + src/primitives-3d.cpp | 1 + + 2 files changed, 4 insertions(+), 2 deletions(-) + +diff --git a/src/matrix.h b/src/matrix.h +index 1053ad9..d7dae5f 100644 +--- a/src/matrix.h ++++ b/src/matrix.h +@@ -14,6 +14,7 @@ + #include <istream> + #include <cassert> + #include <stdexcept> ++#include <unistd.h> + + // -------------------------------------------------------------------- + // uBlas compatible matrix types +@@ -284,7 +285,7 @@ class identity_matrix : public matrix_base<T> + template<typename T> + matrix<T> operator*(const matrix_base<T>& lhs, const matrix_base<T>& rhs) + { +- matrix<T> result(min(lhs.dim_m(), rhs.dim_m()), min(lhs.dim_n(), rhs.dim_n())); ++ matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n())); + + for (uint32 i = 0; i < result.dim_m(); ++i) + { +@@ -310,7 +311,7 @@ matrix<T> operator*(const matrix_base<T>& lhs, T rhs) + template<typename T> + matrix<T> operator-(const matrix_base<T>& lhs, const matrix_base<T>& rhs) + { +- matrix<T> result(min(lhs.dim_m(), rhs.dim_m()), min(lhs.dim_n(), rhs.dim_n())); ++ matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n())); + + for (uint32 i = 0; i < result.dim_m(); ++i) + { +diff --git a/src/primitives-3d.cpp b/src/primitives-3d.cpp +index b04e7c4..4532ecd 100644 +--- a/src/primitives-3d.cpp ++++ b/src/primitives-3d.cpp +@@ -9,6 +9,7 @@ + + #include <valarray> + #include <cmath> ++#include <unistd.h> + + #include <boost/foreach.hpp> + #define foreach BOOST_FOREACH diff --git a/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch b/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch new file mode 100644 index 000000000000..3db40f640ccd --- /dev/null +++ b/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch @@ -0,0 +1,70 @@ + makefile | 24 ++++++++++++++---------- + 1 files changed, 14 insertions(+), 10 deletions(-) + +diff --git a/makefile b/makefile +index df699b7..9d2167b 100644 +--- a/makefile ++++ b/makefile +@@ -2,7 +2,7 @@ + # + # Copyright Maarten L. Hekkelman, Radboud University 2008-2011. + # Distributed under the Boost Software License, Version 1.0. +-# (See accompanying file LICENSE_1_0.txt or copy at ++# (See aCXXompanying file LICENSE_1_0.txt or copy at + # http://www.boost.org/LICENSE_1_0.txt) + # + # This makefile includes a file called make.config. It will create a +@@ -24,22 +24,23 @@ BOOST_LIBS = thread regex filesystem program_options date_time iostreams math_ + LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2 + + DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"' +-CC = c++ ++CXX ?= c++ + +-CFLAGS = $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread +-LDOPTS = $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g -pthread ++CPPFLAGS += $(INC_DIR:%=-I%) -iquote src ++CXXFLAGS += -Wall -Wno-multichar -pthread ++LDOPTS = $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -pthread + + OBJ_DIR = obj + + ifeq ($(DEBUG),1) + OBJ_DIR := $(OBJ_DIR).dbg +-CFLAGS += -g3 ++CFLAGS += + else + DEFINES += NDEBUG +-CFLAGS += -O3 ++CFLAGS += + endif + +-CFLAGS += $(DEFINES:%=-D%) ++CPPFLAGS += $(DEFINES:%=-D%) + + DIST_NAME = dssp-$(VERSION) + +@@ -49,17 +50,20 @@ OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ + + mkdssp: $(OBJECTS) + @ echo linking $@ +- @ $(CC) -static -o $@ $^ $(LDOPTS) ++ $(CXX) $(LDFLAGS) -o $@ $^ $(LDOPTS) + @ echo OK + + include $(OBJECTS:%.o=%.d) + + $(OBJECTS:.o=.d): + +-$(OBJ_DIR)/%.o: %.cpp ++OBJ_DIR: + @ if [ ! -d $(OBJ_DIR) ]; then mkdir $(OBJ_DIR); fi ++ ++ ++$(OBJ_DIR)/%.o: %.cpp OBJ_DIR + @ echo compiling $@ +- @ $(CC) -MD -c -o $@ $< $(CFLAGS) ++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -MD -c -o $@ $< + + clean: + rm -rf $(OBJ_DIR)/* mkdssp diff --git a/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch b/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch new file mode 100644 index 000000000000..15198feaea19 --- /dev/null +++ b/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch @@ -0,0 +1,60 @@ + makefile | 21 +++++++++++---------- + 1 file changed, 11 insertions(+), 10 deletions(-) + +diff --git a/makefile b/makefile +index d6f335e..68736c6 100644 +--- a/makefile ++++ b/makefile +@@ -25,22 +25,23 @@ BOOST_LIBS = thread filesystem program_options iostreams system + LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2 + + DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"' +-CXX = g++ ++CXX ?= g++ + +-CFLAGS += $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread +-LDOPTS += $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g -pthread ++CPPFLAGS += $(INC_DIR:%=-I%) -iquote src ++CXXFLAGS += -Wall -Wno-multichar -pthread ++LDOPTS += $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -pthread + + OBJ_DIR = obj + + ifeq ($(DEBUG),1) + OBJ_DIR := $(OBJ_DIR).dbg +-CFLAGS += -g3 ++CFLAGS += + else + DEFINES += NDEBUG +-CFLAGS += -O3 ++CFLAGS += + endif + +-CFLAGS += $(DEFINES:%=-D%) ++CPPFLAGS += $(DEFINES:%=-D%) + + DIST_NAME = dssp-$(VERSION) + +@@ -50,18 +51,18 @@ OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ + + mkdssp: $(OBJECTS) + @ echo linking $@ +- @ $(CXX) -static -o $@ $^ $(LDOPTS) ++ $(CXX) $(LDFLAGS) -o $@ $^ $(LDOPTS) + + include $(OBJECTS:%.o=%.d) + + $(OBJECTS:.o=.d): + +-$(OBJ_DIR): ++OBJ_DIR: + @ mkdir -p $(OBJ_DIR) + +-$(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR) ++$(OBJ_DIR)/%.o: %.cpp OBJ_DIR + @ echo compiling $@ +- @ $(CXX) -MD -c -o $@ $< $(CFLAGS) ++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -MD -c -o $@ $< + + clean: + install -d $(BIN_DIR) $(MAN_DIR) diff --git a/sci-chemistry/dssp/metadata.xml b/sci-chemistry/dssp/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/dssp/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/easychem/Manifest b/sci-chemistry/easychem/Manifest new file mode 100644 index 000000000000..8c12b1a64218 --- /dev/null +++ b/sci-chemistry/easychem/Manifest @@ -0,0 +1 @@ +DIST easychem-0.6.tar.gz 265458 SHA256 1dba1a1ed1862c723cd77184a90ee7571a26ebcb0d3c22e7e032af1cbafe284d SHA512 83f877d1813287592a460f4dc3769feda88e45d8f77cd728c4055b60521babe253b4432033941ff429c753cfe675a642714052a01736534147398d6972e47051 WHIRLPOOL 7869025a921b2a6ada516f60c3e79247b1ad74a0bb904f7dd9b7bd993b3b5166ccd3f266f6c2e85198c8bde1ddaf863518a7adea7a6fd9b22bf789e1df7103fe diff --git a/sci-chemistry/easychem/easychem-0.6-r1.ebuild b/sci-chemistry/easychem/easychem-0.6-r1.ebuild new file mode 100644 index 000000000000..932cf7709daa --- /dev/null +++ b/sci-chemistry/easychem/easychem-0.6-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Chemical structure drawing program - focused on presentation" +HOMEPAGE="http://easychem.sourceforge.net/" +SRC_URI="mirror://sourceforge/easychem/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + x11-libs/gtk+:2 + app-text/ghostscript-gpl + media-gfx/pstoedit" +DEPEND="${RDEPEND} + dev-lang/perl + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + tc-export CC +} + +src_compile() { + ln -s Makefile.linux Makefile || die + DGS_PATH="${EPREFIX}"/usr/bin DPSTOEDIT_PATH="${EPREFIX}"/usr/bin \ + C_FLAGS="${CFLAGS}" emake -e +} + +src_install () { + dobin easychem + dodoc TODO +} diff --git a/sci-chemistry/easychem/files/0.6-gentoo.patch b/sci-chemistry/easychem/files/0.6-gentoo.patch new file mode 100644 index 000000000000..000e4373b3c2 --- /dev/null +++ b/sci-chemistry/easychem/files/0.6-gentoo.patch @@ -0,0 +1,65 @@ +diff --git a/Makefile.linux b/Makefile.linux +index 6638394..5da56b0 100644 +--- a/Makefile.linux ++++ b/Makefile.linux +@@ -1,5 +1,5 @@ + # The C compiler +-CC=gcc ++CC ?= gcc + + # The following line must be uncommented if you want to specify a place + # where the 'gs' (or 'pstoedit') program is. +@@ -25,11 +25,10 @@ GTK_LIBS=`pkg-config --libs gtk+-2.0` + # The list of important files + OBJECTS=auxi.o bonds.o easychem.o export.o dialogs.o detect.o library.o drawing.o + +-all: easychem po/ ++all: easychem po + +-easychem: postscript/ graph/ $(OBJECTS) +- $(CC) -o easychem $(OBJECTS) $(GTK_LIBS) $(C_FLAGS) +- strip easychem ++easychem: postscript graph $(OBJECTS) ++ $(CC) $(C_FLAGS) $(LDFLAGS) -o easychem $(OBJECTS) $(GTK_LIBS) -lm + + clean: FORCE + -cd graph; make clean +@@ -37,7 +36,7 @@ clean: FORCE + -cd po; make clean + -rm $(OBJECTS) easychem + +-export.o: export.c common.h bonds.h postscript/ ++export.o: export.c common.h bonds.h postscript + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c export.c + bonds.o: bonds.c common.h bonds.h + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c bonds.c +@@ -49,20 +48,22 @@ library.o: library.c common.h library.h + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c library.c + drawing.o: drawing.c common.h drawing.h + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c drawing.c +-dialogs.o: dialogs.c common.h dialogs.h graph/ ++dialogs.o: dialogs.c common.h dialogs.h graph + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c dialogs.c + detect.o: detect.c common.h detect.h + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c detect.c + + # The rules for subdirectories +-graph/: FORCE +- cd graph; make all ++graph: ++ +make -C $@ + +-postscript/: FORCE +- cd postscript; make all ++postscript: ++ +make -C $@ + +-po/: FORCE +- cd po; make all ++po: ++ +make -C $@ + + # This is used to force an update + FORCE: ++ ++.PHONY: graph postscript po diff --git a/sci-chemistry/easychem/files/easychem-0.6-prestrip.patch b/sci-chemistry/easychem/files/easychem-0.6-prestrip.patch new file mode 100644 index 000000000000..a1cbbb055d0c --- /dev/null +++ b/sci-chemistry/easychem/files/easychem-0.6-prestrip.patch @@ -0,0 +1,10 @@ +--- Makefile.linux.orig 2009-02-23 21:17:25.000000000 +0200 ++++ Makefile.linux 2009-02-23 21:17:50.000000000 +0200 +@@ -29,7 +29,6 @@ + + easychem: postscript/ graph/ $(OBJECTS) + $(CC) -o easychem $(OBJECTS) $(GTK_LIBS) $(C_FLAGS) +- strip easychem + + clean: FORCE + -cd graph; make clean diff --git a/sci-chemistry/easychem/metadata.xml b/sci-chemistry/easychem/metadata.xml new file mode 100644 index 000000000000..0a2ea04beeec --- /dev/null +++ b/sci-chemistry/easychem/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> + EasyChem is a program designed to draw chemical molecules, written under + Linux using Gtk+ 2.4. It is implemented with a strong focus on producing + press quality molecules. Easychem can be a little more difficult to learn to + use, but when mastered it can be very fast and powerful. It can draw + ornaments easily, and exports to EPS with LaTeX fonts among other things. + </longdescription> + <upstream> + <remote-id type="sourceforge">easychem</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/eden/Manifest b/sci-chemistry/eden/Manifest new file mode 100644 index 000000000000..c0087f8f962b --- /dev/null +++ b/sci-chemistry/eden/Manifest @@ -0,0 +1 @@ +DIST eden_V5.3.tar.gz 1139981 SHA256 249447f507ace3e188ce0d76796c6e307c043592405db1f6c24f3e90917ec524 SHA512 c59d08004bdb72ef39fe205aef546fbcff9c57ee42942c0391052de9c501c7793ed3bd280569020c2b9ec6133a87362d184a2012b61c6be18b5f6ba9b59716c5 WHIRLPOOL f0329805ab1d3b75febcc07c87583ee30f2ca44d5b5ae5c3512d4891a8763bf45ab7dc94abed831c0326cdbc35502f4bc3904ccb7447b090100b2f7d52b1156b diff --git a/sci-chemistry/eden/eden-5.3-r2.ebuild b/sci-chemistry/eden/eden-5.3-r2.ebuild new file mode 100644 index 000000000000..8dc430e329b1 --- /dev/null +++ b/sci-chemistry/eden/eden-5.3-r2.ebuild @@ -0,0 +1,87 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +MY_P="${PN}_V${PV}" + +DESCRIPTION="A crystallographic real-space electron-density refinement and optimization program" +HOMEPAGE="http://www.gromacs.org/pipermail/eden-users/" +SRC_URI="mirror://gentoo/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="double-precision" + +RDEPEND=" + sci-libs/fftw:2.1 + sci-libs/gsl" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}" + +SRC="${S}/source" + +pkg_setup() { + export EDENHOME="${EPREFIX}/usr/$(get_libdir)/${PN}" +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-makefile-fixes.patch \ + "${FILESDIR}"/${P}-impl-dec.patch \ + "${FILESDIR}"/${P}-format-security.patch + + sed -i \ + -e "s:^\(FFTW.*=\).*:\1 ${EPREFIX}/usr:g" \ + -e "s:^\(LIB.*=.*\$(FFTW)/\).*:\1$(get_libdir):g" \ + -e "s:^\(BIN.*=\).*:\1 ${D}usr/bin:g" \ + -e "s:^\(CFLAGS.*=\).*:\1 ${CFLAGS}:g" \ + -e "s:-lgsl -lgslcblas:$($(tc-getPKG_CONFIG) --libs gsl):g" \ + ${SRC}/Makefile || die + + if ! use double-precision; then + sed -i -e "s:^\(DOUBLESWITCH.*=\).*:\1 OFF:g" ${SRC}/Makefile || die + EDEN_EXE="s${PN}" + else + EDEN_EXE="d${PN}" + fi +} + +src_compile() { + emake CC=$(tc-getCC) -C ${SRC} +} + +src_install() { + emake -C ${SRC} install + + python_foreach_impl python_newscript python/${PN}.py i${PN} + python_foreach_impl python_domodule python/FileListDialog.py + + rm python/*py || die + insinto ${EDENHOME}/python + doins python/* + + insinto ${EDENHOME}/help + doins help/* + + insinto ${EDENHOME}/tools + doins tools/* + + dodoc manual/UserManual.pdf + + cat >> "${T}"/60${PN} <<- EOF + EDENHOME="${EDENHOME}" + EOF + + doenvd "${T}"/60${PN} + + dosym ${EDEN_EXE} /usr/bin/${PN} +} diff --git a/sci-chemistry/eden/files/5.3-makefile-fixes.patch b/sci-chemistry/eden/files/5.3-makefile-fixes.patch new file mode 100644 index 000000000000..632358341784 --- /dev/null +++ b/sci-chemistry/eden/files/5.3-makefile-fixes.patch @@ -0,0 +1,60 @@ + source/Makefile | 17 ++++++++++------- + 1 files changed, 10 insertions(+), 7 deletions(-) + +diff --git a/source/Makefile b/source/Makefile +index 46d89cc..aa751c7 100644 +--- a/source/Makefile ++++ b/source/Makefile +@@ -78,8 +78,10 @@ CFLAGS = -Wall -pipe -g3 + #CFLAGS = -Wall -pipe -marchi686 -pedantic -gdwarf-2 -g3 + #CFLAGS = -Wall -O3 -march=i686 + ifneq ($(FFTW),/usr/local) ++ifneq ($(FFTW),/usr) + CFLAGS += -I$(INC) + endif ++endif + + # NOTE: + # DOUBLESWITCH = ON for double precision; +@@ -91,15 +93,15 @@ endif + DOUBLESWITCH = ON + + ifeq ($(DOUBLESWITCH),ON) +-LDFLAGS = -L$(LIB) -ldfftw -lm ++LIBS = -L$(LIB) -ldfftw -lm + CFLAGS += -DDOUBLE + TARGET = deden + else +-LDFLAGS = -L$(LIB) -lsfftw -lm ++LIBS = -L$(LIB) -lsfftw -lm + TARGET = seden + endif + +-LDFLAGS += -g -lgsl -lgslcblas ++LIBS += -lgsl -lgslcblas + + # GSL_PREFIX:= /sw/lib + # LDFLAGS += -l$(GSL_PREFIX)/libgsl.a -l$(GSL_PREFIX)/libgslcblas.a +@@ -120,17 +122,18 @@ OBJ = addmaps.o apodfc.o apodfo.o back.o cadhkl.o \ + all: eden fbyteswap + + eden: eden.o $(OBJ) +- $(CC) $^ $(LDFLAGS) -o $@ ++ $(CC) $(LDFLAGS) -o $@ $^ $(LIBS) + + fbyteswap: fbyteswap.c +- $(CC) -o $@ $^ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) + + install: all ++ mkdir -p $(BIN) + mv fbyteswap $(BIN) + mv eden $(BIN)/$(TARGET) + chmod 751 $(BIN)/$(TARGET) +- chmod +x mkeden.csh +- ./mkeden.csh $(BIN) $(BIN)/$(TARGET) ++# chmod +x mkeden.csh ++# ./mkeden.csh $(BIN) $(BIN)/$(TARGET) + + dist: clean + cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar diff --git a/sci-chemistry/eden/files/eden-5.3-format-security.patch b/sci-chemistry/eden/files/eden-5.3-format-security.patch new file mode 100644 index 000000000000..04b5ecfddebb --- /dev/null +++ b/sci-chemistry/eden/files/eden-5.3-format-security.patch @@ -0,0 +1,96 @@ + source/back.c | 2 +- + source/concosts.c | 4 ++-- + source/count.c | 4 ++-- + source/eden.c | 2 +- + source/util.c | 4 ++-- + 5 files changed, 8 insertions(+), 8 deletions(-) + +diff --git a/source/back.c b/source/back.c +index fd517b9..185a02b 100644 +--- a/source/back.c ++++ b/source/back.c +@@ -112,7 +112,7 @@ void back_main(int argc, char *argv[]) + ballpark(caller) ; + + if (argc > optind+2) +- sprintf(sf_filename, argv[optind+2]) ; ++ sprintf(sf_filename, "%s", argv[optind+2]) ; + + /********************************************* + Pull off prefix defining whereabouts of input +diff --git a/source/concosts.c b/source/concosts.c +index d62d2e3..590f073 100644 +--- a/source/concosts.c ++++ b/source/concosts.c +@@ -452,7 +452,7 @@ void prepare_singlets(char *filename) + sprintf(message, + "s=%d, p=%d, n=%d, phase=%g, old phase=%g, delta=%g\n", + s, p, n, phase, *(checks+n), phase-*(checks+n)) ; +- fprintf(fp_log, message) ; ++ fprintf(fp_log, "%s", message) ; + } + } + /*********************************************** +@@ -556,7 +556,7 @@ void prepare_triplets(char *filename) + sprintf(message, + "Triplet (%d %d %d) from input (%d %d %d) corresponds to point w/o fobs info!\n", + newh, newk, newl, t_h[q], t_k[q], t_l[q]) ; +- fprintf(fp_log, message) ; ++ fprintf(fp_log, "%s", message) ; + legal_triplet = FALSE ; + } + } +diff --git a/source/count.c b/source/count.c +index c3bc390..ca13008 100644 +--- a/source/count.c ++++ b/source/count.c +@@ -460,12 +460,12 @@ void print_el_count(char *filename, + } + + sprintf(message, "\nTotal no. of electrons is %g\n", totnump*volvox) ; +- fprintf(fp, message) ; ++ fprintf(fp, "%s", message) ; + printTwice(message) ; + + sprintf(message, "Count of all remaining electrons: %g %g %g\n", + remainder0*volvox, remainder1*volvox, remainder2*volvox) ; +- fprintf(fp, message) ; ++ fprintf(fp, "%s", message) ; + printTwice(message) ; + + fclose(fp) ; +diff --git a/source/eden.c b/source/eden.c +index dea3246..5a9b389 100644 +--- a/source/eden.c ++++ b/source/eden.c +@@ -319,7 +319,7 @@ int main(int argc, char *argv[]) + + get_unique_logname() ; + +- sprintf(command_line, argv[0]) ; ++ sprintf(command_line, "%s", argv[0]) ; + + for (k = 1; k < argc; k++) { + strcat(command_line, " ") ; +diff --git a/source/util.c b/source/util.c +index 6fff179..41c624c 100644 +--- a/source/util.c ++++ b/source/util.c +@@ -266,7 +266,7 @@ void printTwice(char *mess) /* send info to terminal (stdout) and to log */ + + void prompt(char *mess) /* Send message to user, await reply */ + { +- fprintf(stdout, mess) ; ++ fprintf(stdout, "%s", mess) ; + + while (fgets(terminp, MAXSTRING, stdin) != NULL) { + if ((int)strlen(terminp) > 0) +@@ -722,7 +722,7 @@ void start_record() + int k ; + + rec_length = k = sprintf(record, "\n") ; +- rec_length += sprintf(record+k, timestamp()) ; ++ rec_length += sprintf(record+k, "%s", timestamp()) ; + k = rec_length ; + + if ((cwd = getcwd(NULL, 120)) == NULL) diff --git a/sci-chemistry/eden/files/eden-5.3-impl-dec.patch b/sci-chemistry/eden/files/eden-5.3-impl-dec.patch new file mode 100644 index 000000000000..af67508d090e --- /dev/null +++ b/sci-chemistry/eden/files/eden-5.3-impl-dec.patch @@ -0,0 +1,28 @@ + source/fbyteswap.c | 1 + + source/util.c | 1 + + 2 files changed, 2 insertions(+), 0 deletions(-) + +diff --git a/source/fbyteswap.c b/source/fbyteswap.c +index 83015b9..c9033c3 100644 +--- a/source/fbyteswap.c ++++ b/source/fbyteswap.c +@@ -39,6 +39,7 @@ and shall not be used for advertising or product endorsement purposes. + + #include <stdio.h> + #include <fcntl.h> ++#include <unistd.h> + #include <sys/stat.h> + #include <sys/types.h> + void byteswap(); +diff --git a/source/util.c b/source/util.c +index 6fff179..ca7a957 100644 +--- a/source/util.c ++++ b/source/util.c +@@ -89,6 +89,7 @@ and shall not be used for advertising or product endorsement purposes. + + *******************************************************************************/ + #include <sys/time.h> /* ... for picking up date & time */ ++#include <time.h> + #include <signal.h> /* ... for capturing kill */ + #include "util.h" + diff --git a/sci-chemistry/eden/files/makefile-fixes.patch b/sci-chemistry/eden/files/makefile-fixes.patch new file mode 100644 index 000000000000..4cfff3f515df --- /dev/null +++ b/sci-chemistry/eden/files/makefile-fixes.patch @@ -0,0 +1,25 @@ +diff -ur eden.orig/source/Makefile eden/source/Makefile +--- eden.orig/source/Makefile 2004-10-18 10:40:03.000000000 -0700 ++++ eden/source/Makefile 2005-12-15 22:32:45.000000000 -0800 +@@ -78,8 +78,10 @@ + #CFLAGS = -Wall -pipe -marchi686 -pedantic -gdwarf-2 -g3 + #CFLAGS = -Wall -O3 -march=i686 + ifneq ($(FFTW),/usr/local) ++ifneq ($(FFTW),/usr) + CFLAGS += -I$(INC) + endif ++endif + + # NOTE: + # DOUBLESWITCH = ON for double precision; +@@ -129,8 +131,8 @@ + mv fbyteswap $(BIN) + mv eden $(BIN)/$(TARGET) + chmod 751 $(BIN)/$(TARGET) +- chmod +x mkeden.csh +- ./mkeden.csh $(BIN) $(BIN)/$(TARGET) ++# chmod +x mkeden.csh ++# ./mkeden.csh $(BIN) $(BIN)/$(TARGET) + + dist: clean + cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar diff --git a/sci-chemistry/eden/metadata.xml b/sci-chemistry/eden/metadata.xml new file mode 100644 index 000000000000..732277b2b750 --- /dev/null +++ b/sci-chemistry/eden/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <use> + <flag name="double-precision">More precise calculations at the expense of + speed</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/elem/Manifest b/sci-chemistry/elem/Manifest new file mode 100644 index 000000000000..49bd992fc961 --- /dev/null +++ b/sci-chemistry/elem/Manifest @@ -0,0 +1 @@ +DIST elem-src-1.0.3-Linux.tgz 58364 SHA256 a570736165b939841a9dbf273110a6c01ddfd77559e5b020574aad8e3f5af296 diff --git a/sci-chemistry/elem/elem-1.0.3-r1.ebuild b/sci-chemistry/elem/elem-1.0.3-r1.ebuild new file mode 100644 index 000000000000..386caa804b61 --- /dev/null +++ b/sci-chemistry/elem/elem-1.0.3-r1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit toolchain-funcs + +DESCRIPTION="periodic table of the elements" +HOMEPAGE="http://elem.sourceforge.net/" +SRC_URI="mirror://sourceforge/elem/${PN}-src-${PV}-Linux.tgz" +LICENSE="GPL-2" +KEYWORDS="amd64 sparc x86" +SLOT="0" +IUSE="" + +DEPEND="x11-libs/xforms" +RDEPEND="${DEPEND}" + +src_unpack() { + unpack ${A} + cd "${S}" + sed -e 's:\(^LIBS = .*\):\1 -lXpm:' -i Makefile || die "sed failed" +} + +src_compile () { + emake COMPILER="$(tc-getCC)" FLAGS="${CFLAGS}" all || die "Build failed." +} + +src_install () { + into /usr + dobin elem elem-de elem-en + dohtml -r doc/* +} diff --git a/sci-chemistry/elem/elem-1.0.3-r2.ebuild b/sci-chemistry/elem/elem-1.0.3-r2.ebuild new file mode 100644 index 000000000000..c52107340659 --- /dev/null +++ b/sci-chemistry/elem/elem-1.0.3-r2.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit toolchain-funcs + +DESCRIPTION="periodic table of the elements" +HOMEPAGE="http://elem.sourceforge.net/" +SRC_URI="mirror://sourceforge/elem/${PN}-src-${PV}-Linux.tgz" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~sparc ~x86" +SLOT="0" +IUSE="" + +DEPEND="x11-libs/xforms" +RDEPEND="${DEPEND}" + +src_unpack() { + unpack ${A} + cd "${S}" + sed -e 's:\(^LIBS = .*\):\1 -lXpm:' \ + -e "s:\${FLAGS} -o elem:\$(LDFLAGS) &:" \ + -i Makefile || die #336190 + sed -e "/string.h/ i #include <stdlib.h>" \ + -i elem_cb.c || die #implicit exit() +} + +src_compile () { + emake COMPILER="$(tc-getCC)" FLAGS="${CFLAGS}" all || die "Build failed." +} + +src_install () { + dobin elem elem-de elem-en || die + dohtml -r doc/* || die +} diff --git a/sci-chemistry/elem/metadata.xml b/sci-chemistry/elem/metadata.xml new file mode 100644 index 000000000000..841c9b22af92 --- /dev/null +++ b/sci-chemistry/elem/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">elem</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/freeon/Manifest b/sci-chemistry/freeon/Manifest new file mode 100644 index 000000000000..39a7e4aedcc1 --- /dev/null +++ b/sci-chemistry/freeon/Manifest @@ -0,0 +1,2 @@ +DIST freeon-1.0.10.tar.bz2 5872019 SHA256 01f0086a53930afb3078a2794baa1fccdacdc4a23082725cb016068d5a10ec38 SHA512 5bae89d6421600792bf986f6fb7504d321d5d51782587237ecba35191e54c1ec6c5ea1fdc50ed2d339551c527e4efcc5421048ccce0404c4b06875cbd0800862 WHIRLPOOL 84fcf7ca4d62e5a2407f2920f9a13fd2a4930f2637d098954b3be81f540e4a10344d17053a1d05046c2743f317a8898886148439d51364ce10dc66a313eadb8b +DIST freeon-1.0.8.tar.bz2 5957707 SHA256 ae14c1b640e4dcd9f18d2807f2debf9fc005b7451401e3e5d7b9dc76919f381d SHA512 1227f670a73b4ea39beb26e4136ad535e126ad17d66171c31b3bd403a3886eee150cda865806a2d9dad85646ccb086a6be4f645455eab24603cb064fb725efbd WHIRLPOOL b41a3b1e4bb152309a12ac0c4fec07c932809bb465af4b08cb76f6e0bf089c4d91682e1428c47d1adb449d153a1338cd3d540e860ca22774a299e21da44a16c1 diff --git a/sci-chemistry/freeon/files/freeon-1.0.8-blas.patch b/sci-chemistry/freeon/files/freeon-1.0.8-blas.patch new file mode 100644 index 000000000000..46fca7fa2a52 --- /dev/null +++ b/sci-chemistry/freeon/files/freeon-1.0.8-blas.patch @@ -0,0 +1,165 @@ + FreeON/Makefile.am | 2 +- + HiCu/Makefile.am | 2 +- + ONX/Makefile.am | 1 + + OneE/Makefile.am | 2 +- + QCTC/Makefile.am | 2 +- + SCFeqs/Makefile.am | 2 +- + configure.ac | 12 ++++++++---- + make.inc | 2 +- + tests/Makefile.am | 8 ++++---- + tools/Makefile.am | 2 +- + 10 files changed, 20 insertions(+), 15 deletions(-) + +diff --git a/FreeON/Makefile.am b/FreeON/Makefile.am +index 18e0283..12db056 100644 +--- a/FreeON/Makefile.am ++++ b/FreeON/Makefile.am +@@ -50,7 +50,7 @@ FreeON_DEPENDENCIES = $(LIBRARY_DEPENDENCY_FILES) + + SOURCES_DEPCHECK = $(FreeON_SOURCES) + +-FreeON_LDADD = $(LDADD_MODULES) ++FreeON_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + AM_CPPFLAGS += \ + -DFREEON_BASISSETS=\"$(datadir)/$(PACKAGE)/BasisSets\" \ +diff --git a/HiCu/Makefile.am b/HiCu/Makefile.am +index 1847354..cc4ebef 100644 +--- a/HiCu/Makefile.am ++++ b/HiCu/Makefile.am +@@ -27,7 +27,7 @@ EXTRA_DIST = \ + MMA/CubeRules/RuleD.Inc \ + MMA/CubeRules/RuleE.Inc + +-LDADD = $(LDADD_MODULES) ++LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + EXTRA_INCLUDES = -I$(top_srcdir)/Modules/MMA/Functionals + AM_CPPFLAGS += -DRULE7 -DEXPLICIT_SOURCE +diff --git a/ONX/Makefile.am b/ONX/Makefile.am +index 4d25029..b27b149 100644 +--- a/ONX/Makefile.am ++++ b/ONX/Makefile.am +@@ -61,6 +61,7 @@ EXTRA_INCLUDES = \ + + LDADD = \ + $(LDADD_MODULES) \ ++ $(LAPACK_LIBS) \ + $(builddir)/../TwoE/libfreeonTwoE.la + + # In case we have ctags installed, make the necessary tags files. +diff --git a/OneE/Makefile.am b/OneE/Makefile.am +index 784bede..ea86ae7 100644 +--- a/OneE/Makefile.am ++++ b/OneE/Makefile.am +@@ -46,7 +46,7 @@ EXTRA_DIST = \ + MMA/QQuad32.Inc \ + MMA/QQuad64.Inc + +-LDADD = $(LDADD_MODULES) ++LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + EXTRA_INCLUDES = -I$(srcdir)/MMA + +diff --git a/QCTC/Makefile.am b/QCTC/Makefile.am +index 3ec39f0..53c358c 100644 +--- a/QCTC/Makefile.am ++++ b/QCTC/Makefile.am +@@ -105,7 +105,7 @@ EXTRA_DIST = \ + PBCTensor/Majik_Kubic_WS2.Inc + + EXTRA_INCLUDES = -I$(top_builddir)/OneE -I$(top_srcdir)/Modules/MMA/LookUpTables_800_6x +-LDADD = $(LDADD_MODULES) libktrax.la ++LDADD = $(LDADD_MODULES) libktrax.la $(LAPACK_LIBS) + + # In case we have ctags installed, make the necessary tags files. + .PHONY : tags +diff --git a/SCFeqs/Makefile.am b/SCFeqs/Makefile.am +index 2ee640f..709f220 100644 +--- a/SCFeqs/Makefile.am ++++ b/SCFeqs/Makefile.am +@@ -57,7 +57,7 @@ SOURCES_DEPCHECK = \ + $(P2Use_SOURCES) \ + $(DIIS_SOURCES) + +-LDADD = $(LDADD_MODULES) ++LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + # In case we have ctags installed, make the necessary tags files. + .PHONY : tags +diff --git a/configure.ac b/configure.ac +index e0c6a77..726c880 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -784,12 +784,16 @@ END PROGRAM test_compiler + you use a version >= 4.2.0])]) + + # Check for BLAS. +-AC_SEARCH_LIBS([dgemm], [blas], [], +- [AC_MSG_FAILURE([specify the location of dgemm()])]) ++PKG_CHECK_MODULES([BLAS],[blas],[], ++ AC_SEARCH_LIBS([dgemm], [blas], [], ++ [AC_MSG_FAILURE([specify the location of dgemm()])]) ++ ) + + # Check for LAPACK. +-AC_SEARCH_LIBS([dsyev], [lapack], [], +- [AC_MSG_FAILURE([specify the library that contains dsyev()])]) ++PKG_CHECK_MODULES([LAPACK],[lapack],[], ++ AC_SEARCH_LIBS([dsyev], [lapack], [], ++ [AC_MSG_FAILURE([specify the library that contains dsyev()])]) ++ ) + + AC_ARG_VAR([H5CC], [h5cc compiler wrapper command]) + +diff --git a/make.inc b/make.inc +index cf35e40..5766ff9 100644 +--- a/make.inc ++++ b/make.inc +@@ -9,7 +9,7 @@ AM_CPPFLAGS = @AM_CPPFLAGS@ + # Fix for bug in autoconf-2.59 + builddir = . + +-LDADD_MODULES = $(top_builddir)/Modules/libfreeonmodules.la ++LDADD_MODULES = $(top_builddir)/Modules/libfreeonmodules.la $(LAPACK_MODULES) + + # On filesystems which are case-insensitive (which really means HFS+ on OS X) + # we can not preprocess into a filename that differs by the case only, i.e. .C +diff --git a/tests/Makefile.am b/tests/Makefile.am +index 6bd89f2..ae9da60 100644 +--- a/tests/Makefile.am ++++ b/tests/Makefile.am +@@ -7,16 +7,16 @@ noinst_PROGRAMS = \ + sendReceive_HGRho + + sleeper_SOURCES = sleeper.F90 +-sleeper_LDADD = $(LDADD_MODULES) ++sleeper_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + lock_SOURCES = lock.F90 +-lock_LDADD = $(LDADD_MODULES) ++lock_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + sendReceive_DBL_RNK2_SOURCES = sendReceive_DBL_RNK2.F90 +-sendReceive_DBL_RNK2_LDADD = $(LDADD_MODULES) ++sendReceive_DBL_RNK2_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + sendReceive_HGRho_SOURCES = sendReceive_HGRho.F90 +-sendReceive_HGRho_LDADD = $(LDADD_MODULES) ++sendReceive_HGRho_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + if HAVE_MPIRUN + MPI_TESTS = locktest +diff --git a/tools/Makefile.am b/tools/Makefile.am +index e0baaff..a6b18b2 100644 +--- a/tools/Makefile.am ++++ b/tools/Makefile.am +@@ -19,7 +19,7 @@ python_PYTHON = \ + bin_PROGRAMS = printBCSR convertBCSR + + printBCSR_SOURCES = printBCSR.F90 +-printBCSR_LDADD = $(top_builddir)/Modules/libfreeonmodules.la ++printBCSR_LDADD = $(top_builddir)/Modules/libfreeonmodules.la $(LAPACK_LIBS) + + convertBCSR_SOURCES = \ + convertBCSR.cc \ diff --git a/sci-chemistry/freeon/freeon-1.0.10.ebuild b/sci-chemistry/freeon/freeon-1.0.10.ebuild new file mode 100644 index 000000000000..f19ae3f6fb89 --- /dev/null +++ b/sci-chemistry/freeon/freeon-1.0.10.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 +FORTRAN_STANDARD=90 +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) + +inherit autotools-utils fortran-2 python-any-r1 + +DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry" +HOMEPAGE="http://www.freeon.org" +SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${PN}-${PV}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + sci-libs/hdf5 + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND} + ${PYTHON_DEPS}" diff --git a/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild b/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild new file mode 100644 index 000000000000..9a847d58768e --- /dev/null +++ b/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 +FORTRAN_STANDARD=90 +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) + +inherit autotools-utils fortran-2 python-any-r1 + +DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry" +HOMEPAGE="http://www.freeon.org" +SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${PN}-${PV}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + sci-libs/hdf5 + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND} + ${PYTHON_DEPS}" + +PATCHES=( "${FILESDIR}"/${P}-blas.patch ) diff --git a/sci-chemistry/freeon/metadata.xml b/sci-chemistry/freeon/metadata.xml new file mode 100644 index 000000000000..eba82069680b --- /dev/null +++ b/sci-chemistry/freeon/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <longdescription lang="en"> + FreeON is an experimental, open source (GPL) suite of programs for linear scaling quantum chemistry. + </longdescription> + <herd>sci-chemistry</herd> + <maintainer> + <email>nicolasbock@gentoo.org</email> + <name>Nicolas Bock</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/gabedit/Manifest b/sci-chemistry/gabedit/Manifest new file mode 100644 index 000000000000..545d0a84c3ae --- /dev/null +++ b/sci-chemistry/gabedit/Manifest @@ -0,0 +1,3 @@ +DIST GabeditSrc246.tar.gz 1964406 SHA256 3881df1f2d4788d4b3660e7d8af0f7318223dd50194fd9ed0072dd58a6beaa12 SHA512 fbd92ff532ce21e97dcc2d012927fb0d19f4634956e88122a8e9a41e9484592ede455c3a88670cbd1c6387a4d0916425f897d2ade1957ebf4b25b89c7365a076 WHIRLPOOL 12be8d5299e6adcb63e4c989542f2fae02136a18bf515ded7ce8f7b3ab4e69f9fb085778be0bd5589b9ae42b7fd80c5ea7fa451a24377e5feedeb09ddff7a6b7 +DIST GabeditSrc247.tar.gz 1990187 SHA256 e9f84aae6751146f72e5cd8d3f33ec68f057f720edc68e3a89d53c5a2c3c9020 SHA512 a562dd650f9dc90a3c28a6d6b45212dc1d945548c9021f84e25a96022e67f95309030ded30bc20c052526783d0613f328830c640955822237828fcbac6d91b95 WHIRLPOOL f6a69e8e6a60fb48ef23849538a8718f507abc4e09de97abe10016ecf7b4ae101c09135f2762d7db7d764c4a66f9a268bd194ece9f05d6162b94a70b36ccec7a +DIST GabeditSrc248.tar.gz 1992373 SHA256 38d6437a18280387b46fd136f2201a73b33e45abde13fa802c64806b6b64e4d3 SHA512 d06b54693c4887e3cecb6bb20b98307db8aeb7f32ff87b85af536a4034f2d6af04f30809c04e29ed6fb4744e6290dcd276c9f85b2940daa71a595f6bd5f154da WHIRLPOOL c47cf238b7080dbeddb3992162e6bb31f17a33623299a0bc4608aa86d2d4ff71f18159f3ca952d71251b039ace9bca0d3736a56af3e1dc8305200395c2a422e3 diff --git a/sci-chemistry/gabedit/files/CONFIG.Gentoo b/sci-chemistry/gabedit/files/CONFIG.Gentoo new file mode 100644 index 000000000000..9cf387c752eb --- /dev/null +++ b/sci-chemistry/gabedit/files/CONFIG.Gentoo @@ -0,0 +1,14 @@ +GTKLIB = `pkg-config --libs gtk+-2.0 gtkglext-1.0` +GTKCFLAGS = `pkg-config --cflags gtk+-2.0 gtkglext-1.0` +OGLLIB = `pkg-config --libs glu` +OGLCFLAGS = `pkg-config --cflags glu` +X11LIB = `pkg-config --libs x11` +LIBPTHREAD = -lpthread +RM = rm -f +MAKE = make +MKDIR = mkdir -p +WIN32LIB = + +#DRAWGEOMGL= +DRAWGEOMGL=-DDRAWGEOMGL + diff --git a/sci-chemistry/gabedit/files/gabedit-2.4.2-gold.patch b/sci-chemistry/gabedit/files/gabedit-2.4.2-gold.patch new file mode 100644 index 000000000000..68823d0d7663 --- /dev/null +++ b/sci-chemistry/gabedit/files/gabedit-2.4.2-gold.patch @@ -0,0 +1,16 @@ + Makefile | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/Makefile b/Makefile +index ae08e60..eee2b46 100644 +--- a/Makefile ++++ b/Makefile +@@ -62,7 +62,7 @@ all: gabedit + gabedit: $(SUBDIRS)
+ $(MKDIR) tmp
+ cp $(OBJECTS) tmp
+- $(CC) $(LDFLAGS) tmp/*.o -o gabedit $(GLTOPS) $(X11LIB) $(GTKLIB) $(OGLLIB) $(JPEGLIB) $(LIBPTHREAD) $(WIN32LIB) $(OMPLIB) -g
++ $(CC) $(LDFLAGS) tmp/*.o -o gabedit $(GLTOPS) $(X11LIB) $(GTKLIB) $(OGLLIB) $(JPEGLIB) $(LIBPTHREAD) $(WIN32LIB) $(OMPLIB) -g -lm
+ @$(RMTMP) > ptmp
+ rmdir tmp
+ @$(RM) ptmp
diff --git a/sci-chemistry/gabedit/gabedit-2.4.6.ebuild b/sci-chemistry/gabedit/gabedit-2.4.6.ebuild new file mode 100644 index 000000000000..2b6d8659c53c --- /dev/null +++ b/sci-chemistry/gabedit/gabedit-2.4.6.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +MY_PN=${PN/g/G} +MY_PV=$(delete_all_version_separators) +MY_P="${MY_PN}Src${MY_PV}" + +DESCRIPTION="GUI for computational chemistry packages" +HOMEPAGE="http://gabedit.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="openmp" + +RDEPEND=" + dev-libs/glib:2 + x11-libs/cairo + x11-libs/gdk-pixbuf:2 + x11-libs/gtk+:2 + x11-libs/gtkglext + x11-libs/gl2ps + x11-libs/pango + virtual/opengl + virtual/glu" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -i "/rmdir tmp/d" "${S}"/Makefile || die + sed \ + -e "/GTK_DISABLE_DEPRECATED/s:define:undef:g" \ + -i "${S}/Config.h" || die + sed -e 's:-g::g' -i Makefile || die + cp "${FILESDIR}"/CONFIG.Gentoo "${S}"/CONFIG + + if use openmp && tc-has-openmp; then + cat <<- EOF >> "${S}/CONFIG" + OMPLIB=-fopenmp + OMPCFLAGS=-DENABLE_OMP -fopenmp + EOF + fi + echo "COMMONCFLAGS = ${CFLAGS} -DENABLE_DEPRECATED \$(OMPCFLAGS) \$(DRAWGEOMGL)" >> CONFIG + + tc-export CC +} + +src_compile() { + emake clean + emake external_gl2ps=1 +} + +src_install() { + local size + dobin ${PN} + dodoc ChangeLog + for size in 16 24 32 48; do + doicon -s ${size} icons/Gabedit${size}.* + done +} diff --git a/sci-chemistry/gabedit/gabedit-2.4.7.ebuild b/sci-chemistry/gabedit/gabedit-2.4.7.ebuild new file mode 100644 index 000000000000..bdfd10250b7d --- /dev/null +++ b/sci-chemistry/gabedit/gabedit-2.4.7.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +MY_PN=${PN/g/G} +MY_PV=$(delete_all_version_separators) +MY_P="${MY_PN}Src${MY_PV}" + +DESCRIPTION="GUI for computational chemistry packages" +HOMEPAGE="http://gabedit.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="openmp" + +RDEPEND=" + dev-libs/glib:2 + x11-libs/cairo + x11-libs/gdk-pixbuf:2 + x11-libs/gtk+:2 + x11-libs/gtkglext + x11-libs/gl2ps + x11-libs/pango + virtual/opengl + virtual/glu" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -i "/rmdir tmp/d" "${S}"/Makefile || die + sed \ + -e "/GTK_DISABLE_DEPRECATED/s:define:undef:g" \ + -i "${S}/Config.h" || die + sed -e 's:-g::g' -i Makefile || die + cp "${FILESDIR}"/CONFIG.Gentoo "${S}"/CONFIG + + if use openmp && tc-has-openmp; then + cat <<- EOF >> "${S}/CONFIG" + OMPLIB=-fopenmp + OMPCFLAGS=-DENABLE_OMP -fopenmp + EOF + fi + echo "COMMONCFLAGS = ${CFLAGS} -DENABLE_DEPRECATED \$(OMPCFLAGS) \$(DRAWGEOMGL)" >> CONFIG + + tc-export CC +} + +src_compile() { + emake clean + emake external_gl2ps=1 +} + +src_install() { + local size + dobin ${PN} + dodoc ChangeLog + for size in 16 24 32 48; do + doicon -s ${size} icons/Gabedit${size}.* + done +} diff --git a/sci-chemistry/gabedit/gabedit-2.4.8.ebuild b/sci-chemistry/gabedit/gabedit-2.4.8.ebuild new file mode 100644 index 000000000000..9d3e7d191505 --- /dev/null +++ b/sci-chemistry/gabedit/gabedit-2.4.8.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +MY_PN=${PN/g/G} +MY_PV=$(delete_all_version_separators) +MY_P="${MY_PN}Src${MY_PV}" + +DESCRIPTION="GUI for computational chemistry packages" +HOMEPAGE="http://gabedit.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="openmp" + +RDEPEND=" + dev-libs/glib:2 + x11-libs/cairo + x11-libs/gdk-pixbuf:2 + x11-libs/gtk+:2 + x11-libs/gtkglext + x11-libs/gl2ps + x11-libs/pango + virtual/opengl + virtual/glu" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -i "/rmdir tmp/d" "${S}"/Makefile || die + sed \ + -e "/GTK_DISABLE_DEPRECATED/s:define:undef:g" \ + -i "${S}/Config.h" || die + sed -e 's:-g::g' -i Makefile || die + cp "${FILESDIR}"/CONFIG.Gentoo "${S}"/CONFIG + + if use openmp && tc-has-openmp; then + cat <<- EOF >> "${S}/CONFIG" + OMPLIB=-fopenmp + OMPCFLAGS=-DENABLE_OMP -fopenmp + EOF + fi + echo "COMMONCFLAGS = ${CFLAGS} -DENABLE_DEPRECATED \$(OMPCFLAGS) \$(DRAWGEOMGL)" >> CONFIG + + tc-export CC +} + +src_compile() { + emake clean + emake external_gl2ps=1 +} + +src_install() { + local size + dobin ${PN} + dodoc ChangeLog + for size in 16 24 32 48; do + doicon -s ${size} icons/Gabedit${size}.* + done +} diff --git a/sci-chemistry/gabedit/metadata.xml b/sci-chemistry/gabedit/metadata.xml new file mode 100644 index 000000000000..574871e7938f --- /dev/null +++ b/sci-chemistry/gabedit/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <description>Tree Proxy for Max</description> + </maintainer> + <upstream> + <remote-id type="sourceforge">gabedit</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/gamess/Manifest b/sci-chemistry/gamess/Manifest new file mode 100644 index 000000000000..d6cb7f6ac130 --- /dev/null +++ b/sci-chemistry/gamess/Manifest @@ -0,0 +1,2 @@ +DIST gamess-20110811.1.tar.gz 21105973 SHA256 b7b7af0eb141c140da31bcd9ef29fbafd82fbe45c087cadd7948d4c0a3cefe57 +DIST tinker.tar.Z 1902051 SHA256 7c52454ade7dd81d1b70a7e7722eda3672c644a3ba67ab444824a0212b4a7a8c diff --git a/sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch b/sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch new file mode 100644 index 000000000000..7bf5797bf513 --- /dev/null +++ b/sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch @@ -0,0 +1,263 @@ +diff -urN gamess.orig/comp gamess/comp +--- gamess.orig/comp 2011-08-11 17:37:48.000000000 +0200 ++++ gamess/comp 2011-10-11 15:17:23.349829478 +0200 +@@ -1444,7 +1444,7 @@ + # g77 does not support FORTRAN logical units above 99, or 128 bit math. + # + case g77: +- set OPT = '-O2' ++ set gentoo-OPT = '-O2' + if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3 + if ($MODULE == zheev) set OPT='-O0' # defensive compiling + if (($MODULE == qeigen) || ($MODULE == int2c)) then +@@ -1474,7 +1474,7 @@ + # -std=legacy suppresses warnings about use of f77 constructs. + # + case gfortran: +- set OPT='-O2' ++ set gentoo-OPT = '-O2' + if ($MODULE == zheev) set OPT='-O0' # defensive compiling + if ($MODULE == pcmcv2) set OPT='-O1' # EFP+CPCM, ala Francois, v4.1.2 + if (($MODULE == qeigen) || ($MODULE == int2c)) then +@@ -1500,7 +1500,7 @@ + # optimizations in 32 bit mode, as a function of the ifort version. + # + case ifort: +- set OPT = '-O3' ++ set gentoo-OPT = '-O2' + if ($MODULE == delocl) set OPT='-O0' # from Cheol + if ($MODULE == prpamm) set OPT='-O0' # for exam13 + if ($MODULE == zheev) set OPT='-O0' +@@ -1617,7 +1617,7 @@ + case gfortran: + # -finit-real=<zero|inf|-inf|nan> could be interesting debug opt + # -fno-automatic forces static storage of all local variables +- set OPT='-O2' ++ set gentoo-OPT = '-O2' + if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS" + if ($MODULE == zheev) set OPT='-O0' # defensive compiling + if (($MODULE == qeigen) || ($MODULE == int2c)) then +@@ -1648,7 +1648,7 @@ + # -WB means warn but don't fail on out-of-bounds array references + # -ftz flushes underflow results to zero + # +- set OPT = '-O2' ++ set gentoo-OPT = '-O2' + if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS" + # alas, I'm so tired of hearing about so many versions failing to + # diagonalize, that this time critical code is run w/o optimization. +diff -urN gamess.orig/compall gamess/compall +--- gamess.orig/compall 2011-05-17 22:53:33.000000000 +0200 ++++ gamess/compall 2011-10-11 12:13:30.041087251 +0200 +@@ -84,12 +84,11 @@ + endif + endif + if ($TARGET == linux32) set extraflags='-DLINUX32' +-if ($TARGET == linux64) then ++if ($TARGET == linux64) then ++ set chip=`uname -m` + # Ubuntu uses the non-standard -m flag, its -p replies "unknown" +- set chip=`uname -p` +- if ($chip == unknown) set chip=`uname -m` +- if ($chip == x86_64) set extraflags='-DLINUX64 -m64' +- if ($chip == ia64) set extraflags='-DLINUX64' # this always 64 bits ++ if ($chip == x86_64) set extraflags='-DLINUX64 -m64' ++ if ($chip == ia64) set extraflags='-DLINUX64' # this always 64 bits + endif + if ($TARGET == mac32) set extraflags='-DLINUX32' + if ($TARGET == mac64) set extraflags='-DLINUX64 -m64 -I/usr/include/malloc' +diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi +--- gamess.orig/ddi/compddi 2011-02-15 21:31:30.000000000 +0100 ++++ gamess/ddi/compddi 2011-10-11 12:23:45.513796580 +0200 +@@ -634,7 +634,7 @@ + + set FORTRAN=$GMS_FORTRAN # might be g77, gfortran, ifort, pgf77, f2c + +- set CC = 'gcc' ++ set gentoo-CC = 'gcc' + set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./" + set CLIBS = "-lpthread" + +@@ -687,7 +687,7 @@ + set ARCH='-m64' + if (`uname -p` == ia64) set ARCH='' + +- set CC = 'gcc' ++ set gentoo-CC = 'gcc' + set CFLAGS = "-DLINUX $ARCH -O3 -fstrict-aliasing -I./" + set CLIBS = "-lpthread" + +diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c +--- gamess.orig/ddi/kickoff/ddikick.c 2008-05-06 12:16:12.000000000 +0200 ++++ gamess/ddi/kickoff/ddikick.c 2011-10-11 12:25:11.862714681 +0200 +@@ -105,7 +105,7 @@ + remoteshell = argv[++i]; + } else { + if((remoteshell = getenv("DDI_RSH")) == NULL) { +- remoteshell = (char *) strdup("rsh"); ++ remoteshell = (char *) strdup("ssh"); + } + } + +diff -urN gamess.orig/lked gamess/lked +--- gamess.orig/lked 2011-08-11 17:41:02.000000000 +0200 ++++ gamess/lked 2011-10-11 12:26:38.564634821 +0200 +@@ -53,7 +53,7 @@ + # + # 3. optional Nuclear-Electronic Orbital method, using NEO code + # +-set NEO=false ++set NEO=true + # + # 4. optional Nvidia/CUDA code, for closed shell SCF Fock construction + # see ~/gamess/libcchem/aaa.readme.1st for more information +@@ -356,17 +356,17 @@ + switch ($GMS_FORTRAN) + case g77: + set LDR='g77' +- set LDOPTS=' ' # add '-Wl,-M' to see load map ++ set gentoo-LDOPTS=' ' # add '-Wl,-M' to see load map + set FORTLIBS=' ' + breaksw + case gfortran: + set LDR='gfortran' +- set LDOPTS=' ' ++ set gentoo-LDOPTS=' ' + set FORTLIBS=' ' + breaksw + case ifort: + set LDR='ifort' +- set LDOPTS=' ' # add '-Wl,-M' to see load map ++ set gentoo-LDOPTS=' ' # add '-Wl,-M' to see load map + set FORTLIBS='-Vaxlib' + breaksw + case pgf77: +@@ -376,7 +376,7 @@ + breaksw + case f2c: + set LDR='gcc' +- set LDOPTS=' ' ++ set gentoo-LDOPTS=' ' + set FORTLIBS='-lf2c -lm' + breaksw + default: +@@ -427,12 +427,7 @@ + # Otherwise, attempt a link against shared object libs. + # See the 64 bit Atlas below for a way to fix the linker's + # not being able to locate -lf77blas, if that happens. +- if (-e $GMS_MATHLIB_PATH/libf77blas.a) then +- set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a" +- set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a" +- else +- set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas" +- endif ++ set MATHLIBS=`${PKG_CONFIG} --libs blas` + set BLAS=' ' + breaksw + +@@ -466,12 +461,12 @@ + switch ($GMS_FORTRAN) + case gfortran: + set LDR='gfortran' +- set LDOPTS=' ' ++ set gentoo-LDOPTS=' ' + set FORTLIBS=' ' + breaksw + case ifort: + set LDR='ifort' +- set LDOPTS='-i8' # -Wl,-M generates a load map ++ set gentoo-LDOPTS=' ' # -Wl,-M generates a load map + # this auxiliary library seems to have disappeared in ifort 10 + set FORTLIBS=' ' + if($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib' +@@ -556,12 +551,7 @@ + # ln -s liblapack_atlas.so.3.0 liblapack.so + # ln -s liblapack.so.3.0 liblapack.so + # It is strange the RPM's don't do these soft links for us. +- if (-e $GMS_MATHLIB_PATH/libf77blas.a) then +- set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a" +- set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a" +- else +- set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas" +- endif ++ set MATHLIBS=`${PKG_CONFIG} --libs blas` + set BLAS=' ' + breaksw + +diff -urN gamess.orig/runall gamess/runall +--- gamess.orig/runall 2009-02-28 00:57:18.000000000 +0100 ++++ gamess/runall 2011-10-11 12:27:32.195586568 +0200 +@@ -10,7 +10,6 @@ + # + # Only the following two lines need to be customized: + # +-chdir /u1/mike/gamess + set VERNO=00 + # + # Loop over all Ntest jobs supplied with GAMESS +@@ -27,7 +26,7 @@ + gms -v $VERNO -q ti -l exam$NUM.log exam$NUM + sleep 5 + else +- ./rungms exam$NUM $VERNO 1 >& exam$NUM.log ++ rungms exam$NUM $VERNO 1 >& exam$NUM.log + endif + @ i++ + end +diff -urN gamess.orig/rungms gamess/rungms +--- gamess.orig/rungms 2011-08-04 21:03:11.000000000 +0200 ++++ gamess/rungms 2011-10-11 12:30:05.244448126 +0200 +@@ -55,7 +55,7 @@ + # one for LoadLeveler "ll-gms" on the IBM SP line. + # + set TARGET=sockets +-set SCR=/scr/$USER ++set SCR=`pwd` + # + set JOB=$1 # name of the input file xxx.inp, give only the xxx part + set VERNO=$2 # revision number of the executable created by 'lked' step +@@ -144,7 +144,7 @@ + # used by the NEO method. See NEO's documentation for more details. + # + set echo +-setenv AUXDATA ~mike/gamess/auxdata ++setenv AUXDATA /usr/share/gamess + setenv EXTBAS /dev/null + setenv NUCBAS /dev/null + setenv POSBAS /dev/null +@@ -153,12 +153,12 @@ + setenv MCPPATH $AUXDATA/MCP + setenv BASPATH $AUXDATA/BASES + setenv QUANPOL $AUXDATA/QUANPOL +-setenv MAKEFP ~$USER/scr/$JOB.efp +-setenv GAMMA ~$USER/scr/$JOB.gamma +-setenv TRAJECT ~$USER/scr/$JOB.trj +-setenv RESTART ~$USER/scr/$JOB.rst ++setenv MAKEFP $SCR/$JOB.efp ++setenv GAMMA $SCR/$JOB.gamma ++setenv TRAJECT $SCR/$JOB.trj ++setenv RESTART $SCR/$JOB.rst + setenv INPUT $SCR/$JOB.F05 +-setenv PUNCH ~$USER/scr/$JOB.dat ++setenv PUNCH $SCR/$JOB.dat + setenv AOINTS $SCR/$JOB.F08 + setenv MOINTS $SCR/$JOB.F09 + setenv DICTNRY $SCR/$JOB.F10 +@@ -347,7 +347,7 @@ + if (null$4 == null) set ELGNAME=ELGFILE + set echo + setenv AOINTS $SCR/$ELGNAME.F08 +- setenv ELGDOS ~$USER/scr/$JOB.ldos ++ setenv ELGDOS $SCR/$JOB.ldos + setenv ELGDAT $SCR/$ELGNAME.F71 + setenv ELGPAR $SCR/$ELGNAME.F72 + setenv ELGCUT $SCR/$ELGNAME.F74 +@@ -500,7 +500,7 @@ + if ($os == AIX) set GMSPATH=/u1/mike/gamess + if ($os == Darwin) set GMSPATH=/Users/mike/desktop/gamess + if ($os == HP-UX) set GMSPATH=/zr/mike/gamess +- if ($os == Linux) set GMSPATH=/cu/mike/gamess ++ if ($os == Linux) set GMSPATH=/usr/bin + if ($os == OSF1) set GMSPATH=/in/mike/gamess + if ($os == SunOS) set GMSPATH=/hf/mike/gamess + # special compilation for Sun E450 uSPARC (uname also= SunOS) diff --git a/sci-chemistry/gamess/files/gamess-checktst.patch b/sci-chemistry/gamess/files/gamess-checktst.patch new file mode 100644 index 000000000000..9fc1547e4540 --- /dev/null +++ b/sci-chemistry/gamess/files/gamess-checktst.patch @@ -0,0 +1,21 @@ +--- gamess.orig/tools/checktst/checktst 2008-12-30 16:33:09.000000000 +0100 ++++ gamess/tools/checktst/checktst 2011-10-11 22:06:26.019798622 +0200 +@@ -6,7 +6,6 @@ + # + # Only the path name in the very next line needs to be customized. + # +-set GMSPATH=~/gamess + + # The Ntest outputs are assumed to be named exam01.log, exam02.log, ... + # but the user will be allowed to specify the directory containing them. +@@ -66,8 +65,8 @@ + setenv tolW 0.1 + setenv tolX 0.00001 + +-set script=$GMSPATH/tools/checktst/exam +-setenv chkabs $GMSPATH/tools/checktst/chkabs ++set script=./exam ++setenv chkabs ./chkabs + + # If we don't see the message about GAMESS exiting normally, + # then there is surely a mistake, and we want to focus the diff --git a/sci-chemistry/gamess/files/gamess-qmmm-tinker-fix-idate.patch b/sci-chemistry/gamess/files/gamess-qmmm-tinker-fix-idate.patch new file mode 100644 index 000000000000..34f291382d41 --- /dev/null +++ b/sci-chemistry/gamess/files/gamess-qmmm-tinker-fix-idate.patch @@ -0,0 +1,20 @@ +diff -urN gamess/tinker.orig/Libtad.f gamess/tinker/Libtad.f +--- gamess/tinker.orig/Libtad.f 2010-05-12 21:41:56.000000000 +0400 ++++ gamess/tinker/Libtad.f 2010-12-08 01:05:31.000000000 +0300 +@@ -1332,11 +1332,15 @@ + c and for Macintosh under Absoft Pro Fortran 5.0 + c + integer hms(3) ++ integer tarray(3) + call itime (hms) + hour = hms(1) + minute = hms(2) + second = hms(3) +- call idate (month,day,year) ++ call idate (tarray) ++ month = tarray(1) ++ day = tarray(2) ++ year = tarray(3) + c + c code for IBM RS/6000 under AIX appends an underscore + c diff --git a/sci-chemistry/gamess/gamess-20110811.1.ebuild b/sci-chemistry/gamess/gamess-20110811.1.ebuild new file mode 100644 index 000000000000..363353adb793 --- /dev/null +++ b/sci-chemistry/gamess/gamess-20110811.1.ebuild @@ -0,0 +1,337 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 flag-o-matic pax-utils toolchain-funcs + +DESCRIPTION="A powerful quantum chemistry package" +LICENSE="gamess" +HOMEPAGE="http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html" +SRC_URI=" + ${P}.tar.gz + qmmm-tinker? ( tinker.tar.Z )" + +SLOT="0" +# NOTE: PLEASE do not stabilize gamess. It does not make sense +# since the tarball has fetch restrictions and upstream only +# provides the latest version. In other words: As soon as a +# new version comes out the stable version will be useless since +# users can not get at the tarball any more. +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="mpi neo pax_kernel qmmm-tinker" + +CDEPEND=" + app-shells/tcsh + mpi? ( virtual/mpi ) + virtual/blas" +DEPEND="${CDEPEND} + virtual/pkgconfig" +RDEPEND="${CDEPEND} + net-misc/openssh" + +S="${WORKDIR}/${PN}" + +RESTRICT="fetch" + +GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html" +GAMESS_VERSION="1 AUG 2011 (R1)" + +pkg_nofetch() { + echo + elog "Please download ${PN}-current.tar.gz from" + elog "${GAMESS_DOWNLOAD}." + elog "Be sure to select the version ${GAMESS_VERSION} tarball!!" + elog "Then move the tarball to" + elog "${DISTDIR}/${P}.tar.gz" + if use qmmm-tinker ; then + elog "Also download http://www.msg.ameslab.gov/GAMESS/tinker.tar.Z" + elog "and place tinker.tar.Z to ${DISTDIR}" + fi + echo +} + +get_fcomp() { + case $(tc-getFC) in + *gfortran* ) + FCOMP="gfortran" ;; + ifort ) + FCOMP="ifc" ;; + * ) + FCOMP=$(tc-getFC) ;; + esac +} + +pkg_setup() { + fortran-2_pkg_setup + get_fcomp + # currently amd64 is only supported with gfortran + if [[ "${ARCH}" == "amd64" ]] && [[ ${FCOMP} != *gfortran* ]]; + then die "You will need gfortran to compile gamess on amd64" + fi + + # note about qmmm-tinker + if use qmmm-tinker; then + einfo "By default MM subsistem is restricted to 1000 atoms" + einfo "if you want larger MM subsystems then you should set" + einfo "QMMM_GAMESS_MAXMM variable to needed value in your make.conf" + einfo "By default maximum number of atom classes types and size of" + einfo "hessian are restricted to 250, 500 and 1000000 respectively" + einfo "If you want larger sizes set:" + einfo "QMMM_GAMESS_MAXCLASS" + einfo "QMMM_GAMESS_MAXCTYP" + einfo "QMMM_GAMESS_MAXHESS" + einfo "in your make.conf" + fi + + #note about mpi + if use mpi; then + ewarn "" + ewarn "You should adjust rungms script for your mpi implentation" + ewarn "because deafult one will not work" + ewarn "" + fi +} + +src_unpack() { + unpack ${A} + + if use qmmm-tinker; then + mv tinker gamess/ || die "failed to move tinker directory" + fi +} + +src_prepare() { + tc-export PKG_CONFIG + # apply LINUX-arch patches to gamess makesfiles + epatch "${FILESDIR}/${P}.gentoo.patch" + epatch "${FILESDIR}/${PN}-checktst.patch" + # select arch + # NOTE: please leave lked alone; it should be good as is!! + cd "${S}" + local active_arch; + if [[ "${ARCH}" == "amd64" ]]; then + active_arch="linux64"; + else + active_arch="linux32"; + fi + + # for hardened-gcc let't turn off ssp, since it breakes + # a few routines + if use pax_kernel && [[ ${FCOMP} == g77 ]]; then + FFLAGS="${FFLAGS} -fno-stack-protector-all" + fi + + # Enable mpi stuff + if use mpi; then + sed -e "s:set COMM = sockets:set COMM = mpi:g" \ + -i ddi/compddi || die "Enabling mpi build failed" + sed -e "s:MPI_INCLUDE_PATH = ' ':MPI_INCLUDE_PATH = '-I/usr/include ':g" \ + -i ddi/compddi || die "Enabling mpi build failed" + sed -e "s:MSG_LIBRARIES='../ddi/libddi.a -lpthread':MSG_LIBRARIES='../ddi/libddi.a -lmpi -lpthread':g" \ + -i lked || die "Enabling mpi build failed" + fi + + # enable NEO + if use neo; then + sed -e "s:NEO=false:NEO=true:" -i compall lked || \ + die "Failed to enable NEO code" + else + sed -e "s:NEO=true:NEO=false:" -i compall lked || \ + die "Failed to disable NEO code" + fi + # enable GAMESS-qmmm + if use qmmm-tinker; then + epatch "${FILESDIR}/${PN}-qmmm-tinker-fix-idate.patch" + sed -e "s:TINKER=false:TINKER=true:" -i compall lked || \ + die "Failed to enable TINKER code" + if [ "x$QMMM_GAMESS_MAXMM" == "x" ]; then + einfo "No QMMM_GAMESS_MAXMM set. Using default value = 1000" + else + einfo "Setting QMMM_GAMESS_MAXMM to $QMMM_GAMESS_MAXMM" + sed -e "s:maxatm=1000:maxatm=$QMMM_GAMESS_MAXMM:g" \ + -i tinker/sizes.i \ + || die "Setting QMMM_GAMESS_MAXMM failed" + sed -e "s:MAXATM=1000:MAXATM=$QMMM_GAMESS_MAXMM:g" \ + -i source/inputb.src \ + || die "Setting QMMM_GAMESS_MAXMM failed" + fi + if [ "x$QMMM_GAMESS_MAXCLASS" == "x" ]; then + einfo "No QMMM_GAMESS_MAXMM set. Using default value = 250" + else + sed -e "s:maxclass=250:maxclass=$QMMM_GAMESS_MAXCLASS:g" \ + -i tinker/sizes.i \ + || die "Setting QMMM_GAMESS_MAXCLASS failed" + fi + if [ "x$QMMM_GAMESS_MAXCTYP" == "x" ]; then + einfo "No QMMM_GAMESS_MAXCTYP set. Using default value = 500" + else + sed -e "s:maxtyp=500:maxtyp=$QMMM_GAMESS_MAXCTYP:g" \ + -i tinker/sizes.i \ + || die "Setting QMMM_GAMESS_MAXCTYP failed" + fi + if [ "x$QMMM_GAMESS_MAXHESS" == "x" ]; then + einfo "No QMMM_GAMESS_MAXHESS set. Usingdefault value = 1000000" + else + sed -e "s:maxhess=1000000:maxhess=$QMMM_GAMESS_MAXHESS:g" \ + -i tinker/sizes.i \ + || die "Setting QMMM_GAMESS_MAXHESS failed" + fi + fi + # greate proper activate sourcefile + cp "./tools/actvte.code" "./tools/actvte.f" || \ + die "Failed to create actvte.f" + sed -e "s/^\*UNX/ /" -i "./tools/actvte.f" || \ + die "Failed to perform UNX substitutions in actvte.f" + + # fix GAMESS' compall script to use proper CC + sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c \$extraflags source/zunix.c|" \ + -i compall || die "Failed setting up compall script" + + # insert proper FFLAGS into GAMESS' comp makefile + # in case we're using ifc let's strip all the gcc + # specific stuff + if [[ ${FCOMP} == "ifort" ]]; then + sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \ + -i comp || die "Failed setting up comp script" + elif ! use x86; then + sed -e "s/-malign-double //" \ + -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \ + -i comp || die "Failed setting up comp script" + else + sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \ + -i comp || die "Failed setting up comp script" + fi + + # fix up GAMESS' linker script; + sed -e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \ + -i lked || die "Failed setting up lked script" + # fix up GAMESS' ddi TCP/IP socket build + sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \ + -i ddi/compddi || die "Failed setting up compddi script" + # Creating install.info + cat > install.info <<-EOF + #!/bin/csh + setenv GMS_PATH $WORKDIR/gamess + setenv GMS_TARGET $active_arch + setenv GMS_FORTRAN $FCOMP + setenv GMS_MATHLIB atlas + setenv GMS_MATHLIB_PATH /usr/$(get_libdir)/atlas + setenv GMS_DDI_COMM sockets + EOF + +} + +src_compile() { + # build actvte + cd "${S}"/tools + ${FCOMP} -o actvte.x actvte.f || \ + die "Failed to compile actvte.x" + + # for hardened (PAX) users and ifc we need to turn + # MPROTECT off + if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then + pax-mark -PemRxS actvte.x + fi + + # build gamess + cd "${S}" + ./compall || die "compall failed" + + # build the ddi TCP/IP socket stuff + cd ${S}/"ddi" + ./compddi || die "compddi failed" + + # finally, link it all together + cd "${S}" + ./lked || die "lked failed" + + # for hardened (PAX) users and ifc we need to turn + # MPROTECT off + if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then + pax-mark -PemRxS ${PN}.00.x + fi +} + +src_install() { + # the executables + dobin ${PN}.00.x rungms \ + || die "Failed installing binaries" + if use !mpi; then + dobin ddi/ddikick.x \ + || die "Failed installing binaries" + fi + + # the docs + dodoc *.DOC qmnuc/*.DOC || die "Failed installing docs" + + # install ericftm + insinto /usr/share/${PN} + doins auxdata/ericfmt.dat || die "Failed installing ericfmt.dat" + + # install mcpdata + insinto /usr/share/${PN}/MCP + doins auxdata/MCP/* || die "Failed installing MCP" + + # install BASES + insinto /usr/share/${PN}/BASES + doins auxdata/BASES/* || die "Failed installing BASES" + + # install QUANPOL + insinto /usr/share/${PN}/QUANPOL + doins auxdata/QUANPOL/* || die "Failed installing QUANPOL" + + # install tinker params in case of qmmm + if use qmmm-tinker ; then + dodoc tinker/simomm.doc || die "Failed installing docs" + insinto /usr/share/${PN} + doins -r tinker/params51 || die "Failed to install Tinker params" + fi + + # install the tests the user should run, and + # fix up the runscript; also grab a copy of rungms + # so the user is ready to run the tests + insinto /usr/share/${PN}/tests + insopts -m0644 + doins tests/* || die "Failed installing tests" + insopts -m0744 + doins runall || die "Failed installing tests" + doins tools/checktst/checktst tools/checktst/chkabs || \ + die "Failed to install main test checker" + doins tools/checktst/exam* || \ + die "Failed to install individual test files" + + insinto /usr/share/${PN}/neotests + insopts -m0644 + doins -r qmnuc/neotests/* || die "Failed to install NEO tests" +} + +pkg_postinst() { + echo + einfo "Before you use GAMESS for any serious work you HAVE" + einfo "to run the supplied test files located in" + einfo "/usr/share/gamess/tests and check them thoroughly." + einfo "Otherwise all scientific publications resulting from" + einfo "your GAMESS runs should be immediately rejected :)" + einfo "To do so copy the content of /usr/share/gamess/tests" + einfo "to some temporary location and execute './runall'. " + einfo "Then run the checktst script in the same directory to" + einfo "validate the tests." + einfo "Please consult TEST.DOC and the other docs!" + + if [[ ${FCOMP} == "ifort" ]]; then + echo + ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away" + ewarn "from ifc-9.0 for now and use the ifc-8.1 series of" + ewarn "compilers UNLESS you can run through ALL of the " + ewarn "test cases (see above) successfully." + fi + + echo + einfo "If you want to run on more than a single CPU" + einfo "you will have to acquaint yourself with the way GAMESS" + einfo "does multiprocessor runs and adjust rungms according to" + einfo "your target network architecture." + echo +} diff --git a/sci-chemistry/gamess/metadata.xml b/sci-chemistry/gamess/metadata.xml new file mode 100644 index 000000000000..65e218a68820 --- /dev/null +++ b/sci-chemistry/gamess/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <herd>sci-chemistry</herd> + <use> + <flag name="neo">Enable NEO for nuclear basis support</flag> + <flag name="pax_kernel">Make this package work on PAX kernels</flag> + <flag name="qmmm-tinker">Enable tinker qmmm code</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/gamessq/Manifest b/sci-chemistry/gamessq/Manifest new file mode 100644 index 000000000000..de14dc2be506 --- /dev/null +++ b/sci-chemistry/gamessq/Manifest @@ -0,0 +1 @@ +DIST gamessq-1.2.tar.gz 293747 SHA256 f122cb78ba5c01d10dd20a9525215a82e4024ae3a3ec19bf895cddcfabbb246a diff --git a/sci-chemistry/gamessq/gamessq-1.2.ebuild b/sci-chemistry/gamessq/gamessq-1.2.ebuild new file mode 100644 index 000000000000..5d7745574da3 --- /dev/null +++ b/sci-chemistry/gamessq/gamessq-1.2.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +WX_GTK_VER="2.8" + +inherit eutils wxwidgets + +DESCRIPTION="Simple job manager for GAMESS-US" +HOMEPAGE="http://www.msg.chem.iastate.edu/GAMESS/GamessQ/" +SRC_URI="http://www.msg.chem.iastate.edu/GAMESS/GamessQ/download/${P}.tar.gz" + +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86" +SLOT="0" +IUSE="" + +DEPEND="x11-libs/wxGTK:${WX_GTK_VER}" +RDEPEND="${DEPEND}" + +src_install() { + default + doicon src/icons/${PN}.ico + make_desktop_entry ${PN} gamessq ${PN}.ico "Science;Education" +} diff --git a/sci-chemistry/gamessq/metadata.xml b/sci-chemistry/gamessq/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/gamessq/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/gelemental/Manifest b/sci-chemistry/gelemental/Manifest new file mode 100644 index 000000000000..6369272c939d --- /dev/null +++ b/sci-chemistry/gelemental/Manifest @@ -0,0 +1,2 @@ +DIST gelemental-1.2.0.tar.bz2 460757 SHA256 4f2797200af98d74c71db0065506f99a97820392f39f67cf3ef42de6dca3859b SHA512 2e6ef2c22b389cff69728b01e1eb397578974362356f5132098f29a9e01a64be228a24686738bd84ea575cee5aef068d9ab3d6c20233f995ccc5f1a1cb5d5673 WHIRLPOOL 6814ce64ad66a872073af31460e9938f2ac385500af9a94a60d3ce28c85bad467ef09ce9a2596e0b3e508121959b662e77cba685a6d3359a5d840a9af9fa34bb +DIST gelemental_1.2.0-8.debian.tar.gz 29877 SHA256 b03ddad5587fdfb279d570388105ea5fb3b16eebbb2626f1f293ff283456869e SHA512 83c236e3b91af304c96f28c0f12577821ee2f47c9e01fb1f3664228afb002dc19b1a71e6dcd6040d09ea991d131b147ea5b36283d8ead290d50014c15e69878c WHIRLPOOL 16bc07c03b88e7a0c161677302d2a9d2cdb74aa6baf702b0d6d2c2a6f2ec8fe21d626cc58ecb34850da8369bccb36b889f5391c013e0861c338bd68c1f38e3ca diff --git a/sci-chemistry/gelemental/files/gelemental-1.2.0-doxygen.patch b/sci-chemistry/gelemental/files/gelemental-1.2.0-doxygen.patch new file mode 100644 index 000000000000..8c904e844586 --- /dev/null +++ b/sci-chemistry/gelemental/files/gelemental-1.2.0-doxygen.patch @@ -0,0 +1,30 @@ +Author: Joachim Reichel <reichel@debian.org> +Description: Skip installing (no longer generated) .dot and .gif files +Origin: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=590382#15 +Bug-Debian: http://bugs.debian.org/590382 +Reviewed-By: Michael Banck <mbanck@debian.org> +Forwarded: no +Last-Update: 2010-09-22 + +--- a/docs/api/Makefile.am ++++ b/docs/api/Makefile.am +@@ -12,7 +12,7 @@ + install-api: $(srcdir)/html/index.html + @$(NORMAL_INSTALL) + $(mkinstalldirs) $(DESTDIR)/$(apidir) +- @dir='$(<D)'; for p in $$dir/*.html $$dir/*.css $$dir/*.png $$dir/*.gif $$dir/*.dot ; do \ ++ @dir='$(<D)'; for p in $$dir/*.html $$dir/*.css $$dir/*.png ; do \ + f="`echo $$p | sed -e 's|^.*/||'`"; \ + echo " $(INSTALL_DATA) $$p $(DESTDIR)$(apidir)/$$f"; \ + $(INSTALL_DATA) $$p $(DESTDIR)$(apidir)/$$f; \ +--- a/docs/api/Makefile.in ++++ b/docs/api/Makefile.in +@@ -393,7 +393,7 @@ + install-api: $(srcdir)/html/index.html + @$(NORMAL_INSTALL) + $(mkinstalldirs) $(DESTDIR)/$(apidir) +- @dir='$(<D)'; for p in $$dir/*.html $$dir/*.css $$dir/*.png $$dir/*.gif $$dir/*.dot ; do \ ++ @dir='$(<D)'; for p in $$dir/*.html $$dir/*.css $$dir/*.png ; do \ + f="`echo $$p | sed -e 's|^.*/||'`"; \ + echo " $(INSTALL_DATA) $$p $(DESTDIR)$(apidir)/$$f"; \ + $(INSTALL_DATA) $$p $(DESTDIR)$(apidir)/$$f; \ diff --git a/sci-chemistry/gelemental/files/gelemental-1.2.0-gcc4.3.patch b/sci-chemistry/gelemental/files/gelemental-1.2.0-gcc4.3.patch new file mode 100644 index 000000000000..8e69e98a5437 --- /dev/null +++ b/sci-chemistry/gelemental/files/gelemental-1.2.0-gcc4.3.patch @@ -0,0 +1,12 @@ +diff -Naru gelemental-1.2.0/libelemental/value.tcc gelemental-1.2.0.new/libelemental/value.tcc +--- gelemental-1.2.0/libelemental/value.tcc 2007-09-25 01:10:16.000000000 -0400 ++++ gelemental-1.2.0.new/libelemental/value.tcc 2008-10-19 10:08:35.000000000 -0400 +@@ -26,6 +26,8 @@ + #error "value.tcc must be included from value.hh." + #endif + ++#include <limits> ++ + namespace Elemental { + + diff --git a/sci-chemistry/gelemental/files/gelemental-1.2.0-glib-2.32.patch b/sci-chemistry/gelemental/files/gelemental-1.2.0-glib-2.32.patch new file mode 100644 index 000000000000..eab2ad1f194e --- /dev/null +++ b/sci-chemistry/gelemental/files/gelemental-1.2.0-glib-2.32.patch @@ -0,0 +1,46 @@ + libelemental/misc/extras.cc | 2 +- + libelemental/misc/widgets.cc | 2 +- + src/main.cc | 4 ++-- + 3 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/libelemental/misc/extras.cc b/libelemental/misc/extras.cc +index a8e5720..c042604 100644 +--- a/libelemental/misc/extras.cc ++++ b/libelemental/misc/extras.cc +@@ -21,7 +21,7 @@ + + #include <algorithm> + #include <stdexcept> +-#include <glib/gmem.h> ++#include <glib.h> + #include <glibmm/utility.h> + + namespace misc { +diff --git a/libelemental/misc/widgets.cc b/libelemental/misc/widgets.cc +index 002310c..941d881 100644 +--- a/libelemental/misc/widgets.cc ++++ b/libelemental/misc/widgets.cc +@@ -20,7 +20,7 @@ + #include "macros.hh" + #include "widgets.hh" + +-#include <glib/gmessages.h> ++#include <glib.h> + #include <gtkmm/alignment.h> + #include <gtkmm/image.h> + #include <gtkmm/label.h> +diff --git a/src/main.cc b/src/main.cc +index 41cfe03..68bbb4c 100644 +--- a/src/main.cc ++++ b/src/main.cc +@@ -26,8 +26,8 @@ + #include <clocale> + #include <iostream> + #include <locale> +-#include <glib/goption.h> +-#include <glib/gutils.h> ++#include <glib.h> ++#include <glib.h> + #include <glibmm/optionentry.h> + #include <gtk/gtkaboutdialog.h> + #include <gtk/gtkversion.h> diff --git a/sci-chemistry/gelemental/gelemental-1.2.0-r1.ebuild b/sci-chemistry/gelemental/gelemental-1.2.0-r1.ebuild new file mode 100644 index 000000000000..78bfcff23630 --- /dev/null +++ b/sci-chemistry/gelemental/gelemental-1.2.0-r1.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools-utils fdo-mime gnome2-utils eutils + +DESCRIPTION="Periodic table viewer that provides detailed information on the chemical elements" +HOMEPAGE="http://freecode.com/projects/gelemental/" +SRC_URI=" + http://www.kdau.com/files/${P}.tar.bz2 + mirror://debian/pool/main/g/${PN}/${PN}_${PV}-8.debian.tar.gz" + +LICENSE="GPL-3 MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc static-libs" + +RDEPEND=" + dev-cpp/gtkmm:2.4 + dev-cpp/glibmm:2" +DEPEND="${RDEPEND} + virtual/pkgconfig + sys-devel/gettext + dev-util/intltool + doc? ( app-doc/doxygen )" + +PATCHES=( + "${FILESDIR}"/${P}-gcc4.3.patch + "${FILESDIR}"/${P}-glib-2.32.patch + "${FILESDIR}"/${P}-doxygen.patch + "${WORKDIR}"/debian/patches/579183_adjust_size_middle_button.patch + "${WORKDIR}"/debian/patches/604612_fix_menu_category.patch + "${WORKDIR}"/debian/patches/604618_scrollable_properties_dialog.patch + "${WORKDIR}"/debian/patches/656372_element_renames.patch + "${WORKDIR}"/debian/patches/add_new_wave_theme.patch + "${WORKDIR}"/debian/patches/czech_translation_559028.patch + "${WORKDIR}"/debian/patches/fix_gtkmm_2.18.patch + "${WORKDIR}"/debian/patches/fix_zinc_german_translation.patch + "${WORKDIR}"/debian/patches/ftbfs_missing_limits.patch + "${WORKDIR}"/debian/patches/lp673285_link_in_about.patch + ) + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +src_configure() { + local myeconfargs=( $(use_enable doc api-docs) ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install apidir="/usr/share/doc/${PF}/html" +} + +pkg_postinst() { + gnome2_icon_cache_update + fdo-mime_desktop_database_update +} + +pkg_postrm() { + gnome2_icon_cache_update + fdo-mime_desktop_database_update +} diff --git a/sci-chemistry/gelemental/gelemental-1.2.0.ebuild b/sci-chemistry/gelemental/gelemental-1.2.0.ebuild new file mode 100644 index 000000000000..fe562c2ce32b --- /dev/null +++ b/sci-chemistry/gelemental/gelemental-1.2.0.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools-utils fdo-mime gnome2-utils eutils + +DESCRIPTION="Periodic table viewer that provides detailed information on the chemical elements" +HOMEPAGE="http://freecode.com/projects/gelemental/" +SRC_URI="http://www.kdau.com/files/${P}.tar.bz2" + +LICENSE="GPL-3 MIT" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="doc static-libs" + +RDEPEND=" + dev-cpp/gtkmm:2.4 + dev-cpp/glibmm:2" +DEPEND="${RDEPEND} + virtual/pkgconfig + sys-devel/gettext + dev-util/intltool + doc? ( app-doc/doxygen )" + +PATCHES=( + "${FILESDIR}"/${P}-gcc4.3.patch + "${FILESDIR}"/${P}-glib-2.32.patch + "${FILESDIR}"/${P}-doxygen.patch ) + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +src_configure() { + local myeconfargs=( $(use_enable doc api-docs) ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install apidir="/usr/share/doc/${PF}/html" +} + +pkg_postinst() { + gnome2_icon_cache_update + fdo-mime_desktop_database_update +} + +pkg_postrm() { + gnome2_icon_cache_update + fdo-mime_desktop_database_update +} diff --git a/sci-chemistry/gelemental/metadata.xml b/sci-chemistry/gelemental/metadata.xml new file mode 100644 index 000000000000..d63987f1d9ef --- /dev/null +++ b/sci-chemistry/gelemental/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <upstream> + <remote-id type="freecode">gelemental</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/ghemical/Manifest b/sci-chemistry/ghemical/Manifest new file mode 100644 index 000000000000..f2af4d9880c3 --- /dev/null +++ b/sci-chemistry/ghemical/Manifest @@ -0,0 +1,2 @@ +DIST ghemical-2.99.2.tar.gz 2168844 SHA256 dbe4796582f8a125121e70c0171bc834d4a8121200354f2ef620583b767e6c4d +DIST ghemical-3.0.0.tar.gz 2196716 SHA256 babb2bda93cf0c20f234452eeb7d19d1d8c0e4c4d611734f110f8de066a1bcb2 SHA512 d4dd0b063a4dea33fa7430e77a2da253c74079fd8b5f21e8c2b5da1383f3689b93305417e1bf0d4908b87c91afb33c3266dd6bd6fbcd768cc98614a3f730ee94 WHIRLPOOL 80dcc426bbd17d57a346d6703d2b5366c7489666f33bb9ec2a1f36cf0e133e2b6c944a5f328cd3882241812b0856c59b3b3cd1648d59498ca80467ea65fe7971 diff --git a/sci-chemistry/ghemical/files/2.99.2-docs.patch b/sci-chemistry/ghemical/files/2.99.2-docs.patch new file mode 100644 index 000000000000..85f31dfd729f --- /dev/null +++ b/sci-chemistry/ghemical/files/2.99.2-docs.patch @@ -0,0 +1,22 @@ +diff --git a/docs/user-docs/Makefile.am b/docs/user-docs/Makefile.am +index 030f67c..dcb207b 100644 +--- a/docs/user-docs/Makefile.am ++++ b/docs/user-docs/Makefile.am +@@ -1,6 +1,6 @@ + SUBDIRS = images + +-helpfilesdir = $(datadir)/ghemical/@APPVERSION@/user-docs ++helpfilesdir = $(datadir)/doc/ghemical-@APPVERSION@/html + helpfiles_DATA = *.css *.html + + EXTRA_DIST = $(helpfiles_DATA) +diff --git a/docs/user-docs/images/Makefile.am b/docs/user-docs/images/Makefile.am +index fae0ffd..a569151 100644 +--- a/docs/user-docs/images/Makefile.am ++++ b/docs/user-docs/images/Makefile.am +@@ -1,4 +1,4 @@ +-helpimagesdir = $(datadir)/ghemical/@APPVERSION@/user-docs/images ++helpimagesdir = $(datadir)/doc/ghemical-@APPVERSION@/html/images + helpimages_DATA = *.png + + EXTRA_DIST = $(helpimages_DATA) diff --git a/sci-chemistry/ghemical/files/ghemical-gcc43.patch b/sci-chemistry/ghemical/files/ghemical-gcc43.patch new file mode 100644 index 000000000000..93557d48720c --- /dev/null +++ b/sci-chemistry/ghemical/files/ghemical-gcc43.patch @@ -0,0 +1,14 @@ +--- src-orig/pangofont_wcl.cpp 2008-11-30 16:15:23.932475487 -0600 ++++ src/pangofont_wcl.cpp 2008-11-30 16:16:09.620396370 -0600 +@@ -22,6 +22,10 @@ + + #include <gtk/gtkgl.h> + ++#include <string.h> ++ ++#include <cstdlib> ++using namespace std; + /*################################################################################################*/ + + pangofont_wcl::pangofont_wcl(ogl_camera * cam) : + diff --git a/sci-chemistry/ghemical/ghemical-2.99.2-r2.ebuild b/sci-chemistry/ghemical/ghemical-2.99.2-r2.ebuild new file mode 100644 index 000000000000..a87d1c1bba33 --- /dev/null +++ b/sci-chemistry/ghemical/ghemical-2.99.2-r2.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit autotools eutils + +DESCRIPTION="Chemical quantum mechanics and molecular mechanics" +HOMEPAGE="http://bioinformatics.org/ghemical/" +SRC_URI="http://bioinformatics.org/ghemical/download/current/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="openbabel seamonkey threads" + +RDEPEND=" + dev-libs/glib:2 + gnome-base/libglade:2.0 + sci-chemistry/mpqc + >=sci-libs/libghemical-2.99 + >=x11-libs/liboglappth-0.98 + virtual/opengl + x11-libs/pango + x11-libs/gtk+:2 + x11-libs/gtkglext + openbabel? ( sci-chemistry/openbabel )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-docs.patch + eautoreconf +} + +src_configure() { +# With amd64, if you want gamess I recommend adding gamess and gtk-gamess to package.provided for now. + +# Change the built-in help browser. + if use seamonkey ; then + sed -i -e 's|mozilla|seamonkey|g' src/gtk_app.cpp || die "sed failed for seamonkey!" + else + sed -i -e 's|mozilla|firefox|g' src/gtk_app.cpp || die "sed failed for firefox!" + fi + + econf \ + $(use_enable openbabel) \ + $(use_enable threads) +} + +src_install() { + emake DESTDIR="${D}" install || die "install failed" + make_desktop_entry /usr/bin/ghemical Ghemical /usr/share/ghemical/${PV}/pixmaps/ghemical.png +} diff --git a/sci-chemistry/ghemical/ghemical-3.0.0.ebuild b/sci-chemistry/ghemical/ghemical-3.0.0.ebuild new file mode 100644 index 000000000000..df7a67c05f3f --- /dev/null +++ b/sci-chemistry/ghemical/ghemical-3.0.0.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit autotools eutils + +DESCRIPTION="Chemical quantum mechanics and molecular mechanics" +HOMEPAGE="http://bioinformatics.org/ghemical/" +SRC_URI="http://bioinformatics.org/ghemical/download/current/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="openbabel seamonkey threads" + +RDEPEND=" + dev-libs/glib:2 + gnome-base/libglade:2.0 + sci-chemistry/mpqc + >=sci-libs/libghemical-3.0.0 + >=x11-libs/liboglappth-1.0.0 + virtual/opengl + x11-libs/pango + x11-libs/gtk+:2 + x11-libs/gtkglext + openbabel? ( sci-chemistry/openbabel )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/2.99.2-docs.patch + eautoreconf +} + +src_configure() { +# With amd64, if you want gamess I recommend adding gamess and gtk-gamess to package.provided for now. + +# Change the built-in help browser. + if use seamonkey ; then + sed -i -e 's|mozilla|seamonkey|g' src/gtk_app.cpp || die "sed failed for seamonkey!" + else + sed -i -e 's|mozilla|firefox|g' src/gtk_app.cpp || die "sed failed for firefox!" + fi + + econf \ + $(use_enable openbabel) \ + $(use_enable threads) +} + +src_install() { + emake DESTDIR="${D}" install || die "install failed" + make_desktop_entry /usr/bin/ghemical Ghemical /usr/share/ghemical/${PV}/pixmaps/ghemical.png +} diff --git a/sci-chemistry/ghemical/metadata.xml b/sci-chemistry/ghemical/metadata.xml new file mode 100644 index 000000000000..631ea739d033 --- /dev/null +++ b/sci-chemistry/ghemical/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-chemistry</herd> +<longdescription> +Ghemical supports both quantum-mechanics (semi-empirical and ab initio) models +and molecular mechanics models (there is an experimental Tripos 5.2-like force +field for organic molecules). Also a tool for reduced protein models is +included. Geometry optimization, molecular dynamics and a large set of +visualization tools are currently available. +</longdescription> +<use> + <flag name='openbabel'>Use <pkg>sci-chemistry/openbabel</pkg> for file + conversions</flag> +</use> +</pkgmetadata> diff --git a/sci-chemistry/gopenmol/Manifest b/sci-chemistry/gopenmol/Manifest new file mode 100644 index 000000000000..087c602229b0 --- /dev/null +++ b/sci-chemistry/gopenmol/Manifest @@ -0,0 +1 @@ +DIST gopenmol-3.00-linux.tar.gz 29615195 SHA256 314494a751f65c28d015fee854d2ee347fecbca6ccf31bb7e04db7eda6a16a23 SHA512 e28fb607fcfdd543f4e62d3d1bf8ba789bafda608bb6a16e534bfd48bb4f2e2741a9fa98b7ead25db7d5572bb92064c73ba59987b0c3c3193477c3735babefd3 WHIRLPOOL eed5015c81b2c6e4cb14faf3f3176b979a3e79d1bb014dbd10fd606de0452f502b004b4bcb85e5cea57191ed782b3f9afeee5027c155d48370f8960cbca12d75 diff --git a/sci-chemistry/gopenmol/files/3.00-impl-dec.patch b/sci-chemistry/gopenmol/files/3.00-impl-dec.patch new file mode 100644 index 000000000000..e1d66c7aaa5d --- /dev/null +++ b/sci-chemistry/gopenmol/files/3.00-impl-dec.patch @@ -0,0 +1,80 @@ + density/density.c | 1 + + utility/g94cub2pl.c | 1 + + utility/gamess2plt.c | 1 + + utility/gcube2plt.c | 1 + + utility/jaguar2plt.c | 1 + + vss/vssmod.c | 1 + + 6 files changed, 6 insertions(+) + +diff --git a/density/density.c b/density/density.c +index 130a48e..ee218c5 100755 +--- a/density/density.c ++++ b/density/density.c +@@ -13,6 +13,7 @@ + #include <string.h> + #include <sys/types.h> + #include <malloc.h> ++#include <stdlib.h> + + #define VERBOSE 0 + #define BUFF_LEN 500 +diff --git a/utility/g94cub2pl.c b/utility/g94cub2pl.c +index e773ab2..94fbcfd 100755 +--- a/utility/g94cub2pl.c ++++ b/utility/g94cub2pl.c +@@ -315,6 +315,7 @@ which can be read by gOpenMol or SCARECROW. + #include <sys/types.h> + #include <malloc.h> + #include <string.h> ++#include <stdlib.h> + + #define BUFF_LEN 256 + #define BOHR_RADIUS 0.52917715 /* conversion constant */ +diff --git a/utility/gamess2plt.c b/utility/gamess2plt.c +index 3f6108e..5da481d 100755 +--- a/utility/gamess2plt.c ++++ b/utility/gamess2plt.c +@@ -86,6 +86,7 @@ which can be read by gOpenMol or SCARECROW. + #include <sys/types.h> + #include <malloc.h> + #include <string.h> ++#include <stdlib.h> + + #define BUFF_LEN 256 + #define BOHR_RADIUS 0.52917715 /* conversion constant */ +diff --git a/utility/gcube2plt.c b/utility/gcube2plt.c +index c5f7b5e..711bad3 100755 +--- a/utility/gcube2plt.c ++++ b/utility/gcube2plt.c +@@ -306,6 +306,7 @@ which can be read by gOpenMol or SCARECROW. + #include <sys/types.h> + #include <malloc.h> + #include <string.h> ++#include <stdlib.h> + + #define BUFF_LEN 256 + #define BOHR_RADIUS 0.52917715 /* conversion constant */ +diff --git a/utility/jaguar2plt.c b/utility/jaguar2plt.c +index 657128c..96d6ac1 100755 +--- a/utility/jaguar2plt.c ++++ b/utility/jaguar2plt.c +@@ -26,6 +26,7 @@ fastes running coordinate. + #include <sys/types.h> + #include <malloc.h> + #include <string.h> ++#include <stdlib.h> + + #define BUFF_LEN 256 + #define BOHR_RADIUS 0.52917715 /* conversion constant */ +diff --git a/vss/vssmod.c b/vss/vssmod.c +index 957d2e5..9d73978 100755 +--- a/vss/vssmod.c ++++ b/vss/vssmod.c +@@ -20,6 +20,7 @@ C- for the potentials + #include <math.h> + #include <string.h> + #include <malloc.h> ++#include <stdlib.h> + + #define LINE_LEN 80 + #define BUFF_LEN 500 diff --git a/sci-chemistry/gopenmol/files/3.00-include-config-for-plugins.patch b/sci-chemistry/gopenmol/files/3.00-include-config-for-plugins.patch new file mode 100644 index 000000000000..a8602d07a03e --- /dev/null +++ b/sci-chemistry/gopenmol/files/3.00-include-config-for-plugins.patch @@ -0,0 +1,11 @@ +--- gOpenMol-3.00.orig/src/plugins/Makefile 2005-12-02 19:38:08.000000000 -0800 ++++ gOpenMol-3.00/src/plugins/Makefile 2005-12-02 19:37:29.000000000 -0800 +@@ -8,6 +8,8 @@ + # Coded by: Eero Häkkinen + ############################################################################## + ++include config.mk ++ + build-all: build FORCE ; + + all install install-local uninstall: FORCE diff --git a/sci-chemistry/gopenmol/files/3.00-multilib.patch b/sci-chemistry/gopenmol/files/3.00-multilib.patch new file mode 100644 index 000000000000..9ca263808622 --- /dev/null +++ b/sci-chemistry/gopenmol/files/3.00-multilib.patch @@ -0,0 +1,104 @@ +diff --git a/src/config.mk.ac b/src/config.mk.ac +index b1061d9..374bc77 100755 +--- a/src/config.mk.ac ++++ b/src/config.mk.ac +@@ -18,7 +18,7 @@ gomroot = $(libdir)/$(gomsubdir) + gomdataroot = $(datadir)/$(gomsubdir) + gombindir = $(gomroot)/bin + gomincdir = $(includedir)/$(gomsubdir) +-gomlibdir = $(gomroot)/bin ++gomlibdir = $(gomroot)/GENTOOLIBDIR + # Tcl/Tk entries. + TCL_LIBRARY = @TCL_LIBRARY@ + TK_LIBRARY = @TK_LIBRARY@ +diff --git a/src/plugins/Makefile b/src/plugins/Makefile +index bb9af64..cf8a97d 100755 +--- a/src/plugins/Makefile ++++ b/src/plugins/Makefile +@@ -22,7 +22,7 @@ all install install-local uninstall: FORCE + build compile clean clean-libs clean-objs: FORCE + -@for dir in *; do \ + if test -f "$$dir/Makefile"; then \ +- ( cd "$$dir" && $(MAKE) $(MFLAGS) $@ ) ;\ ++ ( cd "$$dir" && $(MAKE) $(MFLAGS) $@ ) || exit 1;\ + fi ;\ + done + +diff --git a/src/plugins/config.mk.ac b/src/plugins/config.mk.ac +index 03e3f6b..eb30ea8 100755 +--- a/src/plugins/config.mk.ac ++++ b/src/plugins/config.mk.ac +@@ -11,7 +11,7 @@ gomdataroot = ${datadir}/${gomsubdir} + gombindir = ${gomroot}/bin + gomincdir = ${gomsrcdir}/include/gomlib + #INS gomincdir = ${includedir}/${gomsubdir} +-gomlibdir = ${gomroot}/bin ++gomlibdir = ${gomroot}/GENTOOLIBDIR + gomsrcdir = @abs_top_srcdir@ + gombltdir = @abs_top_builddir@ + #INS gomsrcdir = ${gomroot}/src +diff --git a/src/plugins/rules.mk b/src/plugins/rules.mk +index d41ed47..da133c6 100755 +--- a/src/plugins/rules.mk ++++ b/src/plugins/rules.mk +@@ -43,12 +43,12 @@ $(LIBRARY): $(libdeps) + @$(RM) alldeps.dT + + link-CC: FORCE +- $(GOM_LINK_CC) $(PLUG_CFLAGS) -o $(LIBRARY) $(OBJECTS) \ +- $(PLUG_LDFLAGS) $(PLUG_LIBS) $(GOM_LINKFLAGS) ++ $(GOM_LINK_CC) $(GOM_LINKFLAGS) $(PLUG_CFLAGS) -o $(LIBRARY) $(OBJECTS) \ ++ $(PLUG_LDFLAGS) $(PLUG_LIBS) + + link-CXX: FORCE +- $(GOM_LINK_CXX) $(PLUG_CXXFLAGS) -o $(LIBRARY) $(OBJECTS) \ +- $(PLUG_LDFLAGS) $(PLUG_LIBS) $(GOM_LINKFLAGS) ++ $(GOM_LINK_CXX) $(GOM_LINKFLAGS) $(PLUG_CXXFLAGS) -o $(LIBRARY) $(OBJECTS) \ ++ $(PLUG_LDFLAGS) $(PLUG_LIBS) + + # Rule to compile the source files. + # First make: +diff --git a/src/unix/make/install.mk b/src/unix/make/install.mk +index 3018946..98c061a 100755 +--- a/src/unix/make/install.mk ++++ b/src/unix/make/install.mk +@@ -36,7 +36,7 @@ mkinstalldirs: mkinstalldirs-local mkinstalldirs-shared FORCE ; + mkinstalldirs-local: FORCE + $(MKDIR_P) '$(gomroot)' || test -d '$(gomroot)' + @$(set_show); set -e; \ +- for dir in bin src/plugins src/unix; do \ ++ for dir in bin lib src/plugins src/unix; do \ + dir='$(gomroot)'/$$dir; \ + $$show $(MKDIR_P) "$$dir"; \ + $(MKDIR_P) "$$dir" || test -d "$$dir"; \ +diff --git a/src/unix/make/utility.mk.ac b/src/unix/make/utility.mk.ac +index 21ad59d..ee25ac7 100755 +--- a/src/unix/make/utility.mk.ac ++++ b/src/unix/make/utility.mk.ac +@@ -47,8 +47,7 @@ BINARIES_F = ambera2b$(EXEEXT) \ + xmol2bamber$(EXEEXT) \ + xplor2charmm$(EXEEXT) \ + gridasc2plt$(EXEEXT) \ +- gridbin2plt$(EXEEXT) \ +- icon8$(EXEEXT) ++ gridbin2plt$(EXEEXT) + + BINARIES_JAR = xvibs.jar + +@@ -76,13 +75,13 @@ $(OBJECTS_C): + $(CC) -c $? $(CPPFLAGS) $(CFLAGS) + + $(BINARIES_C): +- $(CC) -o $@ $? $(CPPFLAGS) $(CFLAGS) $(STD_LIBS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $@ $? $(CPPFLAGS) $(CFLAGS) $(STD_LIBS) + + $(BINARIES_CXX): +- $(CXX) -o $@ $? $(CPPFLAGS) $(CXXFLAGS) $(STD_LIBS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o $@ $? $(CPPFLAGS) $(CXXFLAGS) $(STD_LIBS) + + $(BINARIES_F): +- $(F77) -o $@ $? $(FFLAGS) $(STD_LIBS) $(LDFLAGS) ++ $(F77) $(LDFLAGS) -o $@ $? $(FFLAGS) $(STD_LIBS) + + $(BINARIES_JAR): + cp $? $@ diff --git a/sci-chemistry/gopenmol/files/3.00-tcl8.6.patch b/sci-chemistry/gopenmol/files/3.00-tcl8.6.patch new file mode 100644 index 000000000000..a4c3bce12468 --- /dev/null +++ b/sci-chemistry/gopenmol/files/3.00-tcl8.6.patch @@ -0,0 +1,32 @@ + src/graphics/g_Mmain.c | 2 +- + src/parser/p_parser.c | 4 ++-- + 2 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/src/graphics/g_Mmain.c b/src/graphics/g_Mmain.c +index b9bb340..f044568 100755 +--- a/src/graphics/g_Mmain.c ++++ b/src/graphics/g_Mmain.c +@@ -487,7 +487,7 @@ int gomp_Mmain(int argc, const char *argv[]) + { + Tcl_Interp *interp; + interp = gomp_GetTclInterp(); +- sprintf(Temp,"'%s' problems creating the Tk window",interp->result); ++ sprintf(Temp,"'%s' problems creating the Tk window",Tcl_GetStringResult(interp)); + gomp_PrintERROR(Temp); + return(1); + } +diff --git a/src/parser/p_parser.c b/src/parser/p_parser.c +index c9fd8ce..62eb05c 100755 +--- a/src/parser/p_parser.c ++++ b/src/parser/p_parser.c +@@ -809,8 +809,8 @@ int gomp_TclRunScript() + if(value != (const char *)NULL) { + code = Tcl_EvalFile(interp , value); + if(code != TCL_OK) { +- if(*interp->result != (char)NULL) { +- gomp_PrintERROR(interp->result); ++ if(*Tcl_GetStringResult(interp) != (char)NULL) { ++ gomp_PrintERROR(Tcl_GetStringResult(interp)); + return(1); + } + } diff --git a/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild b/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild new file mode 100644 index 000000000000..1a50d785d368 --- /dev/null +++ b/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild @@ -0,0 +1,92 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +PYTHON_DEPEND="2" + +inherit eutils multilib python + +DESCRIPTION="Tool for the visualization and analysis of molecular structures" +HOMEPAGE="http://www.csc.fi/gopenmol/" +SRC_URI="${HOMEPAGE}/distribute/${P}-linux.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-lang/tk + dev-tcltk/bwidget + media-libs/freeglut + virtual/jpeg + virtual/opengl + x11-libs/libICE + x11-libs/libXau + x11-libs/libXdmcp + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXxf86vm" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}/gOpenMol-${PV}/src" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-include-config-for-plugins.patch \ + "${FILESDIR}"/${PV}-multilib.patch + + sed \ + -e "s:GENTOOLIBDIR:$(get_libdir):g" \ + -i config.mk.ac plugins/config.mk.ac || die + sed "/GOM_TEMP/s:^.*$:GOM_TEMP=\"${EPREFIX}/tmp/:g" -i ../environment.txt || die +} + +src_compile() { + default + + # Plugins and Utilities are not built by default + cd "${S}"/plugins && emake + cd "${S}"/utility && emake +} + +src_install() { + einstall + + cd "${S}"/plugins && einstall + cd "${S}"/utility && einstall + + dosym ../$(get_libdir)/gOpenMol-${PV}/bin/${PN} /usr/bin/${PN} + + dodoc "${ED}"/usr/share/gOpenMol-${PV}/{docs/*,README*} || die + + dodir /usr/share/doc/${PF}/html + mv -T "${ED}"/usr/share/gOpenMol-${PV}/help "${ED}"/usr/share/doc/${PF}/html || die + mv "${ED}"/usr/share/gOpenMol-${PV}/utility "${ED}"/usr/share/doc/${PF}/html || die + + rm -rf \ + "${ED}"/usr/$(get_libdir)/gOpenMol-${PV}/{src,install} \ + "${ED}"/usr/share/gOpenMol-${PV}/{docs,README*,COPYRIGHT} || die + + cat >> "${T}"/20${PN} <<- EOF + GOM_ROOT="${EPREFIX}"/usr/$(get_libdir)/gOpenMol-${PV}/ + GOM_DATA="${EPREFIX}"/usr/share/gOpenMol-${PV}/data + GOM_HELP="${EPREFIX}"/usr/share/doc/${PVR}/html + GOM_DEMO="${EPREFIX}"/usr/share/gOpenMol-${PV}/demo + EOF + + doenvd "${T}"/20${PN} +} + +pkg_postinst() { + einfo "Run gOpenMol using the rungOpenMol script." +} diff --git a/sci-chemistry/gopenmol/gopenmol-3.00-r3.ebuild b/sci-chemistry/gopenmol/gopenmol-3.00-r3.ebuild new file mode 100644 index 000000000000..b936d437e5a0 --- /dev/null +++ b/sci-chemistry/gopenmol/gopenmol-3.00-r3.ebuild @@ -0,0 +1,91 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-single-r1 + +DESCRIPTION="Tool for the visualization and analysis of molecular structures" +HOMEPAGE="http://www.csc.fi/gopenmol/" +SRC_URI="${HOMEPAGE}/distribute/${P}-linux.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + dev-lang/tk + dev-tcltk/bwidget + media-libs/freeglut + virtual/jpeg + virtual/opengl + x11-libs/libICE + x11-libs/libXau + x11-libs/libXdmcp + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXxf86vm" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" +S="${WORKDIR}/gOpenMol-${PV}/src" + +src_prepare() { + cd .. + epatch \ + "${FILESDIR}"/${PV}-include-config-for-plugins.patch \ + "${FILESDIR}"/${PV}-multilib.patch \ + "${FILESDIR}"/${PV}-tcl8.6.patch \ + "${FILESDIR}"/${PV}-impl-dec.patch + + sed \ + -e "s:GENTOOLIBDIR:$(get_libdir):g" \ + -i src/{config.mk.ac,plugins/config.mk.ac} || die + sed "/GOM_TEMP/s:^.*$:GOM_TEMP=\"${EPREFIX}/tmp/:g" -i environment.txt || die +} + +src_compile() { + default + + # Plugins and Utilities are not built by default + cd "${S}"/plugins && emake + cd "${S}"/utility && emake +} + +src_install() { + einstall + + cd "${S}"/plugins && einstall + cd "${S}"/utility && einstall + + dosym ../$(get_libdir)/gOpenMol-${PV}/bin/${PN} /usr/bin/${PN} + + dodoc "${ED}"/usr/share/gOpenMol-${PV}/{docs/*,README*} || die + + dodir /usr/share/doc/${PF}/html + mv -T "${ED}"/usr/share/gOpenMol-${PV}/help "${ED}"/usr/share/doc/${PF}/html || die + mv "${ED}"/usr/share/gOpenMol-${PV}/utility "${ED}"/usr/share/doc/${PF}/html || die + + rm -rf \ + "${ED}"/usr/$(get_libdir)/gOpenMol-${PV}/{src,install} \ + "${ED}"/usr/share/gOpenMol-${PV}/{docs,README*,COPYRIGHT} || die + + cat >> "${T}"/20${PN} <<- EOF + GOM_ROOT="${EPREFIX}"/usr/$(get_libdir)/gOpenMol-${PV}/ + GOM_DATA="${EPREFIX}"/usr/share/gOpenMol-${PV}/data + GOM_HELP="${EPREFIX}"/usr/share/doc/${PVR}/html + GOM_DEMO="${EPREFIX}"/usr/share/gOpenMol-${PV}/demo + EOF + + doenvd "${T}"/20${PN} +} + +pkg_postinst() { + einfo "Run gOpenMol using the rungOpenMol script." +} diff --git a/sci-chemistry/gopenmol/metadata.xml b/sci-chemistry/gopenmol/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/gopenmol/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/gperiodic/Manifest b/sci-chemistry/gperiodic/Manifest new file mode 100644 index 000000000000..659d4e28d9ce --- /dev/null +++ b/sci-chemistry/gperiodic/Manifest @@ -0,0 +1 @@ +DIST gperiodic-2.0.10.tar.gz 131213 SHA256 78d72870c51c39e4a35c804c05b8ef5e39f88d42eced52b2934e21d74fb8d096 SHA512 23d0074ad5b0f9e25e8eee63f8c375e2448b1ee7c00f89e965b7dd8ce3f60f20251d7699a2f7a767228316144b946a5ac204a3e478c395767133f7fc801b51ba WHIRLPOOL b758b622bfb980aad45b0bb6e2850579408959c3bf700f4dbb21d4bc64168d2a589a9ed5974f75b5eaf7f6c9d593c69dbc9b470957b01457caa30eb356850f14 diff --git a/sci-chemistry/gperiodic/files/gperiodic-2.0.10-makefile.patch b/sci-chemistry/gperiodic/files/gperiodic-2.0.10-makefile.patch new file mode 100644 index 000000000000..abdb5caae4f2 --- /dev/null +++ b/sci-chemistry/gperiodic/files/gperiodic-2.0.10-makefile.patch @@ -0,0 +1,64 @@ +Respect CC, CFLAGS, LDFLAGS +Fix install paths +Fix parallel build +Drop DEPRECATED flags, bug #391099 + +--- Makefile ++++ Makefile +@@ -1,6 +1,5 @@ +-CC := gcc +-CFLAGS := `pkg-config --cflags gtk+-2.0` -I. -DG_DISABLE_DEPRECATED -DGDK_DISABLE_DEPRECATED -DGDK_PIXBUF_DISABLE_DEPRECATED -DGTK_DISABLE_DEPRECATED +-LIBS :=`pkg-config --libs gtk+-2.0` ++CFLAGS += `pkg-config --cflags gtk+-2.0` -I. ++LIBS +=`pkg-config --libs gtk+-2.0` + bindir ?= /usr/bin + datadir ?= /usr/share + enable_nls ?= 1 +@@ -8,12 +7,11 @@ + .c.o: + $(CC) -c $(CFLAGS) $(CPPFLAGS) $< + +-all: +- make gperiodic +- make -C po/ all enable_nls=$(enable_nls) ++all: gperiodic ++ $(MAKE) -C po/ all enable_nls=$(enable_nls) + + gperiodic: gperiodic.o +- $(CC) $(CFLAGS) -o gperiodic gperiodic.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o gperiodic gperiodic.o $(LIBS) + ifeq ($(strip),1) + strip gperiodic + endif +@@ -23,24 +21,21 @@ + gperiodic.o: gperiodic.c gperiodic.h table_data.h + + install: +- mkdir -p $(DESTDIR)$(bindir) +- install -m 755 gperiodic $(DESTDIR)$(bindir) +- mkdir -p $(DESTDIR)$(datadir)/applications +- install -m 644 gperiodic.desktop $(DESTDIR)$(datadir)/applications +- mkdir -p $(DESTDIR)$(datadir)/pixmaps +- install -m 644 gperiodic.png $(DESTDIR)$(datadir)/pixmaps +- install -m 644 gperiodic-crystal.png $(DESTDIR)$(datadir)/pixmaps +- make -C po/ install enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) ++ install -D -m 755 gperiodic $(DESTDIR)$(bindir)/gperiodic ++ install -D -m 644 gperiodic.desktop $(DESTDIR)$(datadir)/applications/gperiodic.desktop ++ install -D -m 644 gperiodic.png $(DESTDIR)$(datadir)/pixmaps/gperiodic.png ++ install -m 644 gperiodic-crystal.png $(DESTDIR)$(datadir)/pixmaps/gperiodic-crystal.png ++ $(MAKE) -C po/ install enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) + + uninstall: + rm -f $(bindir)/gperiodic \ + $(datadir)/applications/gperiodic.desktop + $(datadir)/pixmaps/gperiodic.png \ + $(datadir)/pixmaps/gperiodic-crystal.png +- make -C po/ uninstall enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) ++ $(MAKE) -C po/ uninstall enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) + + clean: + rm -f *.o gperiodic +- make -C po/ clean ++ $(MAKE) -C po/ clean + + .PHONY: install uninstall clean diff --git a/sci-chemistry/gperiodic/files/gperiodic-2.0.10-nls.patch b/sci-chemistry/gperiodic/files/gperiodic-2.0.10-nls.patch new file mode 100644 index 000000000000..de0bea04dc14 --- /dev/null +++ b/sci-chemistry/gperiodic/files/gperiodic-2.0.10-nls.patch @@ -0,0 +1,20 @@ + po/Makefile | 2 ++ + 1 files changed, 2 insertions(+), 0 deletions(-) + +diff --git a/po/Makefile b/po/Makefile +index d7d7d78..179dad6 100644 +--- a/po/Makefile ++++ b/po/Makefile +@@ -26,10 +26,12 @@ endif + + install: + $(MAKE) all ++ifeq ($(enable_nls),1) + for f in $(FILES_MO) ; do \ + mkdir -p $(DESTDIR)$(LOCALEDIR)/`basename $$f .mo`/LC_MESSAGES ; \ + install -m 644 $$f $(DESTDIR)$(LOCALEDIR)/`basename $$f .mo`/LC_MESSAGES/$(PACKAGE).mo ; \ + done ++endif + + uninstall: + for f in $(FILES_MO) ; do \ diff --git a/sci-chemistry/gperiodic/gperiodic-2.0.10-r2.ebuild b/sci-chemistry/gperiodic/gperiodic-2.0.10-r2.ebuild new file mode 100644 index 000000000000..9c7dca1e1d0c --- /dev/null +++ b/sci-chemistry/gperiodic/gperiodic-2.0.10-r2.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Periodic table application for Linux" +HOMEPAGE="http://www.frantz.fi/software/gperiodic.php" +SRC_URI="http://www.frantz.fi/software/${P}.tar.gz" + +KEYWORDS="amd64 x86" +SLOT="0" +LICENSE="GPL-2" +IUSE="nls" + +RDEPEND=" + sys-libs/ncurses:5 + x11-libs/gtk+:2 + x11-libs/cairo[X] + nls? ( sys-devel/gettext )" + +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-makefile.patch \ + "${FILESDIR}"/${P}-nls.patch + sed \ + -e '/Encoding/d' \ + -i ${PN}.desktop || die +} + +src_compile() { + local myopts + use nls && myopts="enable_nls=1" || myopts="enable_nls=0" + emake CC=$(tc-getCC) ${myopts} +} + +src_install() { + local myopts + use nls && myopts="enable_nls=1" || myopts="enable_nls=0" + emake DESTDIR="${D}" ${myopts} install + dodoc AUTHORS ChangeLog README NEWS + newdoc po/README README.translation +} diff --git a/sci-chemistry/gperiodic/gperiodic-2.0.10.ebuild b/sci-chemistry/gperiodic/gperiodic-2.0.10.ebuild new file mode 100644 index 000000000000..f317a6b77afe --- /dev/null +++ b/sci-chemistry/gperiodic/gperiodic-2.0.10.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Periodic table application for Linux" +HOMEPAGE="http://www.frantz.fi/software/gperiodic.php" +SRC_URI="http://www.frantz.fi/software/${P}.tar.gz" + +KEYWORDS="amd64 x86" +SLOT="0" +LICENSE="GPL-2" +IUSE="nls" + +RDEPEND=" + sys-libs/ncurses:5 + x11-libs/gtk+:2 + x11-libs/cairo[X] + nls? ( sys-devel/gettext )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + # The author has removed "unnecessary automake/autoconf setup" + + sed -i -e "s|-DGTK_DISABLE_DEPRECATED|${CFLAGS}|" Makefile || die + sed -i -e "/make clean/d" Makefile || die + sed -i -e "s|CC=gcc|CC=$(tc-getCC)|" Makefile || die + if ! use nls; then + sed -i -e "/make -C po/d" Makefile || die + fi +} + +src_install() { + sed -i -e "s|/usr/bin|${ED}/usr/bin|" Makefile || die + sed -i -e "s|/usr/share|${ED}/usr/share|" Makefile || die + sed -i -e "s|/usr/share|${ED}/usr/share|" po/Makefile || die + + # Create directories - Makefile is quite broken. + dodir \ + /usr/bin \ + /usr/share/pixmaps \ + /usr/share/applications + + default + + # The man page seems to have been removed too. + newdoc po/README README.translation +} diff --git a/sci-chemistry/gperiodic/metadata.xml b/sci-chemistry/gperiodic/metadata.xml new file mode 100644 index 000000000000..e87a8759836d --- /dev/null +++ b/sci-chemistry/gperiodic/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> + GPeriodic is a program for looking up various data about elements from the + periodic table, based on the GTK2 toolkit. It also features a command line + interface. + </longdescription> +</pkgmetadata> diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest new file mode 100644 index 000000000000..7cf2e013ff01 --- /dev/null +++ b/sci-chemistry/gromacs/Manifest @@ -0,0 +1,6 @@ +DIST gromacs-5.0.4.tar.gz 26342095 SHA256 78068eeccc0b950018ddb45c41280e53c8bedae4639dca48e17c940f8896b23b SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee WHIRLPOOL d8458d3d563e015e830622ae0c924e896765a6329ffe4cb1a31c7aef3c804f392d29e3f1db5617051e85058403422f7d69a160a6c7cc810564696d88f9d50bd4 +DIST gromacs-5.0.5.tar.gz 26343524 SHA256 952c9d14879a12d03362b2233e47c51385dc99325bdde5223a2942938739bf4e SHA512 b45b2da5de48b0aa272b6d8583fd717762512fbd291ac35b414d23c430bf7b6db470f64e641728658e94784de9ddcde04242cfba09ff47931e01b85b8ca8fd73 WHIRLPOOL cc1f5f60d70780f8694acb16c96634d2aa8a16ff3d52be5ed4572dd37f80d9591f8060a0256f3e0f4a55069247398b8b52ad05efed691a0ab8619bc77aa64f76 +DIST gromacs-5.0.6.tar.gz 26351063 SHA256 e07e950c4cd6cb84b83b145b70a15c25338ad6a7d7d1a0a83cdbd51cad954952 SHA512 5bd11d2ab79cc94c1ecf10bb05c239f7a4aed426ba3da0e536076e5145ff854889f9f0808d87a8ce007d86fce8eff9b6a809ae5fb68478528ea405c335dbffb2 WHIRLPOOL e5898fa247016a4c52e7ddc77ba03f0d39df2b863607a79f4b88f7029a2467e22cd84a507c18b52b4015619341699bbede28939be485613ac145b499a7d0998d +DIST regressiontests-5.0.4.tar.gz 65193251 SHA256 89ad9bc067035ac8f340319b538c446983d937b910067e871911d7afe2ecb3f0 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 WHIRLPOOL e15ccab0a0beefac41aeff11e2e596e971167f1590eed159ff82c4a8e3aec1d234287be597026951904ecfe6099f30ef3bcd48f2098b9f5201bde62e15fbc4f9 +DIST regressiontests-5.0.5.tar.gz 65204335 SHA256 e48b9934de89c23a63c9adc8ba9a5aa397cf5a4d1746165d833c556d5ce54833 SHA512 1a1d1a3398ba5d3cc9f68e0f401437ccbdf3265f3ea1100b3b0d314d61ccd467ce3e8492ee09a645c5aaf9c1ca0acdf5ed6213a61bbd689833f3ca002bd5c79b WHIRLPOOL 882c9d8fa45720a5a71811db898aa33b9323bfe60340e8c4f4e2ef537f02efb531c0f3a721ead0e98bdb96f1e9d71df24d1d0faae448ab3da096c694e2a9b593 +DIST regressiontests-5.0.6.tar.gz 65203643 SHA256 fd0a2408250dfc088ac9b401bc8702b8ba398a81db56c214d55f68f838d7c079 SHA512 dec41fbaa93784fb6438887eeef9f523add06032ae9801b83c492f5924872cd9b6a17e07d61cd7d8f999193d46384112e4c8046f4b2a3c28eb0c08f11c1ad8c6 WHIRLPOOL e6a8e99abc3b59be0f246769de0ebdef528caa24b930999dfbe0167a58696a68a31d0b819d2503e312977f0ec4d1ee2acb60e8eb691fab45e608250f2dfde728 diff --git a/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild b/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild new file mode 100644 index 000000000000..b5d7896aa556 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild @@ -0,0 +1,284 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + git://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + EGIT_BRANCH="release-5-0" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + boost? ( >=dev-libs/boost-1.55 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="master" EGIT_COMMIT="master" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + $(cmake-utils_use X GMX_X11) + $(cmake-utils_use blas GMX_EXTERNAL_BLAS) + $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) + $(cmake-utils_use openmp GMX_OPENMP) + $(cmake-utils_use offensive GMX_COOL_QUOTES) + $(cmake-utils_use boost GMX_EXTERNAL_BOOST) + $(cmake-utils_use tng GMX_USE_TNG) + $(cmake-utils_use doc GMX_BUILD_MANUAL) + $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF + -DGMX_USE_GCC44_BUG_WORKAROUND=OFF + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + $(cmake-utils_use threads GMX_THREAD_MPI) + "${cuda[@]}" + -DGMX_OPENMM=OFF + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # generate bash completion, not 100% necessary for + # rel ebuilds as bundled + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile completion + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + #release ebuild does this automatically + if [[ $PV = *9999* ]]; then + cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die + echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) + #little hacckery as some gmx-completion* newlines ,so cat won't work + for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do + echo $(<${x}) + done > "${T}"/gmx-bashcomp || die + newbashcomp "${T}"/gmx-bashcomp gmx + bashcomp_alias gmx mdrun + rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die + if use double-precision && use single-precision; then + bashcomp_alias gmx gmx_d + bashcomp_alias gmx mdrun_d + fi + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "http://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-5.0.4.ebuild b/sci-chemistry/gromacs/gromacs-5.0.4.ebuild new file mode 100644 index 000000000000..6d59d9789888 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-5.0.4.ebuild @@ -0,0 +1,279 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + git://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + EGIT_BRANCH="release-5-0" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" + KEYWORDS="~alpha amd64 arm ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + boost? ( >=dev-libs/boost-1.55 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="master" EGIT_COMMIT="master" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + $(cmake-utils_use X GMX_X11) + $(cmake-utils_use blas GMX_EXTERNAL_BLAS) + $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) + $(cmake-utils_use openmp GMX_OPENMP) + $(cmake-utils_use offensive GMX_COOL_QUOTES) + $(cmake-utils_use boost GMX_EXTERNAL_BOOST) + $(cmake-utils_use tng GMX_USE_TNG) + $(cmake-utils_use doc GMX_BUILD_MANUAL) + $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF + -DGMX_USE_GCC44_BUG_WORKAROUND=OFF + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + $(cmake-utils_use threads GMX_THREAD_MPI) + "${cuda[@]}" + -DGMX_OPENMM=OFF + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # generate bash completion, not 100% necessary for + # rel ebuilds as bundled + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile completion + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + #release ebuild does this automatically + if [[ $PV = *9999* ]]; then + cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die + echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) + #little hacckery as some gmx-completion* newlines ,so cat won't work + for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do + echo $(<${x}) + done > "${T}"/gmx-bashcomp || die + newbashcomp "${T}"/gmx-bashcomp gmx + bashcomp_alias gmx mdrun + rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die + if use double-precision && use single-precision; then + bashcomp_alias gmx gmx_d + bashcomp_alias gmx mdrun_d + fi + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "http://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-5.0.5.ebuild b/sci-chemistry/gromacs/gromacs-5.0.5.ebuild new file mode 100644 index 000000000000..b5d7896aa556 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-5.0.5.ebuild @@ -0,0 +1,284 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + git://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + EGIT_BRANCH="release-5-0" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + boost? ( >=dev-libs/boost-1.55 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="master" EGIT_COMMIT="master" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + $(cmake-utils_use X GMX_X11) + $(cmake-utils_use blas GMX_EXTERNAL_BLAS) + $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) + $(cmake-utils_use openmp GMX_OPENMP) + $(cmake-utils_use offensive GMX_COOL_QUOTES) + $(cmake-utils_use boost GMX_EXTERNAL_BOOST) + $(cmake-utils_use tng GMX_USE_TNG) + $(cmake-utils_use doc GMX_BUILD_MANUAL) + $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF + -DGMX_USE_GCC44_BUG_WORKAROUND=OFF + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + $(cmake-utils_use threads GMX_THREAD_MPI) + "${cuda[@]}" + -DGMX_OPENMM=OFF + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # generate bash completion, not 100% necessary for + # rel ebuilds as bundled + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile completion + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + #release ebuild does this automatically + if [[ $PV = *9999* ]]; then + cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die + echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) + #little hacckery as some gmx-completion* newlines ,so cat won't work + for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do + echo $(<${x}) + done > "${T}"/gmx-bashcomp || die + newbashcomp "${T}"/gmx-bashcomp gmx + bashcomp_alias gmx mdrun + rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die + if use double-precision && use single-precision; then + bashcomp_alias gmx gmx_d + bashcomp_alias gmx mdrun_d + fi + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "http://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-5.0.6.ebuild b/sci-chemistry/gromacs/gromacs-5.0.6.ebuild new file mode 100644 index 000000000000..b5d7896aa556 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-5.0.6.ebuild @@ -0,0 +1,284 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + git://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + EGIT_BRANCH="release-5-0" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + boost? ( >=dev-libs/boost-1.55 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="master" EGIT_COMMIT="master" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + $(cmake-utils_use X GMX_X11) + $(cmake-utils_use blas GMX_EXTERNAL_BLAS) + $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) + $(cmake-utils_use openmp GMX_OPENMP) + $(cmake-utils_use offensive GMX_COOL_QUOTES) + $(cmake-utils_use boost GMX_EXTERNAL_BOOST) + $(cmake-utils_use tng GMX_USE_TNG) + $(cmake-utils_use doc GMX_BUILD_MANUAL) + $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF + -DGMX_USE_GCC44_BUG_WORKAROUND=OFF + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + $(cmake-utils_use threads GMX_THREAD_MPI) + "${cuda[@]}" + -DGMX_OPENMM=OFF + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # generate bash completion, not 100% necessary for + # rel ebuilds as bundled + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile completion + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + #release ebuild does this automatically + if [[ $PV = *9999* ]]; then + cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die + echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) + #little hacckery as some gmx-completion* newlines ,so cat won't work + for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do + echo $(<${x}) + done > "${T}"/gmx-bashcomp || die + newbashcomp "${T}"/gmx-bashcomp gmx + bashcomp_alias gmx mdrun + rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die + if use double-precision && use single-precision; then + bashcomp_alias gmx gmx_d + bashcomp_alias gmx mdrun_d + fi + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "http://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml new file mode 100644 index 000000000000..083289348b0d --- /dev/null +++ b/sci-chemistry/gromacs/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <use> + <flag name="cuda">Enable cuda non-bonded kernels</flag> + <flag name="double-precision">More precise calculations at the expense of speed</flag> + <flag name="single-precision">Single precision version of gromacs (default)</flag> + <flag name="boost">Enable external boost library</flag> + <flag name="tng">Enable new trajectory format - tng</flag> + <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag> + <!-- acceleration optimization flags --> + <flag name="offensive">Enable gromacs partly offensive quotes</flag> + <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/gsim/Manifest b/sci-chemistry/gsim/Manifest new file mode 100644 index 000000000000..faf3cd3e2c9b --- /dev/null +++ b/sci-chemistry/gsim/Manifest @@ -0,0 +1 @@ +DIST gsim-21.3.tar.gz 4100589 SHA256 d3dd161078862fa990b40ff5df988bb82c8469e17dda8e81eda5f1419742de47 SHA512 0a65ec416a11893fe9f249126ed8e7b9f7991dc8f02d6b62b01962de6dfabda805acdc3d7fc6939b609ff018f16cefff616f37ee906776712209460374bb225d WHIRLPOOL d8dde220a52608b5dc48e494fb1b0bad49f13f770e132641b9671cd544c951cdd03a4578bf983492dfb0b74567e51ef716ecbb828ba40b2a3385d26788b83bea diff --git a/sci-chemistry/gsim/files/0.20.1-build.conf.patch b/sci-chemistry/gsim/files/0.20.1-build.conf.patch new file mode 100644 index 000000000000..e0c68d222323 --- /dev/null +++ b/sci-chemistry/gsim/files/0.20.1-build.conf.patch @@ -0,0 +1,44 @@ + gsim.pro | 25 +++++++++++++++---------- + 1 files changed, 15 insertions(+), 10 deletions(-) + +diff --git a/gsim.pro b/gsim.pro +index 7316aee..9278b6a 100755 +--- a/gsim.pro ++++ b/gsim.pro +@@ -16,21 +16,26 @@ + #CONFIG+=use_script + + # Change directories locations for libcmatrix, MinUIT and muParser libraries +-unix:INCLUDEPATH += /home/vjuser/gsim/libcmatrixR3/include \ +- /home/vjuser/gsim/Minuit2/include \ +- /usr/include/muParser ++#unix:INCLUDEPATH += /home/vjuser/gsim/libcmatrixR3/include \ ++# /home/vjuser/gsim/Minuit2/include \ ++# /usr/include/muParser + +-win32:INCLUDEPATH += "C:\gsim\libcmatrixR3\include" "C:\gsim\Minuit2\include" "C:\gsim\muparser\include" ++#win32:INCLUDEPATH += "C:\gsim\libcmatrixR3\include" "C:\gsim\Minuit2\include" "C:\gsim\muparser\include" + +-unix:LIBS += -lcmatrix -L/home/vjuser/gsim/libcmatrixR3/lib -lMinuit2 -L/home/vjuser/gsim/Minuit2/lib -L/home/vjuser/gsim/muparser/lib -lmuparser ++#unix:LIBS += -lcmatrix -L/home/vjuser/gsim/libcmatrixR3/lib -lMinuit2 -L/home/vjuser/gsim/Minuit2/lib -L/home/vjuser/gsim/muparser/lib -lmuparser + +-win32:LIBS += -lcmatrix -L"C:\gsim\libcmatrixR3\lib" -lMinuit2 -L"C:\gsim\Minuit2\lib" -L"C:\gsim\muparser\lib" -lmuparser ++#win32:LIBS += -lcmatrix -L"C:\gsim\libcmatrixR3\lib" -lMinuit2 -L"C:\gsim\Minuit2\lib" -L"C:\gsim\muparser\lib" -lmuparser + + #Change directories location for libEMF (if used) +-use_emf { +- DEFINES+=USE_EMF_OUTPUT +- unix:LIBS +=-lEMF -L/usr/include/libEmf +- win32:LIBS +=-lgdi32 ++#use_emf { ++# DEFINES+=USE_EMF_OUTPUT ++# unix:LIBS +=-lEMF -L/usr/include/libEmf ++# win32:LIBS +=-lgdi32 ++#} ++ ++GSIM_ROOT = . ++!include( $$GSIM_ROOT/build.conf ) { ++ message( "You need a build.conf file with local settings!" ) + } + + ################################################################################################# diff --git a/sci-chemistry/gsim/files/gsim-21.0-build.conf.patch b/sci-chemistry/gsim/files/gsim-21.0-build.conf.patch new file mode 100644 index 000000000000..cbd529a49ac4 --- /dev/null +++ b/sci-chemistry/gsim/files/gsim-21.0-build.conf.patch @@ -0,0 +1,42 @@ + gsim.pro | 23 ++++++++++++++--------- + 1 file changed, 14 insertions(+), 9 deletions(-) + +diff --git a/gsim.pro b/gsim.pro +index f06e5d2..6e28178 100755 +--- a/gsim.pro ++++ b/gsim.pro +@@ -16,20 +16,25 @@ + #CONFIG+=use_script + + # Change directories locations for libcmatrix, MinUIT and muParser libraries +-unix:INCLUDEPATH += /home/dch1vz/libcmatrixR3/include \ +- /home/dch1vz/Minuit2/include \ ++#unix:INCLUDEPATH += /home/dch1vz/libcmatrixR3/include \ ++# /home/dch1vz/Minuit2/include \ + +-win32:INCLUDEPATH += "C:\gsim\libcmatrixR3\include" "C:\gsim\Minuit2\include" "C:\gsim\muparser\include" ++#win32:INCLUDEPATH += "C:\gsim\libcmatrixR3\include" "C:\gsim\Minuit2\include" "C:\gsim\muparser\include" + +-unix:LIBS += -lcmatrix -L/home/dch1vz/libcmatrixR3/lib -lMinuit2Base -L/home/dch1vz/Minuit2/lib -lmuparser ++#unix:LIBS += -lcmatrix -L/home/dch1vz/libcmatrixR3/lib -lMinuit2Base -L/home/dch1vz/Minuit2/lib -lmuparser + +-win32:LIBS += -lcmatrix -L"C:\gsim\libcmatrixR3\lib" -lMinuit2 -L"C:\gsim\Minuit2\lib" -L"C:\gsim\muparser\lib" -lmuparser ++#win32:LIBS += -lcmatrix -L"C:\gsim\libcmatrixR3\lib" -lMinuit2 -L"C:\gsim\Minuit2\lib" -L"C:\gsim\muparser\lib" -lmuparser + + #Change directories location for libEMF (if used) +-use_emf { +- DEFINES+=USE_EMF_OUTPUT +- unix:LIBS +=-lEMF -L/usr/include/libEmf +- win32:LIBS +=-lgdi32 ++#use_emf { ++# DEFINES+=USE_EMF_OUTPUT ++# unix:LIBS +=-lEMF -L/usr/include/libEmf ++# win32:LIBS +=-lgdi32 ++#} ++ ++GSIM_ROOT = . ++!include( $$GSIM_ROOT/build.conf ) { ++ message( "You need a build.conf file with local settings!" ) + } + + ################################################################################################# diff --git a/sci-chemistry/gsim/files/gsim-21.3-build.conf.patch b/sci-chemistry/gsim/files/gsim-21.3-build.conf.patch new file mode 100644 index 000000000000..da7d7b7b4457 --- /dev/null +++ b/sci-chemistry/gsim/files/gsim-21.3-build.conf.patch @@ -0,0 +1,49 @@ + gsim.pro | 23 ++++++++++++++---------
+ 1 file changed, 14 insertions(+), 9 deletions(-)
+
+diff --git a/gsim.pro b/gsim.pro
+index f88dc8a..579a91c 100755
+--- a/gsim.pro
++++ b/gsim.pro
+@@ -10,27 +10,32 @@
+
+ #Uncomment next line if you want to use EMF output
+ #EMF output requires libEMF or Wine on X11 systems and MAC(?)
+-CONFIG+=use_emf
++#CONFIG+=use_emf
+
+ #DO NOT UNCOMMENT NEXT LINE. The scripting possibilty won't work at the moment
+ #CONFIG+=use_script
+
+ # Change directories locations for libcmatrix, MinUIT and muParser libraries
+-unix:INCLUDEPATH += /home/dch0ph/libcmatrixR3nosse/include \
+- /home/dch1vz/Minuit2/include \
+- /home/dch1vz/muparser/include
++#unix:INCLUDEPATH += /home/dch0ph/libcmatrixR3nosse/include \
++# /home/dch1vz/Minuit2/include \
++# /home/dch1vz/muparser/include
+
+ win32:INCLUDEPATH += "C:\gsim\libcmatrixR3_qt4\include" "C:\gsim\Minuit2_qt4\include" "C:\gsim\muparser_qt4\include"
+
+-unix:LIBS += -lcmatrix -L/home/dch0ph/libcmatrixR3nosse/lib -lMinuit2Base -L/home/dch1vz/Minuit2/lib -L/home/dch1vz/muparser/lib -lmuparser
++#unix:LIBS += -lcmatrix -L/home/dch0ph/libcmatrixR3nosse/lib -lMinuit2Base -L/home/dch1vz/Minuit2/lib -L/home/dch1vz/muparser/lib -lmuparser
+
+ win32:LIBS += -lcmatrix -L"C:\gsim\libcmatrixR3_qt4\lib" -lMinuit2 -L"C:\gsim\Minuit2_qt4\lib" -L"C:\gsim\muparser_qt4\lib" -lmuparser
+
+ #Change directories location for libEMF (if used)
+-use_emf {
+- DEFINES+=USE_EMF_OUTPUT
+- unix:LIBS +=-lEMF -L/usr/include/libEmf
+- win32:LIBS +=-lgdi32
++#use_emf {
++# DEFINES+=USE_EMF_OUTPUT
++# unix:LIBS +=-lEMF -L/usr/include/libEmf
++# win32:LIBS +=-lgdi32
++#}
++
++GSIM_ROOT = .
++!include( $$GSIM_ROOT/build.conf ) {
++ message( "You need a build.conf file with local settings!" )
+ }
+
+ #################################################################################################
diff --git a/sci-chemistry/gsim/gsim-21.3.ebuild b/sci-chemistry/gsim/gsim-21.3.ebuild new file mode 100644 index 000000000000..02d476379b72 --- /dev/null +++ b/sci-chemistry/gsim/gsim-21.3.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils qt4-r2 toolchain-funcs + +DESCRIPTION="Programm for visualisation and processing of experimental and simulated NMR spectra" +HOMEPAGE="http://sourceforge.net/projects/gsim/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="emf opengl" + +RDEPEND=" + dev-cpp/muParser + media-libs/freetype + sci-libs/libcmatrix + sci-libs/minuit + virtual/blas + dev-qt/qtsvg:4 + emf? ( media-libs/libemf ) + opengl? ( dev-qt/qtopengl:4 )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}"/${P}-build.conf.patch ) +DOCS="release.txt README_GSIM.* quickstart.* changes.log programming.*" + +src_prepare() { + edos2unix ${PN}.pro + + qt4-r2_src_prepare + + cat >> build.conf <<- EOF + INCLUDEPATH += "${EPREFIX}/usr/include/libcmatrixR3/" \ + "${EPREFIX}/usr/include/Minuit2" \ + "${EPREFIX}/usr/include" + LIBS += -lcmatrix -lMinuit2 -lmuparser $($(tc-getPKG_CONFIG) --libs cblas) + EOF + + use opengl && echo "CONFIG+=use_opengl" >> build.conf + + if use emf; then + cat >> build.conf <<- EOF + CONFIG+=use_emf + DEFINES+=USE_EMF_OUTPUT + LIBS += -L\"${EPREFIX}/usr/include/libEMF\" -lEMF + EOF + fi + sed \ + -e "s:quickstart.pdf:../share/doc/${PF}/quickstart.pdf:g" \ + -e "s:README_GSIM.pdf:../share/doc/${PF}/README_GSIM.pdf:g" \ + -i mainform.h || die +} + +src_install() { + qt4-r2_src_install + dobin ${PN} + insinto /usr/share/${PN} + doins -r images ${PN}.ico + insinto /usr/share/${PN}/ui + doins *.ui +} diff --git a/sci-chemistry/gsim/metadata.xml b/sci-chemistry/gsim/metadata.xml new file mode 100644 index 000000000000..9ebe36a07183 --- /dev/null +++ b/sci-chemistry/gsim/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <use> + <flag name="emf">Support for .emf export</flag> + </use> + <upstream> + <remote-id type="sourceforge">gsim</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/gtk-gamess/Manifest b/sci-chemistry/gtk-gamess/Manifest new file mode 100644 index 000000000000..01eb84c1022f --- /dev/null +++ b/sci-chemistry/gtk-gamess/Manifest @@ -0,0 +1 @@ +DIST gtk-gamess-2.00.tar.gz 174125 SHA256 f282cdb94ddccba196b2ea0964cc2c26e3a4db5c8ac3b9f51d72a5a0e45f9e0e SHA512 1eb5e4d23f2c1061b46211db4757530cf8223e93f548940f671f5f55b4cab7c183e629254b9b65ef1d5b3147c44f613489d7447e6658c235f3dc9fcd9e998636 WHIRLPOOL 6fe37b9490dccd42bfa67ddf625a55c0e5a5a229a27b05736980b2134803ea07c1ffe03e504cb2fedaaf9c7ca53b2924e87836c356945ca91f25c6e7842e04bd diff --git a/sci-chemistry/gtk-gamess/gtk-gamess-2.00.ebuild b/sci-chemistry/gtk-gamess/gtk-gamess-2.00.ebuild new file mode 100644 index 000000000000..2003819a2b56 --- /dev/null +++ b/sci-chemistry/gtk-gamess/gtk-gamess-2.00.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="GUI for GAMESS, a General Atomic and Molecular Electronic Structure System" +HOMEPAGE="http://sourceforge.net/projects/gtk-gamess/" + +SRC_URI="mirror://sourceforge/gtk-gamess/${P}.tar.gz" +LICENSE="GPL-2" + +SLOT="0" + +KEYWORDS="~amd64 ~ppc ~x86" + +IUSE="" + +RDEPEND=" + gnome-base/libglade:2.0 + x11-libs/gtk+:2 + dev-libs/libxml2:2 + sci-chemistry/gamess" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_install() { + emake DESTDIR="${D}" install + dodoc README +} diff --git a/sci-chemistry/gtk-gamess/metadata.xml b/sci-chemistry/gtk-gamess/metadata.xml new file mode 100644 index 000000000000..0ddae2afddfa --- /dev/null +++ b/sci-chemistry/gtk-gamess/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <longdescription lang="en"> +GTK-Gamess is a frontend to GAMESS that allows users to queue up GAMESS +calculations and run them sequentially. +</longdescription> + <upstream> + <remote-id type="sourceforge">gtk-gamess</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/hollow/Manifest b/sci-chemistry/hollow/Manifest new file mode 100644 index 000000000000..70844b442e80 --- /dev/null +++ b/sci-chemistry/hollow/Manifest @@ -0,0 +1 @@ +DIST hollow-1.2.zip 62554 SHA256 9a2d97ad95fc102c1fd537e4fba3c1041ca0ba28d7d2dc0ddc8968b9d1b8722e SHA512 e253680cc0fae286ec697b2dac822b9e165d509cc7eefb27bbcafae6ab2617c3edc8cd9c8beefcc9ef2eb920c9d839fd0bc25f79d22160d857b1705cefbc05ca WHIRLPOOL 83d5d811defe43f91b3516dec873793d9aa6a6a93b2850289c1dd560d53b48a900c8064a16a33692edadb74d1c95b453c2c6fb3ff589a364b7393342e55f6587 diff --git a/sci-chemistry/hollow/hollow-1.2-r1.ebuild b/sci-chemistry/hollow/hollow-1.2-r1.ebuild new file mode 100644 index 000000000000..f98bc7158495 --- /dev/null +++ b/sci-chemistry/hollow/hollow-1.2-r1.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +DESCRIPTION="Production of surface images of proteins" +HOMEPAGE="http://hollow.sourceforge.net/" +#SRC_URI="mirror://sourceforge/${P}.zip" +SRC_URI="http://hollow.sourceforge.net/${P}.zip" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-3" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="${PYTHON_DEPS} + app-arch/unzip" + +src_install() { + python_setup + esvn_clean + python_foreach_impl python_domodule pdbstruct + python_moduleinto ${PN} + python_foreach_impl python_domodule *.py hollow.txt + + python_foreach_impl python_newscript ${PN}.py ${PN} + + dodoc README + python_optimize +} diff --git a/sci-chemistry/hollow/metadata.xml b/sci-chemistry/hollow/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/hollow/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/icm-browser/Manifest b/sci-chemistry/icm-browser/Manifest new file mode 100644 index 000000000000..6a993f2d9017 --- /dev/null +++ b/sci-chemistry/icm-browser/Manifest @@ -0,0 +1 @@ +DIST icm-browser-3.6-1i.i386.rpm 81669297 SHA256 6be8fdea54b5c744d6f8d164caead7dc49325428e07de6be458d655d8de5aef5 diff --git a/sci-chemistry/icm-browser/files/90icm-browser b/sci-chemistry/icm-browser/files/90icm-browser new file mode 100644 index 000000000000..554bb8a030c0 --- /dev/null +++ b/sci-chemistry/icm-browser/files/90icm-browser @@ -0,0 +1 @@ +MOLBROWSERPROHOME=/opt/icm-browser diff --git a/sci-chemistry/icm-browser/files/icm-browser.xpm b/sci-chemistry/icm-browser/files/icm-browser.xpm new file mode 100644 index 000000000000..f975898bdc6a --- /dev/null +++ b/sci-chemistry/icm-browser/files/icm-browser.xpm @@ -0,0 +1,326 @@ +/* XPM */ +static char *icm_browser[] = { +/* columns rows colors chars-per-pixel */ +"63 64 256 2 ", +" c #7C0E13", +". c #6C171B", +"X c #5F3B3A", 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+"UXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXu.u.k.k.k.k.k.k.x.k.k.x.x.d.x.k.k.k.k.u.u.UXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUX", +"UXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXk.k.u.u.k.k.u.u.k.u.u.k.u.u.k.k.k.UXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUX", +"UXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXu.u.u.u.u.u.u.UXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUX", +"UXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUX", +"UXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUXUX" +}; diff --git a/sci-chemistry/icm-browser/icm-browser-3.6.1i.ebuild b/sci-chemistry/icm-browser/icm-browser-3.6.1i.ebuild new file mode 100644 index 000000000000..e16e92495fea --- /dev/null +++ b/sci-chemistry/icm-browser/icm-browser-3.6.1i.ebuild @@ -0,0 +1,87 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit rpm eutils versionator + +MY_PV=$(replace_version_separator 2 '-' ) +MY_P="$PN-${MY_PV}" +DESCRIPTION="MolSoft LCC ICM Browser" +SRC_URI="${MY_P}.i386.rpm" +HOMEPAGE="http://www.molsoft.com/icm_browser.html" + +LICENSE="MolSoft" +SLOT=0 +KEYWORDS="~amd64 ~x86" +IUSE="" +RESTRICT="fetch" + +RDEPEND="!sci-chemistry/icm + virtual/libstdc++:3.3 + >=app-arch/bzip2-1.0.6-r4[abi_x86_32(-)] + >=media-libs/freetype-2.5.0.1[abi_x86_32(-)] + media-libs/libmng[abi_x86_32(-)] + >=media-libs/mesa-9.1.6[osmesa,abi_x86_32(-)] + >=media-libs/tiff-3.9.7-r1:3[abi_x86_32(-)] + >=sys-apps/keyutils-1.5.9-r1[abi_x86_32(-)] + virtual/jpeg:62[abi_x86_32(-)] + virtual/krb5[abi_x86_32(-)] + virtual/opengl[abi_x86_32(-)] + x11-libs/libICE[abi_x86_32(-)] + x11-libs/libSM[abi_x86_32(-)] + x11-libs/libX11[abi_x86_32(-)] + x11-libs/libXau[abi_x86_32(-)] + x11-libs/libXdamage[abi_x86_32(-)] + x11-libs/libXdmcp[abi_x86_32(-)] + x11-libs/libXext[abi_x86_32(-)] + x11-libs/libXfixes[abi_x86_32(-)] + x11-libs/libXmu[abi_x86_32(-)] + x11-libs/libXrender[abi_x86_32(-)] + x11-libs/libXt[abi_x86_32(-)] + x11-libs/libXxf86vm[abi_x86_32(-)] + x11-libs/libdrm[abi_x86_32(-)] + x11-libs/libxcb[abi_x86_32(-)] +" +DEPEND="" + +S="${WORKDIR}/usr/${PN}-pro-${MY_PV}" + +pkg_nofetch() { + einfo "Please download ${SRC_URI} from " + einfo "${HOMEPAGE}" + einfo "and move it to ${DISTDIR}" +} + +src_unpack() { + rpm_src_unpack +} + +src_install () { + instdir=/opt/icm-browser + dodir "${instdir}" + dodir "${instdir}/licenses" + cp -pPR * "${D}/${instdir}" + doenvd "${FILESDIR}/90icm-browser" + exeinto ${instdir} + doexe "${S}/icmbrowserpro" + doexe "${S}/lmhostid" + doexe "${S}/txdoc" + dosym "${instdir}/icmbrowserpro" /opt/bin/icmbrowserpro + dosym "${instdir}/txdoc" /opt/bin/txdoc + dosym "${instdir}/lmhostid" /opt/bin/lmhostid + # make desktop entry + doicon "${FILESDIR}"/${PN}.xpm + make_desktop_entry "icmbrowserpro -g" "ICM Browser" ${PN} Chemistry +} + +pkg_postinst () { + einfo + einfo "Documentation can be found in ${instdir}/man/" + einfo + einfo "If you want to upgrade free version of browser to pro version" + einfo "you should purchaise license from ${HOMEPAGE} and place it to" + einfo "${instdir}/licenses" + einfo +} diff --git a/sci-chemistry/icm-browser/metadata.xml b/sci-chemistry/icm-browser/metadata.xml new file mode 100644 index 000000000000..3cfdd8f68922 --- /dev/null +++ b/sci-chemistry/icm-browser/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-chemistry</herd> +<maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> +</maintainer> +</pkgmetadata> diff --git a/sci-chemistry/icm/Manifest b/sci-chemistry/icm/Manifest new file mode 100644 index 000000000000..3ccc244f1352 --- /dev/null +++ b/sci-chemistry/icm/Manifest @@ -0,0 +1,2 @@ +DIST icm-3.7-2e-linux.sh 345626160 SHA256 89e2db76b6dbe0b5305e7e5dd67c43c3850924eb2383732881599991083af0cf SHA512 996955f70f24605d705e9ce44397b26306808c8f6742ac38d7b0926c0df11ad678d365c3b25926765a286c20be9ea5f27acba25fa6281f4222ac7859e3593b77 WHIRLPOOL 16d0205fbf2dc72db1d36a537ee43778b4b597ec103497cad146c935b7ed1c3bde1eaed76afa41554504b899f8f5c3ec72e958d4de3c5f29526a05a9f278ab85 +DIST icm-3.7-3b-linux.sh 361208642 SHA256 8dbdf3d0c56ede2d60eb0c32928c6194ed606898c0335a5ffa79c1d33c2d3195 SHA512 b2865623db3acc7b3cf81eceaacd0cacb540b402935a5cd5c1d52efec1cadb243f033f2331cd12748d92b493fd2872bb840068239a3776123904c68d6f19efa2 WHIRLPOOL 48161846010d6fdf58fecda2a330295dee334a20bfe94f3096c4d0bd19e2c2dc115a4b3116162d0ea5f694e8d53fe0c881df2845ac72b2f27c209d1f92ea8a8b diff --git a/sci-chemistry/icm/files/90icm b/sci-chemistry/icm/files/90icm new file mode 100644 index 000000000000..ce8966c406c3 --- /dev/null +++ b/sci-chemistry/icm/files/90icm @@ -0,0 +1,3 @@ +ICMHOME=/opt/icm +LM_LICENSE_FILE=/opt/icm/licenses/license.dat +MANPATH=/opt/icm/man diff --git a/sci-chemistry/icm/files/icm.xpm b/sci-chemistry/icm/files/icm.xpm new file mode 100644 index 000000000000..fd6e1ed3e2ed --- /dev/null +++ b/sci-chemistry/icm/files/icm.xpm @@ -0,0 +1,326 @@ +/* XPM */ +static char *icm[] = { +/* columns rows colors chars-per-pixel */ +"63 64 256 2 ", +" c #7C0E13", +". c #6C171B", +"X c #5F3B3A", +"o c #663436", +"O c #5C554F", +"+ c #6E756A", +"@ c #90090F", +"# c #B70003", +"$ c #AD0C11", +"% c #8A2B2D", +"& c #A02C2E", +"* c #C90104", +"= c #DD050B", +"- c #E30309", +"; c #F2181A", +": c #E71014", +"> c #85605A", +", c #837468", +"< c #976263", +"1 c #6D837A", +"2 c #003EA9", +"3 c #053CB8", +"4 c #002EB9", +"5 c #0044AC", +"6 c #024BAC", +"7 c #0045A6", +"8 c #0D4DB4", +"9 c #0745B6", +"0 c #134EB9", +"q c #1B54BB", +"w c #1754B7", +"e c #0E52B0", +"r c #2057BE", +"t c #59569B", +"y c #534D99", +"u c #556D9C", +"i c #635EA0", +"p c #4574B4", +"a c #4978BA", +"s c #4C6EAB", +"d c #6C69A6", +"f c #7878AE", +"g c 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( || ( app-editors/vim app-editors/gvim ) ) + amd64? ( + 64bit? ( + =media-libs/tiff-3* + media-libs/libmng + app-crypt/mit-krb5 + app-arch/bzip2 + media-libs/libpng:1.2 + || ( virtual/jpeg:62 media-libs/jpeg:62 ) + x11-libs/libdrm + x11-libs/libX11 + sys-apps/keyutils + ) + 32bit? ( + virtual/libstdc++:3.3 + >=x11-libs/libX11-1.6.2[abi_x86_32(-)] + ) + ) + x86? ( + =media-libs/tiff-3* + media-libs/libpng:1.2 + media-libs/libmng + app-crypt/mit-krb5 + app-arch/bzip2 + x11-libs/libdrm + x11-libs/libX11 + sys-apps/keyutils + )" +RDEPEND="$DEPEND" + +S="${WORKDIR}" + +pkg_nofetch() { + einfo "Please download ${SRC_URI} from " + einfo "${HOMEPAGE}" + einfo "and move it to ${DISTDIR}" +} + +src_unpack() { + unpack_makeself + unpack ./data.tgz + rm ./data.tgz +} + +src_install () { + instdir=/opt/icm + dodir "${instdir}" + dodir "${instdir}/licenses" + cp -pPR * "${D}/${instdir}" + rm "${D}/${instdir}/unzip" + doenvd "${FILESDIR}/90icm" || die + if use x86; then + dosym "${instdir}/icm" /opt/bin/icm || die + dosym "${instdir}/icmng" /opt/bin/icmng || die + rm "${D}/${instdir}/icm64" || die + rm "${D}/${instdir}/icmng64" || die + rm "${D}/${instdir}/icmora64" || die + rm "${D}/${instdir}/icmora64.bin" || die + rm -rf "${D}/${instdir}/lib64" || die + elif use amd64; then + if use 32bit; then + dosym "${instdir}/icm" /opt/bin/icm || die + dosym "${instdir}/icmng" /opt/bin/icmng || die + fi + if use 64bit; then + dosym "${instdir}/icm64" /opt/bin/icm64 || die + dosym "${instdir}/icmng64" /opt/bin/icmng64 || die + fi + if ! use 64bit; then + rm "${D}/${instdir}/icm64" || die + rm "${D}/${instdir}/icmng64" || die + rm "${D}/${instdir}/icmora64{,.bin}" || die + rm -rf "${D}/${instdir}/lib64" || die + fi + if ! use 32bit; then + rm "${D}/${instdir}/icm" || die + rm "${D}/${instdir}/icmng" || die + rm "${D}/${instdir}/icmora" || die + rm "${D}/${instdir}/icmora.bin" || die + rm -rf "${D}/${instdir}/lib32" || die + fi + fi + dosym "${instdir}/txdoc" /opt/bin/txdoc || die + dosym "${instdir}/lmhostid" /opt/bin/lmhostid || die + # install vim files + if use vim-syntax ; then + insinto /usr/share/vim/vimfiles/ftdetect + doins "${WORKDIR}/icm.vim" + insinto /usr/share/vim/vimfiles/syntax + doins "${WORKDIR}/icm.vim" + rm "${D}/${instdir}/icm.vim" || die + fi + # make desktop entry + doicon "${FILESDIR}/${PN}.xpm" + if use x86; then + make_desktop_entry "icm -g" "ICM Pro" ${PN} Chemistry + elif use amd64; then + use 32bit && make_desktop_entry "icm -g" "ICM Pro (32bit)" ${PN} Chemistry + use 64bit && make_desktop_entry "icm64 -g" "ICM Pro (64bit)" ${PN} Chemistry + fi +} + +pkg_postinst () { + einfo + einfo "Documentation can be found in ${instdir}/man/" + einfo + einfo "You will need to place your license in ${instdir}/licenses/" + einfo + +} diff --git a/sci-chemistry/icm/icm-3.7.3b.ebuild b/sci-chemistry/icm/icm-3.7.3b.ebuild new file mode 100644 index 000000000000..bee2194b3a88 --- /dev/null +++ b/sci-chemistry/icm/icm-3.7.3b.ebuild @@ -0,0 +1,140 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit eutils unpacker versionator + +MY_PV=$(replace_version_separator 2 '-' ) +MY_P="$PN-${MY_PV}" + +DESCRIPTION="MolSoft LCC ICM Pro" +HOMEPAGE="http://www.molsoft.com/icm_pro.html" +SRC_URI="${MY_P}-linux.sh" + +LICENSE="MolSoft" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="32bit 64bit vim-syntax" + +REQUIRED_USE="^^ ( + ( !32bit 64bit ) + ( 32bit !64bit ) + ( 32bit 64bit ) + )" + +RESTRICT="fetch" + +DEPEND="!sci-chemistry/icm-browser + app-arch/unzip + vim-syntax? ( || ( app-editors/vim app-editors/gvim ) ) + amd64? ( + 64bit? ( + =media-libs/tiff-3* + media-libs/libmng + app-crypt/mit-krb5 + app-arch/bzip2 + media-libs/libpng:1.2 + || ( virtual/jpeg:62 media-libs/jpeg:62 ) + x11-libs/libdrm + x11-libs/libX11 + sys-apps/keyutils + ) + 32bit? ( + virtual/libstdc++:3.3 + >=x11-libs/libX11-1.6.2[abi_x86_32(-)] + ) + ) + x86? ( + =media-libs/tiff-3* + media-libs/libpng:1.2 + media-libs/libmng + app-crypt/mit-krb5 + app-arch/bzip2 + x11-libs/libdrm + x11-libs/libX11 + sys-apps/keyutils + )" +RDEPEND="$DEPEND" + +S="${WORKDIR}" + +pkg_nofetch() { + einfo "Please download ${SRC_URI} from " + einfo "${HOMEPAGE}" + einfo "and move it to ${DISTDIR}" +} + +src_unpack() { + unpack_makeself + unpack ./data.tgz + rm ./data.tgz +} + +src_install () { + instdir=/opt/icm + dodir "${instdir}" + dodir "${instdir}/licenses" + cp -pPR * "${D}/${instdir}" + rm "${D}/${instdir}/unzip" + doenvd "${FILESDIR}/90icm" || die + if use x86; then + dosym "${instdir}/icm" /opt/bin/icm || die + dosym "${instdir}/icmng" /opt/bin/icmng || die + rm "${D}/${instdir}/icm64" || die + rm "${D}/${instdir}/icmng64" || die + rm "${D}/${instdir}/icmora64" || die + rm "${D}/${instdir}/icmora64.bin" || die + rm -rf "${D}/${instdir}/lib64" || die + elif use amd64; then + if use 32bit; then + dosym "${instdir}/icm" /opt/bin/icm || die + dosym "${instdir}/icmng" /opt/bin/icmng || die + fi + if use 64bit; then + dosym "${instdir}/icm64" /opt/bin/icm64 || die + dosym "${instdir}/icmng64" /opt/bin/icmng64 || die + fi + if ! use 64bit; then + rm "${D}/${instdir}/icm64" || die + rm "${D}/${instdir}/icmng64" || die + rm "${D}/${instdir}/icmora64{,.bin}" || die + rm -rf "${D}/${instdir}/lib64" || die + fi + if ! use 32bit; then + rm "${D}/${instdir}/icm" || die + rm "${D}/${instdir}/icmng" || die + rm "${D}/${instdir}/icmora" || die + rm "${D}/${instdir}/icmora.bin" || die + rm -rf "${D}/${instdir}/lib32" || die + fi + fi + dosym "${instdir}/txdoc" /opt/bin/txdoc || die + dosym "${instdir}/lmhostid" /opt/bin/lmhostid || die + # install vim files + if use vim-syntax ; then + insinto /usr/share/vim/vimfiles/ftdetect + doins "${WORKDIR}/icm.vim" + insinto /usr/share/vim/vimfiles/syntax + doins "${WORKDIR}/icm.vim" + rm "${D}/${instdir}/icm.vim" || die + fi + # make desktop entry + doicon "${FILESDIR}/${PN}.xpm" + if use x86; then + make_desktop_entry "icm -g" "ICM Pro" ${PN} Chemistry + elif use amd64; then + use 32bit && make_desktop_entry "icm -g" "ICM Pro (32bit)" ${PN} Chemistry + use 64bit && make_desktop_entry "icm64 -g" "ICM Pro (64bit)" ${PN} Chemistry + fi +} + +pkg_postinst () { + einfo + einfo "Documentation can be found in ${instdir}/man/" + einfo + einfo "You will need to place your license in ${instdir}/licenses/" + einfo + +} diff --git a/sci-chemistry/icm/metadata.xml b/sci-chemistry/icm/metadata.xml new file mode 100644 index 000000000000..55d880878df8 --- /dev/null +++ b/sci-chemistry/icm/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <use> + <flag name="32bit">Automatically generated description for 32bit</flag> + <flag name="64bit">Automatically generated description for 64bit</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/imosflm/Manifest b/sci-chemistry/imosflm/Manifest new file mode 100644 index 000000000000..2ce7d893b7fd --- /dev/null +++ b/sci-chemistry/imosflm/Manifest @@ -0,0 +1 @@ +DIST imosflm-1.0.7.zip 941784 SHA256 b067261b4d7ef2f1f7581ddeaa08252d29f889acf89ce190eb0d8b30aa94b107 SHA512 f3163e1f71c5b1e24d6b3fbd5a040bbcebae25485d1258eef4b2725821f5f96c1260adb2bcc3ab57179d7b9b9e538ddf0494ab9b5be259b98d138fddacec8c77 WHIRLPOOL bd2b6bcdcc241fde41fe2ba99bd1e2f47bc444c46ee36a5b332d5c018b81a9d649378110a8bffa48ffc67a19b04ede7e61846b53a250e5fe3058ec0313fda80c diff --git a/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch b/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch new file mode 100644 index 000000000000..5d0dd7010910 --- /dev/null +++ b/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch @@ -0,0 +1,12 @@ +diff --git a/c/tkImageLoad.c b/c/tkImageLoad.c +index e7c46f0..1496a15 100755 +--- a/c/tkImageLoad.c ++++ b/c/tkImageLoad.c +@@ -12,6 +12,7 @@ + #include <tcl.h> + #include <tk.h> + #include <assert.h> ++#include <stdlib.h> + + #define HEADER_LINE_LENGTH 512 + #define BYTES_PER_PIXEL 2 diff --git a/sci-chemistry/imosflm/files/1.0.4-tk.patch b/sci-chemistry/imosflm/files/1.0.4-tk.patch new file mode 100644 index 000000000000..a90175194eb4 --- /dev/null +++ b/sci-chemistry/imosflm/files/1.0.4-tk.patch @@ -0,0 +1,50 @@ +--- c/tkImageLoad.c 2009-08-14 21:10:19.000000000 +0200 ++++ c/tkImageLoad.c.new 2009-08-14 21:10:55.000000000 +0200 +@@ -19,6 +19,7 @@ + //#define BLOCKED 1 + //#define UNBLOCKED 1 + #define IN_BLOCK_FLIP 1 ++#define USE_COMPOSITELESS_PHOTO_PUT_BLOCK + + /* *********************************************************************/ + +--- c/tkImageLoad.c 2009-08-14 21:13:29.000000000 +0200 ++++ c/tkImageLoad.c.new 2009-08-14 21:14:59.000000000 +0200 +@@ -272,9 +272,11 @@ + } + /* put the photo block into the image */ + #ifdef __alpha +- Tk_PhotoPutBlock(dp, &db, 0, 0, width, height); ++ Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, ++ TK_PHOTO_COMPOSITE_OVERLAY); + #else +- Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, TK_PHOTO_COMPOSITE_SET); ++ Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, TK_PHOTO_COMPOSITE_SET, ++ TK_PHOTO_COMPOSITE_OVERLAY); + #endif + + /* Free the photo block's memory now it is finished with */ +@@ -417,9 +419,11 @@ + + /* put the photo block back into the image */ + #ifdef __alpha +- Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height); ++ Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height, ++ TK_PHOTO_COMPOSITE_OVERLAY); + #else +- Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,TK_PHOTO_COMPOSITE_SET); ++ Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,TK_PHOTO_COMPOSITE_SET, ++ TK_PHOTO_COMPOSITE_OVERLAY); + #endif + /* Free the photo block's memory now it is finished with */ + if (block.pixelPtr) { +--- c/tkImageLoad.c 2009-08-14 21:15:06.000000000 +0200 ++++ c/tkImageLoad.c.new 2009-08-14 21:16:53.000000000 +0200 +@@ -9,6 +9,7 @@ + \************************************************************************/ + + #include <stdio.h> ++#include <string.h> + #include <tcl.h> + #include <tk.h> + #include <assert.h> diff --git a/sci-chemistry/imosflm/files/1.0.7-libpng16.patch b/sci-chemistry/imosflm/files/1.0.7-libpng16.patch new file mode 100644 index 000000000000..27efc6f36f4b --- /dev/null +++ b/sci-chemistry/imosflm/files/1.0.7-libpng16.patch @@ -0,0 +1,13 @@ +http://bugs.gentoo.org/467036 + +--- src/contrast.tcl ++++ src/contrast.tcl +@@ -3,7 +3,7 @@ + + package require palette + +-image create photo ::img::pixel_count_v -data "iVBORw0KGgoAAAANSUhEUgAAAA4AAABCCAIAAAGft0AHAAAABGdBTUEAAYagMeiWXwAAASFJREFUKJGtVFEWhCAINJ9H4f4n4jD7YauAA1jGT2EwAxNyMXMppZZu3bv6Q3t3iH7ob3fOPz3wdLoi7y8V1SOZp0NE02Hm7quc6VSVaokFKzMD8qKUUd0tyEQ0z1DchNQaud+JCHclzeIDOUCle7EjcA/XPZU4Klb9y2GDY68LVe8YiAihmXT052G9SQ0+m4yN2J7EZqrvnZpheMdGRLnq5/ViddTusPeux9o5G7fdsskrV9ej8rw3I80LhNUUgqmvwCY8izozZcvo5tGt1owfoGJhoEVtgcXg2da2gJa0JYESseRJ8gvyOYSGlxUkScYFoBoJB+RZrR+H2sWx2vEQrnv0pa4HYkFqF7UHrefRdjE5zQQFAp/Nqwf8XNePZ+AHq5sOPlXtupMAAAAASUVORK5CYII=" ++image create photo ::img::pixel_count_v -data "iVBORw0KGgoAAAANSUhEUgAAAA4AAABCCAIAAAGft0AHAAAABGdBTUEAAYagMeiWXwAAASFJREFUeJytVFEWhCAINJ9H4f4n4jD7YauAA1jGT2EwAxNyMXMppZZu3bv6Q3t3iH7ob3fOPz3wdLoi7y8V1SOZp0NE02Hm7quc6VSVaokFKzMD8qKUUd0tyEQ0z1DchNQaud+JCHclzeIDOUCle7EjcA/XPZU4Klb9y2GDY68LVe8YiAihmXT052G9SQ0+m4yN2J7EZqrvnZpheMdGRLnq5/ViddTusPeux9o5G7fdsskrV9ej8rw3I80LhNUUgqmvwCY8izozZcvo5tGt1owfoGJhoEVtgcXg2da2gJa0JYESseRJ8gvyOYSGlxUkScYFoBoJB+RZrR+H2sWx2vEQrnv0pa4HYkFqF7UHrefRdjE5zQQFAp/Nqwf8XNePZ+AHq5sOPv4fGP4AAAAASUVORK5CYII=" + + class Contrast { + inherit Palette diff --git a/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild b/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild new file mode 100644 index 000000000000..e49667e50dc7 --- /dev/null +++ b/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils multilib toolchain-funcs versionator + +MY_PV="$(delete_all_version_separators ${PV})" + +DESCRIPTION="A new GUI for the Mosflm crystallographic data processing tool" +HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/imosflm" +SRC_URI="${HOMEPAGE}/ver${MY_PV}/downloads/${P}.zip" + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-lang/tcl:0= + >=dev-tcltk/itcl-3.3 + >=dev-tcltk/itk-3.3 + >=dev-tcltk/iwidgets-4 + >=dev-tcltk/tdom-0.8 + >=dev-tcltk/tkimg-1.3 + >=dev-tcltk/tktreectrl-2.1 + dev-tcltk/anigif + dev-tcltk/combobox + dev-tcltk/tablelist + >=sci-chemistry/mosflm-7.0.9" +DEPEND="app-arch/unzip" + +S=${WORKDIR}/${PN} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-libpng16.patch +} + +src_install(){ + rm -rf lib/{*.so,anigif,combobox} + + insinto /usr/$(get_libdir)/${PN} + doins -r "${S}"/{src,bitmaps,lib} + fperms 775 /usr/$(get_libdir)/${PN}/src/imosflm + + cat >> "${T}"/23imosflm <<- EOF + IMOSFLM_VERSION="${PV}" + EOF + + doenvd "${T}"/23imosflm + + make_wrapper imosflm /usr/$(get_libdir)/${PN}/src/imosflm +} diff --git a/sci-chemistry/imosflm/metadata.xml b/sci-chemistry/imosflm/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/imosflm/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest new file mode 100644 index 000000000000..44e86a598441 --- /dev/null +++ b/sci-chemistry/jmol/Manifest @@ -0,0 +1,3 @@ +DIST Jmol-12.0.45-full.tar.gz 26501382 SHA256 f9a3fe242841f9b56a718f8da2efe4130e497afe2c12d77f2e68344c62d7f70e SHA512 b0e999335c039e5bde5e261c076f3eb75dd0c33a351445d5c086995d32b3fd03795b3a11dc57a06bf8ac39e74945f3c9f4547ecfbf18b56d827b9a42f5208c11 WHIRLPOOL d0bbae1fc5c96ddfb4dd29f6e09701e496a333a2f44ba266e2a24c60de2d36d73c2184bd9b8f6054b0955535d49856154d6101644ef0297b825c4f6745cfe3bb +DIST Jmol-12.2.27-full.tar.gz 29493780 SHA256 f2ca3b810ea16a488f6f57003d2a407c8ac040d610479a7ae6d95631157db801 SHA512 a8608e64dc06b6d3b0cb7e911f0a224456a65bdc15c51d6b420ee6abf8d82cdcec9f54f6b1a51cfe032e2e074f173f50a88bcff783311de19ce9b95ad990ebca WHIRLPOOL ae0826eab7eb364acb4f30eb77850450b871a24d8940eaabaf8fe9f3770efc39deb604e3c5f875a695c0d33b516ad47d523982c7a6460f2421f961f50a7680bf +DIST jmol-selfSignedCertificate.store.tar 10240 SHA256 416744934991ef4f1fa298c0afc8e855d43771de2f2278ed3fbc60f707ea46b2 SHA512 2c3e9d1183a0b174273346d0fba0729caa415ef53fe01629a4c47daa2393c9e18ca3f57984911e6340197429cf0ee581c64bb9b6072db902102976030d9f2c23 WHIRLPOOL 79dc2b2c95b304569f44bb986af3aa25150b0c5f8a9fc9b1698a979647800e60d0f20a7a4abbc89533a21f3d7f4b93a430840eed71bbe04b1cc0bdbcfae7fe63 diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch new file mode 100644 index 000000000000..3b43c219d94f --- /dev/null +++ b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch @@ -0,0 +1,96 @@ +diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt +--- jmol-11.0.3-orig/manifest/applet0.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet0.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,6 @@ ++Main-Class: JmolApplet
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
++
+diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt +--- jmol-11.0.3-orig/manifest/applet1.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet1.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,6 @@ ++Name: org/jmol/api/
++Sealed: false
++
++Name: org/jmol/applet/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt +--- jmol-11.0.3-orig/manifest/applet2.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet2.txt 2007-05-16 01:56:19.000000000 -0500 +@@ -0,0 +1,3 @@ ++Name: javax/vecmath/ ++ ++ +diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt +--- jmol-11.0.3-orig/manifest/applet3.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet3.txt 2007-05-16 01:56:47.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/g3d/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt +--- jmol-11.0.3-orig/manifest/applet4.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet4.txt 2007-05-16 01:57:05.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/adapter/smarter/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt +--- jmol-11.0.3-orig/manifest/applet5.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet5.txt 2007-05-16 01:57:23.000000000 -0500 +@@ -0,0 +1,4 @@ ++Name: org/openscience/jmol/ui/ ++Sealed: true ++ ++ +diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt +--- jmol-11.0.3-orig/manifest/applet6.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet6.txt 2007-05-16 01:57:46.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/viewer/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt +--- jmol-11.0.3-orig/manifest/appletMain.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/appletMain.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,5 @@ ++Manifest-Version: 1.0
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
+diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt +--- jmol-11.0.3-orig/manifest/appletMonolithic.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/appletMonolithic.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,7 @@ ++Main-Class: JmolApplet
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt +--- jmol-11.0.3-orig/manifest/applet.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,2 @@ ++Manifest-Version: 1.0
++Sealed: true
+\ No newline at end of file +diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt +--- jmol-11.0.3-orig/manifest/application.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/application.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1 @@ ++Main-Class: org.openscience.jmol.app.Jmol
+diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt +--- jmol-11.0.3-orig/manifest/jvxl.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/jvxl.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1 @@ ++Main-Class: org.openscience.jvxl.Jvxl
diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch new file mode 100644 index 000000000000..c1b22e83c615 --- /dev/null +++ b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch @@ -0,0 +1,313 @@ +--- build.xml 2011-02-25 12:59:43.000000000 -0600 ++++ build.xml.new 2011-02-27 12:16:02.398959959 -0600 +@@ -110,10 +110,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">
+- <srcfiles dir="doc/source"
+- includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -123,14 +119,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -140,14 +128,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolDevelopersGuide.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -157,14 +137,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -385,17 +357,12 @@ + </target>
+
+ <target name="jar" id="jar"
+- depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
++ depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">
+ <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >
+ <fileset dir="build/doc/JmolUserGuide">
+ <include name="**/*.html" />
+ </fileset>
+ </copy>
+- <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >
+- <fileset dir="build/doc/JmolUserGuide_fr">
+- <include name="**/*.html" />
+- </fileset>
+- </copy>
+ <copy todir="${classes.dir}/org/openscience/jmol/Data" >
+ <fileset dir="build/doc/JmolHistory">
+ <include name="**/*.html" />
+@@ -587,18 +554,6 @@ + <fileset dir="${appletjars.dir}" includes="**/*"/>
+ </jar>
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+- </fileset>
+- </jar>
+- </sequential>
+- </for>
+-
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+ <fileset dir="${applet.classes.dir}">
+ <include name="org/jmol/minimize/**" />
+@@ -712,7 +667,6 @@ + <include name="org/jmol/bspt/**" />
+ <include name="org/jmol/g3d/**" />
+ <include name="org/jmol/geodesic/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/modelset/**" />
+ <include name="org/jmol/script/**" />
+ <include name="org/jmol/shape/**" />
+@@ -738,7 +692,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -851,16 +804,6 @@ + keystore="selfSignedCertificate/selfSignedCertificate.store"
+ storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"
+- keystore="selfSignedCertificate/selfSignedCertificate.store"
+- storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+- </sequential>
+- </for>
+-
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- this one must be treated specially because of jar indexing
+ we cannot simply rename the jar file, because the index has
+@@ -906,7 +849,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
+@@ -944,18 +886,6 @@ + </fileset>
+ </jar>
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+- </fileset>
+- </jar>
+- </sequential>
+- </for>
+-
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+ <fileset dir="${applet.classes.dir}">
+ <include name="org/jmol/minimize/**" />
+@@ -1069,7 +999,6 @@ + <include name="org/jmol/bspt/**" />
+ <include name="org/jmol/g3d/**" />
+ <include name="org/jmol/geodesic/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/modelset/**" />
+ <include name="org/jmol/script/**" />
+ <include name="org/jmol/shape/**" />
+@@ -1095,7 +1024,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -1104,7 +1032,7 @@ + </target>
+
+ <target name="dist" id="dist"
+- depends="doc,main-i18n,main,signed-applet">
++ depends="doc,main,signed-applet">
+ <!-- first build binary distribution -->
+ <delete dir="build/dist/jmol-${version}"/>
+ <mkdir dir="build/dist/jmol-${version}"/>
+@@ -1163,7 +1091,6 @@ + <fileset dir=".">
+ <include name="applet.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -1246,7 +1173,6 @@ + <fileset dir=".">
+ <include name="apisio.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -1342,7 +1268,7 @@ + <target name="xclean" id="xclean">
+ </target>
+
+- <target name="spotless" id="spotless" depends="clean,spotless-i18n">
++ <target name="spotless" id="spotless" depends="clean">
+ <delete dir="build"/>
+ <delete dir="${javadoc.dir}"/>
+ <delete dir="packaging/rpm/dist"/>
+@@ -1406,16 +1332,6 @@ + <arg value="../../../doc/source/JmolGuide.docbook.xml" />
+ <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+ </java>
+- <echo message="Generating user's guide (fr)" />
+- <mkdir dir="build/doc/JmolUserGuide_fr" />
+- <java fork="true" dir="build/doc/JmolUserGuide_fr"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <jvmarg value="${proxyHost}" />
+- <jvmarg value="${proxyPort}" />
+- <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />
+- <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolHistory" id="jmolHistory"
+@@ -1430,26 +1346,6 @@ + <arg value="../../../doc/source/JmolHistory.xml" />
+ <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+ </java>
+- <echo message="Generating history of changes (fr)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_fr.html" />
+- <arg value="../../../doc/source/JmolHistory_fr.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=fr" />
+- </java>
+- <echo message="Generating history of changes (nl)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_nl.html" />
+- <arg value="../../../doc/source/JmolHistory_nl.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=nl" />
+- </java>
+ </target>
+
+ <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
+@@ -1463,24 +1359,6 @@ + <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating developer's guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_fr.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating developer's guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_de.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
+@@ -1494,24 +1372,6 @@ + <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating applet guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_fr.html" />
+- <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating applet guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_de.html" />
+- <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="test" id="test" depends="main,compile-tests">
+@@ -1543,12 +1403,4 @@ + <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
+ </target>
+
+- <!-- i18n stuff -->
+- <target name="main-i18n" depends="classes">
+- <ant antfile="tools/build-i18n.xml" target="main-i18n"/>
+- </target>
+- <target name="spotless-i18n">
+- <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>
+- </target>
+-
+ </project>
diff --git a/sci-chemistry/jmol/files/caffeine.xyz b/sci-chemistry/jmol/files/caffeine.xyz new file mode 100644 index 000000000000..f0325b049f3c --- /dev/null +++ b/sci-chemistry/jmol/files/caffeine.xyz @@ -0,0 +1,26 @@ +24 +Caffeine +H -3.3804130 -1.1272367 0.5733036 +N 0.9668296 -1.0737425 -0.8198227 +C 0.0567293 0.8527195 0.3923156 +N -1.3751742 -1.0212243 -0.0570552 +C -1.2615018 0.2590713 0.5234135 +C -0.3068337 -1.6836331 -0.7169344 +C 1.1394235 0.1874122 -0.2700900 +N 0.5602627 2.0839095 0.8251589 +O -0.4926797 -2.8180554 -1.2094732 +C -2.6328073 -1.7303959 -0.0060953 +O -2.2301338 0.7988624 1.0899730 +H 2.5496990 2.9734977 0.6229590 +C 2.0527432 -1.7360887 -1.4931279 +H -2.4807715 -2.7269528 0.4882631 +H -3.0089039 -1.9025254 -1.0498023 +H 2.9176101 -1.8481516 -0.7857866 +H 2.3787863 -1.1211917 -2.3743655 +H 1.7189877 -2.7489920 -1.8439205 +C -0.1518450 3.0970046 1.5348347 +C 1.8934096 2.1181245 0.4193193 +N 2.2861252 0.9968439 -0.2440298 +H -0.1687028 4.0436553 0.9301094 +H 0.3535322 3.2979060 2.5177747 +H -1.2074498 2.7537592 1.7203047 diff --git a/sci-chemistry/jmol/files/index.html b/sci-chemistry/jmol/files/index.html new file mode 100644 index 000000000000..35a5d49217e2 --- /dev/null +++ b/sci-chemistry/jmol/files/index.html @@ -0,0 +1,14 @@ +<html> + <head> + <title>Jmol Test Page</title> + <div align="center"> <b>All the Sugar and Twice the Caffeine.</b> <br><br> + <script src="./Jmol.js"></script> + </head> + <body> + <script> + jmolInitialize("./"); // REQUIRED + jmolApplet(400, "load ./caffeine.xyz"); + </script></div> + </body> +</html> + diff --git a/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch b/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch new file mode 100644 index 000000000000..3b43c219d94f --- /dev/null +++ b/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch @@ -0,0 +1,96 @@ +diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt +--- jmol-11.0.3-orig/manifest/applet0.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet0.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,6 @@ ++Main-Class: JmolApplet
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
++
+diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt +--- jmol-11.0.3-orig/manifest/applet1.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet1.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,6 @@ ++Name: org/jmol/api/
++Sealed: false
++
++Name: org/jmol/applet/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt +--- jmol-11.0.3-orig/manifest/applet2.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet2.txt 2007-05-16 01:56:19.000000000 -0500 +@@ -0,0 +1,3 @@ ++Name: javax/vecmath/ ++ ++ +diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt +--- jmol-11.0.3-orig/manifest/applet3.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet3.txt 2007-05-16 01:56:47.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/g3d/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt +--- jmol-11.0.3-orig/manifest/applet4.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet4.txt 2007-05-16 01:57:05.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/adapter/smarter/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt +--- jmol-11.0.3-orig/manifest/applet5.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet5.txt 2007-05-16 01:57:23.000000000 -0500 +@@ -0,0 +1,4 @@ ++Name: org/openscience/jmol/ui/ ++Sealed: true ++ ++ +diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt +--- jmol-11.0.3-orig/manifest/applet6.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet6.txt 2007-05-16 01:57:46.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/viewer/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt +--- jmol-11.0.3-orig/manifest/appletMain.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/appletMain.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,5 @@ ++Manifest-Version: 1.0
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
+diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt +--- jmol-11.0.3-orig/manifest/appletMonolithic.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/appletMonolithic.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,7 @@ ++Main-Class: JmolApplet
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt +--- jmol-11.0.3-orig/manifest/applet.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,2 @@ ++Manifest-Version: 1.0
++Sealed: true
+\ No newline at end of file +diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt +--- jmol-11.0.3-orig/manifest/application.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/application.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1 @@ ++Main-Class: org.openscience.jmol.app.Jmol
+diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt +--- jmol-11.0.3-orig/manifest/jvxl.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/jvxl.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1 @@ ++Main-Class: org.openscience.jvxl.Jvxl
diff --git a/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch b/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch new file mode 100644 index 000000000000..25fd17e36c68 --- /dev/null +++ b/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch @@ -0,0 +1,266 @@ +--- jmol-11.0.3-orig/build.xml 2007-05-17 09:35:04.000000000 -0500 ++++ jmol-11.0.3/build.xml 2007-05-17 09:40:21.000000000 -0500 +@@ -100,10 +100,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">
+- <srcfiles dir="doc/source"
+- includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -113,14 +109,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -130,14 +118,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolDevelopersGuide.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -147,14 +127,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -332,17 +304,12 @@ + </target>
+
+ <target name="jar" id="jar"
+- depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
++ depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">
+ <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >
+ <fileset dir="build/doc/JmolUserGuide">
+ <include name="**/*.html" />
+ </fileset>
+ </copy>
+- <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >
+- <fileset dir="build/doc/JmolUserGuide_fr">
+- <include name="**/*.html" />
+- </fileset>
+- </copy>
+ <copy todir="${classes.dir}/org/openscience/jmol/Data" >
+ <fileset dir="build/doc/JmolHistory">
+ <include name="**/*.html" />
+@@ -462,7 +429,6 @@ + <!-- note that this class is included in JmolApplet0.jar -->
+ <exclude name="org/jmol/api/JmolAppletInterface.class" />
+ <include name="org/jmol/applet/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/popup/**" />
+ </fileset>
+ </jar>
+@@ -502,12 +468,6 @@ + </fileset>
+ </jar>
+
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet_i18n.jar" manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/**" />
+- </fileset>
+- </jar>
+-
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- changes to this must be replicated below for the signed applet -->
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0.jar"
+@@ -527,7 +487,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet4.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet5.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet6.jar" />
+- <pathelement path="${jmol.applet.build.dir}/JmolApplet_i18n.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -564,10 +523,6 @@ + signedjar="${jmol.applet.build.dir}/JmolAppletSigned6.jar"
+ keystore="selfSignedCertificate/selfSignedCertificate.store"
+ storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+- <signjar jar="${jmol.applet.build.dir}/JmolApplet_i18n.jar"
+- signedjar="${jmol.applet.build.dir}/JmolAppletSigned_i18n.jar"
+- keystore="selfSignedCertificate/selfSignedCertificate.store"
+- storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- this one must be treated specially because of jar indexing
+@@ -589,7 +544,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned4.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned5.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned6.jar" />
+- <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned_i18n.jar" />
+ </indexjars>
+ </jar>
+ <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
+@@ -599,7 +553,7 @@ + </target>
+
+ <target name="dist" id="dist"
+- depends="doc,main-i18n,main,signed-applet">
++ depends="doc,main,signed-applet">
+ <!-- first build binary distribution -->
+ <delete dir="build/dist/jmol-${version}"/>
+ <mkdir dir="build/dist/jmol-${version}"/>
+@@ -655,7 +609,6 @@ + <fileset dir=".">
+ <include name="applet.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -744,7 +697,6 @@ + <fileset dir=".">
+ <include name="apisio.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -839,7 +791,7 @@ + <target name="xclean" id="xclean">
+ </target>
+
+- <target name="spotless" id="spotless" depends="clean,spotless-i18n">
++ <target name="spotless" id="spotless" depends="clean">
+ <delete dir="build"/>
+ <delete dir="${javadoc.dir}"/>
+ <delete dir="packaging/rpm/dist"/>
+@@ -900,16 +852,6 @@ + <arg value="../../../doc/source/JmolGuide.docbook.xml" />
+ <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+ </java>
+- <echo message="Generating user's guide (fr)" />
+- <mkdir dir="build/doc/JmolUserGuide_fr" />
+- <java fork="true" dir="build/doc/JmolUserGuide_fr"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <jvmarg value="${proxyHost}" />
+- <jvmarg value="${proxyPort}" />
+- <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />
+- <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolHistory" id="jmolHistory"
+@@ -924,26 +866,6 @@ + <arg value="../../../doc/source/JmolHistory.xml" />
+ <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+ </java>
+- <echo message="Generating history of changes (fr)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_fr.html" />
+- <arg value="../../../doc/source/JmolHistory_fr.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=fr" />
+- </java>
+- <echo message="Generating history of changes (nl)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_nl.html" />
+- <arg value="../../../doc/source/JmolHistory_nl.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=nl" />
+- </java>
+ </target>
+
+ <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
+@@ -957,24 +879,6 @@ + <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating developer's guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_fr.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating developer's guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_de.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
+@@ -988,24 +892,6 @@ + <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating applet guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_fr.html" />
+- <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating applet guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_de.html" />
+- <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="test" id="test" depends="main,compile-tests">
+@@ -1036,12 +922,4 @@ + <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
+ </target>
+
+- <!-- i18n stuff -->
+- <target name="main-i18n" depends="classes">
+- <ant antfile="build-i18n.xml" target="main-i18n"/>
+- </target>
+- <target name="spotless-i18n">
+- <ant antfile="build-i18n.xml" target="spotless-i18n"/>
+- </target>
+-
+ </project>
diff --git a/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch new file mode 100644 index 000000000000..0a43faaf653d --- /dev/null +++ b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch @@ -0,0 +1,330 @@ +--- orig-build.xml 2012-05-31 13:42:43.943062427 -0500 ++++ build.xml 2012-05-31 14:01:01.691982062 -0500 +@@ -52,8 +52,6 @@ +
+ <property file="proxy.properties" />
+
+- <import file="tools/build-i18n.xml"/>
+-
+ <path id="project.class.path">
+ <fileset dir="${lib.dir}">
+ <include name="*.jar" />
+@@ -111,10 +109,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">
+- <srcfiles dir="doc/source"
+- includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -124,14 +118,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -141,14 +127,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolDevelopersGuide.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -158,14 +136,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -388,17 +358,12 @@ + </target>
+
+ <target name="jar" id="jar"
+- depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
++ depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">
+ <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >
+ <fileset dir="build/doc/JmolUserGuide">
+ <include name="**/*.html" />
+ </fileset>
+ </copy>
+- <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >
+- <fileset dir="build/doc/JmolUserGuide_fr">
+- <include name="**/*.html" />
+- </fileset>
+- </copy>
+ <copy todir="${classes.dir}/org/openscience/jmol/Data" >
+ <fileset dir="build/doc/JmolHistory">
+ <include name="**/*.html" />
+@@ -603,18 +568,6 @@ + <fileset dir="${appletjars.dir}" includes="**/*"/>
+ </jar>
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+- </fileset>
+- </jar>
+- </sequential>
+- </for>
+-
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+ <fileset dir="${applet.classes.dir}">
+ <include name="org/jmol/minimize/**" />
+@@ -729,7 +682,6 @@ + <include name="org/jmol/constant/**" />
+ <include name="org/jmol/g3d/**" />
+ <include name="org/jmol/geodesic/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/modelset/**" />
+ <include name="org/jmol/script/**" />
+ <include name="org/jmol/shape/**" />
+@@ -755,7 +707,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -868,16 +819,6 @@ + keystore="selfSignedCertificate/selfSignedCertificate.store"
+ storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"
+- keystore="selfSignedCertificate/selfSignedCertificate.store"
+- storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+- </sequential>
+- </for>
+-
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- this one must be treated specially because of jar indexing
+ we cannot simply rename the jar file, because the index has
+@@ -905,7 +846,6 @@ + <include name="org/jmol/shape/**" />
+ <include name="org/jmol/viewer/**" />
+ <include name="org/jmol/util/**" />
+- <include name="org/jmol/i18n/**" />
+ </fileset>
+ <indexjars>
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Console.jar" />
+@@ -924,7 +864,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
+@@ -963,18 +902,6 @@ + </fileset>
+ </jar>
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+- </fileset>
+- </jar>
+- </sequential>
+- </for>
+-
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+ <fileset dir="${applet.classes.dir}">
+ <include name="org/jmol/minimize/**" />
+@@ -1088,7 +1015,6 @@ + <include name="org/jmol/constant/**" />
+ <include name="org/jmol/g3d/**" />
+ <include name="org/jmol/geodesic/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/modelset/**" />
+ <include name="org/jmol/script/**" />
+ <include name="org/jmol/shape/**" />
+@@ -1114,7 +1040,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -1123,7 +1048,7 @@ + </target>
+
+ <target name="dist" id="dist"
+- depends="doc,main-i18n,main,signed-applet">
++ depends="doc,main,signed-applet">
+ <!-- first build binary distribution -->
+ <delete dir="build/dist/jmol-${version}"/>
+ <mkdir dir="build/dist/jmol-${version}"/>
+@@ -1183,7 +1108,6 @@ + <fileset dir=".">
+ <include name="applet.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -1278,7 +1202,6 @@ + <fileset dir=".">
+ <include name="apisio.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -1374,7 +1297,7 @@ + <target name="xclean" id="xclean">
+ </target>
+
+- <target name="spotless" id="spotless" depends="clean,spotless-i18n">
++ <target name="spotless" id="spotless" depends="clean">
+ <delete dir="build"/>
+ <delete dir="${javadoc.dir}"/>
+ <delete dir="packaging/rpm/dist"/>
+@@ -1438,16 +1361,6 @@ + <arg value="../../../doc/source/JmolGuide.docbook.xml" />
+ <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+ </java>
+- <echo message="Generating user's guide (fr)" />
+- <mkdir dir="build/doc/JmolUserGuide_fr" />
+- <java fork="true" dir="build/doc/JmolUserGuide_fr"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <jvmarg value="${proxyHost}" />
+- <jvmarg value="${proxyPort}" />
+- <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />
+- <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolHistory" id="jmolHistory"
+@@ -1462,26 +1375,6 @@ + <arg value="../../../doc/source/JmolHistory.xml" />
+ <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+ </java>
+- <echo message="Generating history of changes (fr)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_fr.html" />
+- <arg value="../../../doc/source/JmolHistory_fr.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=fr" />
+- </java>
+- <echo message="Generating history of changes (nl)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_nl.html" />
+- <arg value="../../../doc/source/JmolHistory_nl.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=nl" />
+- </java>
+ </target>
+
+ <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
+@@ -1495,24 +1388,6 @@ + <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating developer's guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_fr.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating developer's guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_de.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
+@@ -1526,24 +1401,6 @@ + <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating applet guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_fr.html" />
+- <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating applet guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_de.html" />
+- <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="test" id="test" depends="main,compile-tests">
+@@ -1575,12 +1432,4 @@ + <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
+ </target>
+
+- <!-- i18n stuff -->
+- <target name="main-i18n" depends="classes">
+- <ant antfile="tools/build-i18n.xml" target="main-i18n"/>
+- </target>
+- <target name="spotless-i18n">
+- <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>
+- </target>
+-
+ </project>
diff --git a/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild new file mode 100644 index 000000000000..0112130458e2 --- /dev/null +++ b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild @@ -0,0 +1,101 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 +WEBAPP_OPTIONAL="yes" + +inherit eutils webapp java-pkg-2 java-ant-2 + +MY_P=Jmol + +DESCRIPTION="Java molecular viever for 3-D chemical structures" +HOMEPAGE="http://jmol.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz + http://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar" + +WEBAPP_MANUAL_SLOT="yes" +SLOT="0" +KEYWORDS="~amd64 ~x86" +LICENSE="LGPL-2.1" +IUSE="client-only vhosts" + +COMMON_DEP=" + dev-java/commons-cli:1 + dev-java/itext:0 + sci-libs/jmol-acme:0 + sci-libs/vecmath-objectclub:0" + +RDEPEND=">=virtual/jre-1.4 + ${COMMON_DEP}" +DEPEND=">=virtual/jdk-1.4 + !client-only? ( ${WEBAPP_DEPEND} ) + ${COMMON_DEP}" + +pkg_setup() { + use client-only || webapp_pkg_setup + java-pkg-2_pkg_setup +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}/${PN}-nointl.patch \ + "${FILESDIR}"/${PV}/${PN}-manifest.patch + + mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory." + cp "${WORKDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \ + || die "Failed to install Cert file." + + rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die + cd "${S}/jars" + +# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along. + if use amd64; then + mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar." + rm -v *.jar *.tar.gz || die "Failed to remove jars." + mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar." + fi + + java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar + java-pkg_jar-from itext iText.jar itext-1.4.5.jar + java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar + java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar + + mkdir -p "${S}/build/appjars" || die +} + +src_compile() { + # prevent absorbing dep's classes + eant -Dlibjars.uptodate=true main +} + +src_install() { + java-pkg_dojar build/Jmol.jar + dohtml -r build/doc/* || die "Failed to install html docs." + dodoc *.txt doc/*license* || die "Failed to install licenses." + + java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \ + --java_args "-Xmx512m" + + if ! use client-only ; then + webapp_src_preinst + cp Jmol.js build/Jmol.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp build/JmolApplet*.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp applet.classes "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/classes/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/appletjars/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/caffeine.xyz "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/index.html "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + + webapp_src_install + fi +} + +pkg_postinst() { + use client-only || webapp_pkg_postinst +} + +pkg_prerm() { + use client-only || webapp_pkg_prerm +} diff --git a/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild b/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild new file mode 100644 index 000000000000..0e48dbb2d725 --- /dev/null +++ b/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild @@ -0,0 +1,99 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 +WEBAPP_OPTIONAL="yes" + +inherit eutils webapp java-pkg-2 java-ant-2 + +MY_P=Jmol + +DESCRIPTION="Java molecular viever for 3-D chemical structures" +HOMEPAGE="http://jmol.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz + http://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar" + +LICENSE="LGPL-2.1" +KEYWORDS="~x86 ~amd64" +IUSE="+client-only vhosts" + +WEBAPP_MANUAL_SLOT="yes" +SLOT="0" + +COMMON_DEP=" + dev-java/commons-cli:1 + dev-java/itext:0 + sci-libs/jmol-acme:0 + sci-libs/vecmath-objectclub:0 + sci-libs/naga" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEP}" +DEPEND=">=virtual/jdk-1.5 + dev-java/saxon:6.5 + !client-only? ( ${WEBAPP_DEPEND} ) + ${COMMON_DEP}" + +pkg_setup() { + use client-only || webapp_pkg_setup + java-pkg-2_pkg_setup +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-nointl.patch + + rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die + cd "${S}/jars" + +# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along. + if use amd64; then + mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar." + rm -v *.jar *.tar.gz || die "Failed to remove jars." + mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar." + fi + + java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar + java-pkg_jar-from itext iText.jar itext-1.4.5.jar + java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar + java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar + java-pkg_jar-from naga + java-pkg_jar-from --build-only saxon-6.5 saxon.jar + + mkdir -p "${S}/build/appjars" || die +} + +src_compile() { + # prevent absorbing dep's classes + eant -Dlibjars.uptodate=true main +} + +src_install() { + java-pkg_dojar build/Jmol.jar + dohtml -r build/doc/* || die "Failed to install html docs." + dodoc *.txt doc/*license* || die "Failed to install licenses." + + java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \ + --java_args "-Xmx512m" + + if ! use client-only ; then + webapp_src_preinst + cp Jmol.js build/Jmol.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp build/JmolApplet*.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp applet.classes "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/classes/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/appletjars/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/caffeine.xyz "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/index.html "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + + webapp_src_install + fi +} + +pkg_postinst() { + use client-only || webapp_pkg_postinst +} + +pkg_prerm() { + use client-only || webapp_pkg_prerm +} diff --git a/sci-chemistry/jmol/metadata.xml b/sci-chemistry/jmol/metadata.xml new file mode 100644 index 000000000000..9e4d1db2e0a2 --- /dev/null +++ b/sci-chemistry/jmol/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <use> + <flag name="client-only">Install the viewer only, no applet files for httpd + </flag> + </use> + <upstream> + <remote-id type="sourceforge">jmol</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/ksdssp/Manifest b/sci-chemistry/ksdssp/Manifest new file mode 100644 index 000000000000..c0946b22157e --- /dev/null +++ b/sci-chemistry/ksdssp/Manifest @@ -0,0 +1 @@ +DIST ksdssp-040728.shar 104347 SHA256 0e47de4147724035519f9e845724407c472b99219bbb41c35f3ae1150ae8ef4c SHA512 17c32bea1f32acfd31353d0378fe2a664a8922db8b929da4b9b10ac279013946911acd2a26ab3ab227ae160352c8313dcf742fae8c139a90ac11f772f17a1689 WHIRLPOOL a5f70b8268150388ec1e21e798c4e651b19503293f08ca581a9a9d73e9ffd40c1472988c12bcbac53bdbae5e1557a27f1a2846b28b96bc338500592cc6604748 diff --git a/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild b/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild new file mode 100644 index 000000000000..e3d856999d94 --- /dev/null +++ b/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit toolchain-funcs + +DESCRIPTION="An open source implementation of sci-chemistry/dssp" +HOMEPAGE="http://www.cgl.ucsf.edu/Overview/software.html" +SRC_URI="mirror://gentoo/${P}.shar" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="sci-libs/libpdb++" +DEPEND="${RDEPEND} + app-arch/sharutils" + +S="${WORKDIR}"/${PN} + +src_unpack() { + "${EPREFIX}/usr/bin/unshar" "${DISTDIR}"/${A} || die +} + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + PDBINCDIR="${EPREFIX}/usr/include/libpdb++" \ + BINDIR="${EPREFIX}/usr/bin" \ + .TARGET="${PN}.csh" \ + .CURDIR="${S}" \ + CC="$(tc-getCXX)" \ + LINKER="$(tc-getCXX)" \ + OPT="${CXXFLAGS}" \ + LFLAGS="${LDFLAGS}" \ + ${PN} ${PN}.csh +} + +src_install() { + dobin ${PN}{,.csh} + dodoc README + dohtml ${PN}.html + doman ${PN}.1 +} diff --git a/sci-chemistry/ksdssp/ksdssp-040728.ebuild b/sci-chemistry/ksdssp/ksdssp-040728.ebuild new file mode 100644 index 000000000000..3910b349697c --- /dev/null +++ b/sci-chemistry/ksdssp/ksdssp-040728.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit toolchain-funcs + +DESCRIPTION="ksdssp is an open source implementation of dssp" +HOMEPAGE="http://www.cgl.ucsf.edu/Overview/software.html" +SRC_URI="mirror://gentoo/${P}.shar" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD" +IUSE="" + +RDEPEND="sci-libs/libpdb++" +DEPEND=" + ${RDEPEND} + app-arch/sharutils" + +S="${WORKDIR}"/${PN} + +src_unpack() { + "${EPREFIX}"/usr/bin/unshar "${DISTDIR}"/${A} +} + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + PDBINCDIR="${EPREFIX}/usr/include/libpdb++" \ + BINDIR="${EPREFIX}/usr/bin" \ + .TARGET="${PN}.csh" \ + .CURDIR="${S}" \ + CC="$(tc-getCXX)" \ + LINKER="$(tc-getCXX)" \ + OPT="${CXXFLAGS}" \ + LFLAGS="${LDFLAGS}" \ + ${PN} ${PN}.csh +} + +src_install() { + dobin ${PN}{,.csh} +} diff --git a/sci-chemistry/ksdssp/metadata.xml b/sci-chemistry/ksdssp/metadata.xml new file mode 100644 index 000000000000..1837bbc07a6e --- /dev/null +++ b/sci-chemistry/ksdssp/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/makecif/Manifest b/sci-chemistry/makecif/Manifest new file mode 100644 index 000000000000..b489a33454fd --- /dev/null +++ b/sci-chemistry/makecif/Manifest @@ -0,0 +1 @@ +DIST makecif-5.6.6.tar.gz 3797710 SHA256 fdcc1bee70583da3161f0d46eb792d965c04f08f0ad3033f730486550e859d1f SHA512 874c69d85b55ef22057c1113418218d7fd0a1e795f04673f3d64cd015230ab47ad8bdb0277ca9b389cc3edf397dc63c2c1cdd35837a86bc5d2a595d9ae534dbc WHIRLPOOL 5ecc1f7d06445d34e1d5d97ad98fd4c9d21db1e1611a9d89e25f0228a7b2cce5fa631b470687b3e6f7085c932cee6c5d8d4da2e6473406a22d63a26645f56be7 diff --git a/sci-chemistry/makecif/files/5.6.6-makefile.patch b/sci-chemistry/makecif/files/5.6.6-makefile.patch new file mode 100644 index 000000000000..186abb92b7d8 --- /dev/null +++ b/sci-chemistry/makecif/files/5.6.6-makefile.patch @@ -0,0 +1,49 @@ +diff --git a/src/makefile b/src/makefile +index 6c8264a..acdec20 100755 +--- a/src/makefile ++++ b/src/makefile +@@ -22,6 +22,8 @@ MAKEDIC = $(MAKECIF)/dic/ + # setenv BLANC_FORT "f77 -O1" + # + ++all: makecif_all libcheck_all modcheck_all emin_all ++ + clean: + rm -f temp_makecif_path.fh + rm -f ../bin/* +@@ -118,7 +120,7 @@ makecif.o: makecif.f lib_com.fh crd_com.fh + $(BLANC_FORT) -c makecif.f + + mkcif: main_makecif.o make_lib11.o make_lib12.o make_lib2.o make_vdw.o make_CIF.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_PDB.o makecif.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o +- $(BLANC_FORT) -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o + # ------------- + libcheck.o: libcheck.f lib_com.fh crd_com.fh + $(BLANC_FORT) -c libcheck.f +@@ -130,7 +132,7 @@ main_libcheck.o: main_libcheck.f libcheck_version.fh + $(BLANC_FORT) -c main_libcheck.f + + lbcheck: main_libcheck.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_unix.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o +- $(BLANC_FORT) -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o + # ------------ + + emin.o: emin.f crd_com.fh atom_com.fh +@@ -143,7 +145,7 @@ main_emin.o: main_emin.f + $(BLANC_FORT) -c main_emin.f + + emn: main_emin.o emin_new.o angle_subr.o make_unix.o make_CIF.o make_subr_2.o make_subr.o +- $(BLANC_FORT) -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o + + # ------------- + +@@ -155,7 +157,7 @@ main_modcheck.o: main_modcheck.f + $(BLANC_FORT) -c main_modcheck.f + + mdcheck: main_modcheck.o modcheck.o mod_subr.o make_CIF.o make_unix.o make_subr_2.o make_subr.o +- $(BLANC_FORT) -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o + + + # ====================================== diff --git a/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild b/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild new file mode 100644 index 000000000000..509117f300af --- /dev/null +++ b/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="PDB --> CIF convertor" +HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html" +SRC_URI="mirror://gentoo/${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +LICENSE="ccp4" +IUSE="" + +S="${WORKDIR}"/${PN} + +DEPEND="" +RDEPEND=" + !>=sci-chemistry/refmac-5.6 + sci-libs/monomer-db" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-makefile.patch +} + +src_compile() { + emake -C src clean + emake \ + -C src \ + BLANC_FORT="$(tc-getFC) ${FFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + dobin bin/* + dodoc readme +} diff --git a/sci-chemistry/makecif/makecif-5.6.6.ebuild b/sci-chemistry/makecif/makecif-5.6.6.ebuild new file mode 100644 index 000000000000..3a5f70a8b259 --- /dev/null +++ b/sci-chemistry/makecif/makecif-5.6.6.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="PDB --> CIF convertor" +HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html" +SRC_URI="mirror://gentoo/${P}.tar.gz" + +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +LICENSE="ccp4" +IUSE="" + +S="${WORKDIR}"/${PN} + +DEPEND="" +RDEPEND=" + !>=sci-chemistry/refmac-5.6 + sci-libs/monomer-db" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-makefile.patch +} + +src_compile() { + cd src && emake clean + emake \ + BLANC_FORT="$(tc-getFC) ${FFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + dobin bin/* + dodoc readme +} diff --git a/sci-chemistry/makecif/metadata.xml b/sci-chemistry/makecif/metadata.xml new file mode 100644 index 000000000000..993c1d1ffcda --- /dev/null +++ b/sci-chemistry/makecif/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +PDB - CIF convertor +check and create correct structure description +create the list of restraints +create dictionary description of new ligands +rebuild missing atoms +create tree like structure +also the part of REFMAC +can use additional user's dictionary +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/mars/Manifest b/sci-chemistry/mars/Manifest new file mode 100644 index 000000000000..6266916bc856 --- /dev/null +++ b/sci-chemistry/mars/Manifest @@ -0,0 +1 @@ +DIST mars-1.2_linux.tar.gz 2058733 SHA256 c909aa781296d806f89c8d51d89b7345c3e94dd33fc8cc72554573a78ff21b2b SHA512 ba7ec4e94cf5918d22405022c75feabf3e5b345d96075eabf50eb24857101575bb41d15e5686822c2b2f25ba554aa7d7a2b65122dd47304939234a4a884ae4d2 WHIRLPOOL 3cbc59474d776cc79d3c392ae55ce6effe13ae088ff544afd3537daf157adc2c14e1074a38b937e197c87d262f37371dc7109d31f758d25c4c210847a5fb6a79 diff --git a/sci-chemistry/mars/mars-1.2.ebuild b/sci-chemistry/mars/mars-1.2.ebuild new file mode 100644 index 000000000000..3e3aa6a7948f --- /dev/null +++ b/sci-chemistry/mars/mars-1.2.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +MY_P="${P}_linux" + +DESCRIPTION="Robust automatic backbone assignment of proteins" +HOMEPAGE="http://www.mpibpc.mpg.de/groups/zweckstetter/_links/software_mars.htm" +SRC_URI="http://www.mpibpc.mpg.de/groups/zweckstetter/_software_files/_${PN}/${MY_P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="all-rights-reserved" +IUSE="examples" + +RDEPEND="sci-biology/psipred" +DEPEND="" + +RESTRICT=mirror + +S="${WORKDIR}"/${MY_P} + +QA_PREBUILT="opt/mars/*" + +src_install() { + dobin bin/runmars* + + exeinto /opt/${PN}/ + doexe bin/{${PN},calcJC-S2,runmars*,*.awk} *.awk + insinto /opt/${PN}/ + doins bin/*.{tab,txt} + if use examples; then + insinto /usr/share/${PN}/ + doins -r examples + fi + + cat >> "${T}"/23mars <<- EOF + MARSHOME="${EPREFIX}/opt/${PN}" + EOF + + doenvd "${T}"/23mars +} diff --git a/sci-chemistry/mars/metadata.xml b/sci-chemistry/mars/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/mars/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/massxpert/Manifest b/sci-chemistry/massxpert/Manifest new file mode 100644 index 000000000000..2288ccad80f4 --- /dev/null +++ b/sci-chemistry/massxpert/Manifest @@ -0,0 +1,2 @@ +DIST massxpert-2.0.5.tar.gz 13603475 SHA256 11f7f1599a587be923ed0b58e753e1f9296e0c3c0acfb5e3980579e768600e5c SHA512 49c1d8fa4324907d04c79dddad66eecae34ba1dded98594838b4cbb88ad022abe3f8fbd7f2aeee73baafc17a03397b1776f2e6fdabf4e2ac4e4f6d6eeb86ca2f WHIRLPOOL dba641144835d303eaf181a70aabee11dc14a43c8fe508ad33eb2ffe3c1c8a11eaa1ae066a8e9134e9d6c891cea5fc2dba503ca5e53acf62eb8b532d52c1bf3e +DIST massxpert-3.4.0.tar.bz2 16544044 SHA256 b06314722b4cbdf68dc76e55933a79487848c655fc65341a8dbc707ed89cc9e8 SHA512 50e8eaab145ab7fa225725b113d6840168b88db7d2ee194b176bc88eabf4f44c20f8dc0680986d659de1f94f2e0c6ae10d54e17e2d8b3b5aa6a9a9bf57a508de WHIRLPOOL 4578801c2dd4eee7390eadb299f3d55af29d0a48365f96ba6d6488a07792e47882e191f8eda05b6b261d9a972bf7f92f160d4a5fbbcc216ed7ffda32fcfee6ed diff --git a/sci-chemistry/massxpert/files/massxpert-2.0.5-gentoo.patch b/sci-chemistry/massxpert/files/massxpert-2.0.5-gentoo.patch new file mode 100644 index 000000000000..63cbe2340008 --- /dev/null +++ b/sci-chemistry/massxpert/files/massxpert-2.0.5-gentoo.patch @@ -0,0 +1,84 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 8085e0a..eaae8ce 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -23,10 +23,10 @@ SET (CMAKE_VERBOSE_MAKEFILE ON) + + ############################################################# + # Enable warnings and treat them as errors +-SET (PEDANTIC TRUE CACHE BOOL "Should we compile with -Wall -Werror.") ++SET (PEDANTIC TRUE CACHE BOOL "Should we compile with -Wall.") + + IF (PEDANTIC) +- ADD_DEFINITIONS (-Wall -Werror) ++ ADD_DEFINITIONS (-Wall) + ENDIF (PEDANTIC) + + ############################################################# +@@ -51,9 +51,9 @@ ENDIF (WIN32) + IF (UNIX AND NOT APPLE) + SET (MASSXPERT_BIN_DIR ${CMAKE_INSTALL_PREFIX}/bin) + SET (MASSXPERT_DATA_DIR ${CMAKE_INSTALL_PREFIX}/share/massxpert) +- SET (MASSXPERT_PLUGIN_DIR ${CMAKE_INSTALL_PREFIX}/lib/massxpert/plugins) ++ SET (MASSXPERT_PLUGIN_DIR ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}/massxpert/plugins) + SET (MASSXPERT_LOCALE_DIR ${CMAKE_INSTALL_PREFIX}/share/massxpert/locales) +- SET (MASSXPERT_DOC_DIR ${CMAKE_INSTALL_PREFIX}/share/doc/massxpert) ++ SET (MASSXPERT_DOC_DIR ${CMAKE_INSTALL_PREFIX}/share/doc/massxpert-${VERSION}) + SET (MASSXPERT_USERMAN_DIR ${MASSXPERT_DOC_DIR}/usermanual) + ENDIF (UNIX AND NOT APPLE) + +@@ -122,10 +122,6 @@ IF (${BUILD_PROGRAM}) + ############### + # install stuff + +- # The license file +- INSTALL (FILES COPYING +- DESTINATION ${MASSXPERT_DOC_DIR}) +- + # The desktop file + IF (UNIX AND NOT APPLE) + INSTALL (FILES massxpert.desktop +@@ -165,10 +161,6 @@ IF (${BUILD_DATA}) + ############### + # install stuff + +- # The license file +- INSTALL (FILES COPYING +- DESTINATION ${MASSXPERT_DOC_DIR}) +- + # The manual pages (data) + IF (UNIX AND NOT APPLE) + INSTALL (FILES massxpert-data.7 +@@ -201,10 +193,6 @@ IF (${BUILD_USERMANUAL}) + ############### + # install stuff + +- # The license file +- INSTALL (FILES COPYING +- DESTINATION ${MASSXPERT_DOC_DIR}) +- + # The manual pages (user manual) + IF (UNIX AND NOT APPLE) + INSTALL (FILES massxpert-doc.7 +diff --git a/gui/configurationSettingsDlg.cpp b/gui/configurationSettingsDlg.cpp +index bf595d5..82cad21 100644 +--- a/gui/configurationSettingsDlg.cpp ++++ b/gui/configurationSettingsDlg.cpp +@@ -309,13 +309,11 @@ namespace massXpert + bool + ConfigurationSettingsDlg::checkLocalizationDir(const QDir &dir) + { +- // At the moment there is the french translation: massxpert_fr.qm ++ // Gentoo provides optional installing of translations. ++ // If you decide not to have translations, then this check ++ // would fail. + +- QString filePath(dir.absolutePath() + +- QDir::separator() + +- "massxpert_fr.qm"); +- +- return QFile::exists(filePath); ++ return true; + } + + diff --git a/sci-chemistry/massxpert/files/massxpert-3.4.0-gentoo.patch b/sci-chemistry/massxpert/files/massxpert-3.4.0-gentoo.patch new file mode 100644 index 000000000000..fc0fc4f606cf --- /dev/null +++ b/sci-chemistry/massxpert/files/massxpert-3.4.0-gentoo.patch @@ -0,0 +1,91 @@ + CMakeLists.txt | 20 ++++---------------- + gui/configurationSettingsDlg.cpp | 10 ++++------ + 2 files changed, 8 insertions(+), 22 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index fec954b..b87d157 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -24,10 +24,10 @@ SET (CMAKE_VERBOSE_MAKEFILE ON) + ############################################################# + # Enable warnings and treat them as errors, on GNU/Linux only + IF (UNIX) +- SET (PEDANTIC TRUE CACHE BOOL "Should we compile with -Wall -Werror.") ++ SET (PEDANTIC TRUE CACHE BOOL "Should we compile with -Wall.") + + IF (PEDANTIC) +- ADD_DEFINITIONS (-Wall -Werror) ++ ADD_DEFINITIONS (-Wall) + ENDIF (PEDANTIC) + ENDIF (UNIX) + +@@ -64,12 +64,12 @@ IF (UNIX AND NOT APPLE) + # Plugin-specific stuff, some distros set CMAKE_INSTALL_LIBDIR to + # /usr/lib64 (Fedora64, for example) + IF (NOT CMAKE_INSTALL_LIBDIR) +- SET (CMAKE_INSTALL_LIBDIR ${CMAKE_INSTALL_PREFIX}/lib) ++ SET (CMAKE_INSTALL_LIBDIR ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}) + ENDIF (NOT CMAKE_INSTALL_LIBDIR) + SET (MASSXPERT_PLUGIN_DIR ${CMAKE_INSTALL_LIBDIR}/massxpert/plugins) + + SET (MASSXPERT_LOCALE_DIR ${CMAKE_INSTALL_PREFIX}/share/massxpert/locales) +- SET (MASSXPERT_DOC_DIR ${CMAKE_INSTALL_PREFIX}/share/doc/massxpert) ++ SET (MASSXPERT_DOC_DIR ${CMAKE_INSTALL_PREFIX}/share/doc/massxpert-${VERSION}) + SET (MASSXPERT_USERMAN_DIR ${MASSXPERT_DOC_DIR}/usermanual) + ENDIF (UNIX AND NOT APPLE) + +@@ -144,10 +144,6 @@ IF (${BUILD_PROGRAM}) + ############### + # install stuff + +- # The license file +- INSTALL (FILES COPYING +- DESTINATION ${MASSXPERT_DOC_DIR}) +- + # The desktop file + IF (UNIX AND NOT APPLE) + INSTALL (FILES massxpert.desktop +@@ -185,10 +181,6 @@ IF (${BUILD_DATA}) + ############### + # install stuff + +- # The license file +- INSTALL (FILES COPYING +- DESTINATION ${MASSXPERT_DOC_DIR}) +- + # The manual pages (data) + IF (UNIX AND NOT APPLE) + INSTALL (FILES massxpert-data.7 +@@ -219,10 +211,6 @@ IF (${BUILD_USERMANUAL}) + ############### + # install stuff + +- # The license file +- INSTALL (FILES COPYING +- DESTINATION ${MASSXPERT_DOC_DIR}) +- + # The manual pages (user manual) + IF (UNIX AND NOT APPLE) + INSTALL (FILES massxpert-doc.7 +diff --git a/gui/configurationSettingsDlg.cpp b/gui/configurationSettingsDlg.cpp +index bf595d5..82cad21 100644 +--- a/gui/configurationSettingsDlg.cpp ++++ b/gui/configurationSettingsDlg.cpp +@@ -309,13 +309,11 @@ namespace massXpert + bool + ConfigurationSettingsDlg::checkLocalizationDir(const QDir &dir) + { +- // At the moment there is the french translation: massxpert_fr.qm ++ // Gentoo provides optional installing of translations. ++ // If you decide not to have translations, then this check ++ // would fail. + +- QString filePath(dir.absolutePath() + +- QDir::separator() + +- "massxpert_fr.qm"); +- +- return QFile::exists(filePath); ++ return true; + } + + diff --git a/sci-chemistry/massxpert/massxpert-2.0.5.ebuild b/sci-chemistry/massxpert/massxpert-2.0.5.ebuild new file mode 100644 index 000000000000..ba0ee2dd9491 --- /dev/null +++ b/sci-chemistry/massxpert/massxpert-2.0.5.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit cmake-utils + +DESCRIPTION="A software suite to predict/analyze mass spectrometric data on (bio)polymers" +HOMEPAGE="http://massxpert.org" +SRC_URI="http://download.tuxfamily.org/${PN}/source/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc" + +RDEPEND="dev-qt/qtsvg:4[debug?]" +DEPEND="${DEPEND} + doc? ( virtual/latex-base )" + +MASSXPERT_LANGS="fr" + +for L in ${MASSXPERT_LANGS}; do + IUSE="${IUSE} linguas_${L}" +done + +src_prepare() { + epatch "${FILESDIR}/${P}-gentoo.patch" + + local langs= + for lingua in ${LINGUAS}; do + if has ${lingua} ${MASSXPERT_LANGS}; then + langs="${langs} ${PN}_${lingua}.qm" + fi + done + + sed -i -e "s/\(SET (massxpert_TRANSLATIONS \).*/\1${langs})/" \ + gui/CMakeLists.txt || die "setting up translations failed" +} + +src_configure() { + local mycmakeargs=( + -DBUILD_PROGRAM=1 + -DBUILD_DATA=1 + ) + use doc && mycmakeargs+=( -DBUILD_USERMANUAL=1 ) + + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + doicon "gui/images/${PN}-icon-32.xpm" || die "installing icon failed" + dodoc TODO || die "dodoc failed" +} diff --git a/sci-chemistry/massxpert/massxpert-3.4.0.ebuild b/sci-chemistry/massxpert/massxpert-3.4.0.ebuild new file mode 100644 index 000000000000..b9aa2467f5d6 --- /dev/null +++ b/sci-chemistry/massxpert/massxpert-3.4.0.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Software suite to predict/analyze mass spectrometric data on (bio)polymers" +HOMEPAGE="http://massxpert.org" +SRC_URI="http://download.tuxfamily.org/${PN}/source/${P}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc" + +RDEPEND="dev-qt/qtsvg:4[debug?]" +DEPEND="${DEPEND} + doc? ( virtual/latex-base )" + +MASSXPERT_LANGS="fr" + +for L in ${MASSXPERT_LANGS}; do + IUSE="${IUSE} linguas_${L}" +done + +src_prepare() { + epatch "${FILESDIR}/${P}-gentoo.patch" + + local langs= + for lingua in ${LINGUAS}; do + if has ${lingua} ${MASSXPERT_LANGS}; then + langs="${langs} ${PN}_${lingua}.qm" + fi + done + + sed -i -e "s/\(SET (massxpert_TRANSLATIONS \).*/\1${langs})/" \ + gui/CMakeLists.txt || die "setting up translations failed" +} + +src_configure() { + local mycmakeargs=( + -DBUILD_PROGRAM=1 + -DBUILD_DATA=1 + ) + use doc && mycmakeargs+=( -DBUILD_USERMANUAL=1 ) + + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + doicon "gui/images/${PN}-icon-32.xpm" + dodoc TODO +} diff --git a/sci-chemistry/massxpert/metadata.xml b/sci-chemistry/massxpert/metadata.xml new file mode 100644 index 000000000000..a4137981114b --- /dev/null +++ b/sci-chemistry/massxpert/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <longdescription lang="en"> +Prediction and analysis of mass spectrometric data for proteomic projects. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/mdanalysis/Manifest b/sci-chemistry/mdanalysis/Manifest new file mode 100644 index 000000000000..a87a92b28ed1 --- /dev/null +++ b/sci-chemistry/mdanalysis/Manifest @@ -0,0 +1 @@ +DIST MDAnalysis-0.7.7.tar.gz 3262287 SHA256 9dd72b776bf7f2be83da562a638895a94f629422798cc309c14965795847eac1 SHA512 c26085c767ec213d5aa27709029e5a3b9df786c10e23e3841ffc9644e2fd66c8add0358f013c51a95fa3452c5c900b44901db736830504b669916ea45a924712 WHIRLPOOL 2acaa02d641d67bef4cd9ec311c787f57884d83bf350b46af9e862ca6d3a03a6d4ff3d71a2e866f5ab57e29036c5a3182a167e3bcc492667e9a5a60778de0b39 diff --git a/sci-chemistry/mdanalysis/mdanalysis-0.7.7.ebuild b/sci-chemistry/mdanalysis/mdanalysis-0.7.7.ebuild new file mode 100644 index 000000000000..aab36560129d --- /dev/null +++ b/sci-chemistry/mdanalysis/mdanalysis-0.7.7.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +MY_PN="MDAnalysis" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="A python library to analyze and manipulate molecular dynamics trajectories" +HOMEPAGE="https://code.google.com/p/mdanalysis/" +SRC_URI="https://mdanalysis.googlecode.com/files/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-biology/biopython[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/scientificpython[${PYTHON_USEDEP}] + dev-python/GridDataFormats[${PYTHON_USEDEP}] + dev-python/netcdf4-python[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND} + test? ( dev-python/nose[${PYTHON_USEDEP}] )" + +S="${WORKDIR}"/${MY_P} diff --git a/sci-chemistry/mdanalysis/metadata.xml b/sci-chemistry/mdanalysis/metadata.xml new file mode 100644 index 000000000000..5ef07a39e7e1 --- /dev/null +++ b/sci-chemistry/mdanalysis/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/mead/Manifest b/sci-chemistry/mead/Manifest new file mode 100644 index 000000000000..b86a2a21886e --- /dev/null +++ b/sci-chemistry/mead/Manifest @@ -0,0 +1 @@ +DIST mead-2.2.7.tar.gz 806319 RMD160 9adf9743e44061779f9ac3b9064abb9164ad3e58 SHA1 6d3bbda29a5f8fdf26600e036ca8debacc37b90e SHA256 fd2a4b357bbd847ac9b255563034d7e71bf16cf59efa371d966b6fbbe9b4cd7c diff --git a/sci-chemistry/mead/files/mead-2.2.7-gcc43.patch b/sci-chemistry/mead/files/mead-2.2.7-gcc43.patch new file mode 100644 index 000000000000..673f25890e74 --- /dev/null +++ b/sci-chemistry/mead/files/mead-2.2.7-gcc43.patch @@ -0,0 +1,22 @@ +--- mead-2.2.7.orig/libmead/AtomSet.h ++++ mead-2.2.7/libmead/AtomSet.h +@@ -31,8 +31,7 @@ + + #include <map> + #include <list> +-#include <string> +-using std::string; ++#include <string.h> + #include "MEAD/Atom.h" + #include "MEAD/Coord.h" + #include "MEAD/AtomID.h" +--- mead-2.2.7.orig/libmead/DielCubeRep.h ++++ mead-2.2.7/libmead/DielCubeRep.h +@@ -31,6 +31,7 @@ + + #include "MEAD/CubeLatSpec.h" + #include "MEAD/globals.h" ++#include <string.h> + + class DielCubeRep { + public: diff --git a/sci-chemistry/mead/files/mead-2.2.7-respect-cflags.patch b/sci-chemistry/mead/files/mead-2.2.7-respect-cflags.patch new file mode 100644 index 000000000000..61c54737778e --- /dev/null +++ b/sci-chemistry/mead/files/mead-2.2.7-respect-cflags.patch @@ -0,0 +1,57 @@ +diff -Naur mead-2.2.7-orig/apps/libmso/Makefile.in mead-2.2.7/apps/libmso/Makefile.in +--- mead-2.2.7-orig/apps/libmso/Makefile.in 2004-12-10 14:33:49.000000000 -0600 ++++ mead-2.2.7/apps/libmso/Makefile.in 2009-02-15 16:32:40.000000000 -0600 +@@ -35,8 +35,8 @@ + INSTALL_PROGRAM = @INSTALL_PROGRAM@ + + ALL_CPPFLAGS = -I. $(LOCALINCS) $(CPPFLAGS) $(REGEX_CPP) $(CXX_DEFS) +-ALL_CXXFLAGS = $(CXX_OPTFLAGS) $(CXX_DEBUGFLAGS) +-ALL_CFLAGS = $(CC_DEBUGFLAGS) $(CC_OPTFLAGS) ++ALL_CXXFLAGS = @CXXFLAGS@ ++ALL_CFLAGS = @CFLAGS@ + + .SUFFIXES: + .SUFFIXES: .cc .o +diff -Naur mead-2.2.7-orig/apps/Makefile.common.in mead-2.2.7/apps/Makefile.common.in +--- mead-2.2.7-orig/apps/Makefile.common.in 2004-11-19 16:49:56.000000000 -0600 ++++ mead-2.2.7/apps/Makefile.common.in 2009-02-15 16:32:22.000000000 -0600 +@@ -36,10 +36,10 @@ + LIBS = @LIBS@ -lm + + ALL_CPPFLAGS = -I. $(LOCALINCS) $(CPPFLAGS) $(REGEX_CPP) $(CXX_DEFS) +-ALL_CXXFLAGS = $(CXX_OPTFLAGS) $(CXX_DEBUGFLAGS) +-ALL_CFLAGS = $(CC_DEBUGFLAGS) $(CC_OPTFLAGS) ++ALL_CXXFLAGS = @CXXFLAGS@ ++ALL_CFLAGS = @CFLAGS@ + +-CXXLINK = $(CXX) $(ALL_CPPFLAGS) $(CXX_DEBUGFLAGS) $(CXX_OPTFLAGS) \ ++CXXLINK = $(CXX) $(ALL_CPPFLAGS) @CXXFLAGS@ \ + $(LDFLAGS) + + .SUFFIXES: .cc .o +diff -Naur mead-2.2.7-orig/libmead/Makefile.in mead-2.2.7/libmead/Makefile.in +--- mead-2.2.7-orig/libmead/Makefile.in 2008-03-04 14:18:22.000000000 -0600 ++++ mead-2.2.7/libmead/Makefile.in 2009-02-15 16:31:56.000000000 -0600 +@@ -99,8 +99,8 @@ + INCLUDES = -I$(top_srcdir) + + ALL_CPPFLAGS = $(INCLUDES) $(CPPFLAGS) $(REGEX_CPP) $(CXX_DEFS) +-ALL_CXXFLAGS = $(CXX_OPTFLAGS) $(CXX_DEBUGFLAGS) $(CXX_SHAREDFLAGS) +-ALL_CFLAGS = $(CC_DEBUGFLAGS) $(CC_OPTFLAGS) ++ALL_CXXFLAGS = @CXXFLAGS@ ++ALL_CFLAGS = @CFLAGS@ + + + +diff -Naur mead-2.2.7-orig/swig/Makefile.in mead-2.2.7/swig/Makefile.in +--- mead-2.2.7-orig/swig/Makefile.in 2007-11-27 15:57:17.000000000 -0600 ++++ mead-2.2.7/swig/Makefile.in 2009-02-15 16:34:35.000000000 -0600 +@@ -58,7 +58,7 @@ + CXX_FLAGS = @CXX_NOOPTFLAGS@ @CXX_DEBUGFLAGS@ @CXX_SHAREDFLAGS@ + CXX_DYNLIB_FLAGS = @CXX_DYNLIB_FLAGS@ + +-ALL_CXXFLAGS = $(CPP_FLAGS) $(CXX_FLAGS) ++ALL_CXXFLAGS = $(CPP_FLAGS) @CXXFLAGS@ @CXX_SHAREDFLAGS@ + + MEADINC = -I$(top_srcdir) -I$(srcdir) + MEADLIBS = -L../libmead -lmead diff --git a/sci-chemistry/mead/files/mead-2.2.7-respect-flags.patch b/sci-chemistry/mead/files/mead-2.2.7-respect-flags.patch new file mode 100644 index 000000000000..9ffb238ece8c --- /dev/null +++ b/sci-chemistry/mead/files/mead-2.2.7-respect-flags.patch @@ -0,0 +1,74 @@ +diff --git a/apps/Makefile.common.in b/apps/Makefile.common.in +index 15c61ae..f15d71d 100644 +--- a/apps/Makefile.common.in ++++ b/apps/Makefile.common.in +@@ -36,10 +36,10 @@ REGEX_CPP = @REGEX_CPP@ + LIBS = @LIBS@ -lm + + ALL_CPPFLAGS = -I. $(LOCALINCS) $(CPPFLAGS) $(REGEX_CPP) $(CXX_DEFS) +-ALL_CXXFLAGS = $(CXX_OPTFLAGS) $(CXX_DEBUGFLAGS) +-ALL_CFLAGS = $(CC_DEBUGFLAGS) $(CC_OPTFLAGS) ++ALL_CXXFLAGS = @CXXFLAGS@ ++ALL_CFLAGS = @CFLAGS@ + +-CXXLINK = $(CXX) $(ALL_CPPFLAGS) $(CXX_DEBUGFLAGS) $(CXX_OPTFLAGS) \ ++CXXLINK = $(CXX) $(ALL_CPPFLAGS) @CXXFLAGS@ \ + $(LDFLAGS) + + .SUFFIXES: .cc .o +diff --git a/apps/libmso/Makefile.in b/apps/libmso/Makefile.in +index 249c25b..9d23665 100644 +--- a/apps/libmso/Makefile.in ++++ b/apps/libmso/Makefile.in +@@ -35,8 +35,8 @@ INSTALL = @INSTALL@ + INSTALL_PROGRAM = @INSTALL_PROGRAM@ + + ALL_CPPFLAGS = -I. $(LOCALINCS) $(CPPFLAGS) $(REGEX_CPP) $(CXX_DEFS) +-ALL_CXXFLAGS = $(CXX_OPTFLAGS) $(CXX_DEBUGFLAGS) +-ALL_CFLAGS = $(CC_DEBUGFLAGS) $(CC_OPTFLAGS) ++ALL_CXXFLAGS = @CXXFLAGS@ ++ALL_CFLAGS = @CFLAGS@ + + .SUFFIXES: + .SUFFIXES: .cc .o +diff --git a/apps/redti/Makefile.in b/apps/redti/Makefile.in +index c4aa5ca..9561bf3 100644 +--- a/apps/redti/Makefile.in ++++ b/apps/redti/Makefile.in +@@ -21,7 +21,7 @@ CFLAGS = @CFLAGS@ + redti_objs = redti.o rfixpro.o rfixprosee.o pfix.o tc.o + + redti : $(redti_objs) +- $(CC) $(CFLAGS) $(redti_objs) -lm -o redti ++ $(CC) $(CFLAGS) $(LDFLAGS) $(redti_objs) -lm -o redti + + appname = redti + include ../Makefile.common +diff --git a/libmead/Makefile.in b/libmead/Makefile.in +index 3d4d5f0..8b4a4ac 100644 +--- a/libmead/Makefile.in ++++ b/libmead/Makefile.in +@@ -99,8 +99,8 @@ PYTHONINC = @PYTHONINC@ + INCLUDES = -I$(top_srcdir) + + ALL_CPPFLAGS = $(INCLUDES) $(CPPFLAGS) $(REGEX_CPP) $(CXX_DEFS) +-ALL_CXXFLAGS = $(CXX_OPTFLAGS) $(CXX_DEBUGFLAGS) $(CXX_SHAREDFLAGS) +-ALL_CFLAGS = $(CC_DEBUGFLAGS) $(CC_OPTFLAGS) ++ALL_CXXFLAGS = @CXXFLAGS@ ++ALL_CFLAGS = @CFLAGS@ + + + +diff --git a/swig/Makefile.in b/swig/Makefile.in +index 81b3b4e..8410307 100644 +--- a/swig/Makefile.in ++++ b/swig/Makefile.in +@@ -58,7 +58,7 @@ CPP_FLAGS = -DSWIG @CPPFLAGS@ + CXX_FLAGS = @CXX_NOOPTFLAGS@ @CXX_DEBUGFLAGS@ @CXX_SHAREDFLAGS@ + CXX_DYNLIB_FLAGS = @CXX_DYNLIB_FLAGS@ + +-ALL_CXXFLAGS = $(CPP_FLAGS) $(CXX_FLAGS) ++ALL_CXXFLAGS = $(CPP_FLAGS) @CXXFLAGS@ @CXX_SHAREDFLAGS@ + + MEADINC = -I$(top_srcdir) -I$(srcdir) + MEADLIBS = -L../libmead -lmead diff --git a/sci-chemistry/mead/mead-2.2.7-r1.ebuild b/sci-chemistry/mead/mead-2.2.7-r1.ebuild new file mode 100644 index 000000000000..fd67abb3c345 --- /dev/null +++ b/sci-chemistry/mead/mead-2.2.7-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit eutils + +DESCRIPTION="Macroscopic Electrostatics with Atomic Detail" +HOMEPAGE="http://www.teokem.lu.se/~ulf/Methods/mead.html" +SRC_URI="ftp://ftp.scripps.edu/pub/bashford/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86" + +IUSE="python" + +RESTRICT="fetch" + +pkg_nofetch() { + elog "Download ${SRC_URI}" + elog "and place it in ${DISTDIR}." + elog + elog "Use \"anonymous\" as a login, and an email address as a password." +} + +src_unpack() { + unpack ${A} + cd "${S}" + + epatch "${FILESDIR}"/${P}-respect-flags.patch + epatch "${FILESDIR}"/${P}-gcc43.patch +} + +src_compile() { + econf \ + ${conf_opts} \ + || die "configure failed" + emake || die "make failed" +} + +src_install() { + # package hates emake DESTDIR="${D}" install + einstall || die "install failed" +} diff --git a/sci-chemistry/mead/mead-2.2.7.ebuild b/sci-chemistry/mead/mead-2.2.7.ebuild new file mode 100644 index 000000000000..fd67abb3c345 --- /dev/null +++ b/sci-chemistry/mead/mead-2.2.7.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit eutils + +DESCRIPTION="Macroscopic Electrostatics with Atomic Detail" +HOMEPAGE="http://www.teokem.lu.se/~ulf/Methods/mead.html" +SRC_URI="ftp://ftp.scripps.edu/pub/bashford/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86" + +IUSE="python" + +RESTRICT="fetch" + +pkg_nofetch() { + elog "Download ${SRC_URI}" + elog "and place it in ${DISTDIR}." + elog + elog "Use \"anonymous\" as a login, and an email address as a password." +} + +src_unpack() { + unpack ${A} + cd "${S}" + + epatch "${FILESDIR}"/${P}-respect-flags.patch + epatch "${FILESDIR}"/${P}-gcc43.patch +} + +src_compile() { + econf \ + ${conf_opts} \ + || die "configure failed" + emake || die "make failed" +} + +src_install() { + # package hates emake DESTDIR="${D}" install + einstall || die "install failed" +} diff --git a/sci-chemistry/mead/metadata.xml b/sci-chemistry/mead/metadata.xml new file mode 100644 index 000000000000..9ac9ffdb3a41 --- /dev/null +++ b/sci-chemistry/mead/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/metadata.xml b/sci-chemistry/metadata.xml new file mode 100644 index 000000000000..c60d4c31553f --- /dev/null +++ b/sci-chemistry/metadata.xml @@ -0,0 +1,38 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE catmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<catmetadata> + <longdescription lang="en"> + The sci-chemistry category contains software that can be used + in chemistral scientific environments. + </longdescription> + <longdescription lang="de"> + Die Kategorie sci-chemistry enthält Software, welche in chemischen + und chemietechnischen Umgebungen genutzt werden kann. + </longdescription> + <longdescription lang="es"> + La categoría sci-chemistry contiene programas que pueden ser utilizados + en entornos relacionados con la química. + </longdescription> + <longdescription lang="ja"> + sci-chemistryカテゴリーには化学の科学的な分野に利用される + フトウェアが含まれています。 + </longdescription> + <longdescription lang="nl"> + De sci-chemistry categorie bevat software die in scheikundige omgevingen + gebruikt kan worden. + </longdescription> + <longdescription lang="vi"> + Nhóm sci-chemistry chứa các phần mềm dùng trong hoá học. + </longdescription> + <longdescription lang="it"> + La categoria sci-chemistry contiene programmi per la chimica. + </longdescription> + <longdescription lang="pt"> + A categoria sci-chemistry contém programas que podem ser usados + em ambientes relacionados a química. + </longdescription> + <longdescription lang="pl"> + Kategoria sci-chemistry zawiera programy naukowe związane z chemią. + </longdescription> +</catmetadata> + diff --git a/sci-chemistry/mm-align/Manifest b/sci-chemistry/mm-align/Manifest new file mode 100644 index 000000000000..a1e08c44269c --- /dev/null +++ b/sci-chemistry/mm-align/Manifest @@ -0,0 +1 @@ +DIST MM-align-20120321.tar.xz 20072 SHA256 0158a93a06257b885630ab7bed3b7bf8dca2ee12217c84d019829a1e34f3eeb3 diff --git a/sci-chemistry/mm-align/files/CMakeLists.txt b/sci-chemistry/mm-align/files/CMakeLists.txt new file mode 100644 index 000000000000..635ffdd67418 --- /dev/null +++ b/sci-chemistry/mm-align/files/CMakeLists.txt @@ -0,0 +1,5 @@ +cmake_minimum_required (VERSION 2.6) +project (MM-align Fortran) +add_executable(MMalign MM-align.f) + +install (TARGETS MMalign DESTINATION bin) diff --git a/sci-chemistry/mm-align/metadata.xml b/sci-chemistry/mm-align/metadata.xml new file mode 100644 index 000000000000..2634f696a953 --- /dev/null +++ b/sci-chemistry/mm-align/metadata.xml @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +MM-align is an algorithm for structurally aligning multiple-chain +protein-protein complexes. The algorithm is built on a heuristic +iteration of a modified Needleman-Wunsch dynamic programming (DP) +algorithm, with the alignment score specified by the inter-complex residue +distances. The multiple chains in each complex are first joined, in every +possible order, and then simultaneously aligned with cross-chain alignments +prevented. The alignments of interface residues are enhanced by an +interface-specific weighting factor. An optimal alignment between two complexes, +as well as the overall TM-score, will be reported for each comparison. +What is the difference between TM-align and MM-align? TM-align is for aligning +monomer protein structures while MM-align is designed for aligning +multiple-chain protein complex structures. Although one can still use TM-align +to align protein complexes after manually joining the chains, this will lead +to suboptimal alignments with unphysical cross alignments. Therefore, the +best result will be obtained if one uses TM-align to monomer structures and +MM-align for multimer structures. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/mm-align/mm-align-20120321.ebuild b/sci-chemistry/mm-align/mm-align-20120321.ebuild new file mode 100644 index 000000000000..c0ef57c832af --- /dev/null +++ b/sci-chemistry/mm-align/mm-align-20120321.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils fortran-2 + +DESCRIPTION="Protein Complex Structural Alignment" +HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/MM-align/" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/MM-align-${PV}.tar.xz" + +SLOT="0" +LICENSE="tm-align" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}" + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die +} diff --git a/sci-chemistry/molden/Manifest b/sci-chemistry/molden/Manifest new file mode 100644 index 000000000000..e78207790325 --- /dev/null +++ b/sci-chemistry/molden/Manifest @@ -0,0 +1,2 @@ +DIST molden4.8.tar.gz 2969701 SHA256 314d9b9bdede2fd63d1e2f26e0212711576952244634fc28ea6c97ce2f7029b1 SHA512 11f2406e54a077d044369b5eee4a8a1c1b10f052188d33d4162af0151a1e76a1d5274d8788bbc3610905ff271b0bd2100990b77540a0290ad608bd5c29b839e3 WHIRLPOOL 838d66a4e17651dfd2bab893fa9b36ca8d722c879b9f10adb00c3c4e59974ae73e13060e6a559286c651ab35e1cea084049677277cc4b455e68a95c6c210dcf9 +DIST molden5.0.tar.gz 3063244 SHA256 c9cf8f656adf2f2c7a8b8b64fa07b5feaa9c3ca36c4803e1f58ac33de1cffdc4 SHA512 bf45849bf4efb67bc552767c28a6df6e5106a7d8ac2d73db2c7218412fb6cd2f2785c2be83a8589a5664ba9c0ca052cef5eb155c665ee1f3d6c7fe208f806a6b WHIRLPOOL ab7f1118b000a8df36cbaf23fddabb21bd291a2388e3aa5599e609ffa792bec01bf7df52a98f7e70125b504f7866e48ec6d5ce029ecd0e40c7bab7b8627c5c86 diff --git a/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch b/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch new file mode 100644 index 000000000000..dd5aba4f17da --- /dev/null +++ b/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch @@ -0,0 +1,12 @@ +diff --git a/silly.c b/silly.c +index 57d07e8..102156a 100644 +--- a/silly.c ++++ b/silly.c +@@ -13,6 +13,7 @@ + #include <stdio.h> + #include <stdlib.h> + #include <math.h> ++#include <string.h> + + #ifndef WIN32 + #include <GL/gl.h> diff --git a/sci-chemistry/molden/files/molden-4.8-ambfor.patch b/sci-chemistry/molden/files/molden-4.8-ambfor.patch new file mode 100644 index 000000000000..1ececa7f57e9 --- /dev/null +++ b/sci-chemistry/molden/files/molden-4.8-ambfor.patch @@ -0,0 +1,12 @@ +diff -Naur molden4.8/ambfor/makefile molden4.8.new/ambfor/makefile +--- molden4.8/ambfor/makefile 2009-12-19 06:14:32.000000000 -0500 ++++ molden4.8.new/ambfor/makefile 2010-02-25 22:33:41.000000000 -0500 +@@ -32,7 +32,7 @@ + $(LDR) -o ambmd md.o verlet.o allocmd.o $(OBJS) $(LIBS) + + ambfor.o: ambfor.f +- ${FC} -c -g -ffast-math -funroll-loops -m32 -o ambfor.o ambfor.f ++ ${FC} $(FFLAGS) -c ambfor.f -o ambfor.o + + allocmd.o: alloc.c + $(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o diff --git a/sci-chemistry/molden/files/molden-4.8-ldflags.patch b/sci-chemistry/molden/files/molden-4.8-ldflags.patch new file mode 100644 index 000000000000..92fa6c665f3f --- /dev/null +++ b/sci-chemistry/molden/files/molden-4.8-ldflags.patch @@ -0,0 +1,26 @@ +diff --git a/makefile b/makefile +index 81147a3..9e2353e 100644 +--- a/makefile ++++ b/makefile +@@ -224,10 +224,10 @@ all: molden gmolden ambfor/ambfor ambfor/ambmd surf/surf + + + molden: $(OBJS) mpdum.o xwin.o +- $(LDR) -o molden $(OBJS) mpdum.o xwin.o $(LIBS) ++ $(LDR) $(LDFLAGS) -o molden $(OBJS) mpdum.o xwin.o $(LIBS) + + gmolden: $(OBJS) mpdum.o xwingl.o +- $(LDR) -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG) ++ $(LDR) $(LDFLAGS) -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG) + + ambfor/ambfor: ambfor/*.f ambfor/*.c + $(MAKE) -C ambfor FC=${FC} FFLAGS="${FFLAGS}" LDR="${LDR}" CFLAGS="${CFLAGS}" +@@ -269,7 +269,7 @@ short_wrl: short_wrl.o + # Moldens OpenGL helper program + + moldenogl: oglmol.o silly.o +- $(CC) -o moldenogl oglmol.o silly.o $(LIBSOGL) ++ $(CC) $(LDFLAGS) -o moldenogl oglmol.o silly.o $(LIBSOGL) + + # conversion of CADPAC output to molden format + diff --git a/sci-chemistry/molden/files/molden-4.8-overflow.patch b/sci-chemistry/molden/files/molden-4.8-overflow.patch new file mode 100644 index 000000000000..7cbd7f436f57 --- /dev/null +++ b/sci-chemistry/molden/files/molden-4.8-overflow.patch @@ -0,0 +1,38 @@ + xwin.c | 10 ++++++---- + 1 files changed, 6 insertions(+), 4 deletions(-) + +diff --git a/xwin.c b/xwin.c +index f395909..092edff 100644 +--- a/xwin.c ++++ b/xwin.c +@@ -13552,7 +13552,7 @@ void NewActiveStruct() + #ifdef CRAY + _fcd ztr; + #else +- char ztr; ++ char ztr[4]; + #endif + #endif + +@@ -13650,8 +13650,10 @@ void NewActiveStruct() + */ + clfpstr->ihashz = 0; + #else +- strncpy(&ztr,HetAtm[j],3); +- parhet_(&j1,&ztr); ++ if (HetAtm[j] != NULL) { ++ strncpy(ztr,HetAtm[j],3); ++ parhet_(&j1,ztr); ++ } + #endif + #endif + } +@@ -27353,7 +27355,7 @@ char *errstr; + UpdateZME(); + RedrawScroll(&zscroll); + } +- strcpy(ZMEerr,errstr); ++ strncpy(ZMEerr,errstr,MAXZMEERR); + RedrawStatus(); + } + diff --git a/sci-chemistry/molden/files/molden-5.0-ambfor.patch b/sci-chemistry/molden/files/molden-5.0-ambfor.patch new file mode 100644 index 000000000000..9656ff7a79be --- /dev/null +++ b/sci-chemistry/molden/files/molden-5.0-ambfor.patch @@ -0,0 +1,16 @@ + ambfor/makefile | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/ambfor/makefile b/ambfor/makefile +index 8627a11..dbc23a1 100644 +--- a/ambfor/makefile ++++ b/ambfor/makefile +@@ -47,7 +47,7 @@ ambmd: md.o verlet.o qvdw.o allocmd.o $(OBJS) + $(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS) + + ambfor.o: ambfor.f +- ${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f ++ ${FC} $(FFLAGS) -c -o ambfor.o ambfor.f + + allocmd.o: alloc.c + $(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o diff --git a/sci-chemistry/molden/files/molden-5.0-overflow.patch b/sci-chemistry/molden/files/molden-5.0-overflow.patch new file mode 100644 index 000000000000..4fc406266935 --- /dev/null +++ b/sci-chemistry/molden/files/molden-5.0-overflow.patch @@ -0,0 +1,16 @@ + xwin.c | 10 ++++++---- + 1 files changed, 6 insertions(+), 4 deletions(-) + +diff --git a/xwin.c b/xwin.c +index f395909..092edff 100644 +--- a/xwin.c ++++ b/xwin.c +@@ -27353,7 +27355,7 @@ char *errstr; + UpdateZME(); + RedrawScroll(&zscroll); + } +- strcpy(ZMEerr,errstr); ++ strncpy(ZMEerr,errstr,MAXZMEERR); + RedrawStatus(); + } + diff --git a/sci-chemistry/molden/metadata.xml b/sci-chemistry/molden/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/molden/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/molden/molden-4.8-r2.ebuild b/sci-chemistry/molden/molden-4.8-r2.ebuild new file mode 100644 index 000000000000..943f7cc4fb05 --- /dev/null +++ b/sci-chemistry/molden/molden-4.8-r2.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 flag-o-matic toolchain-funcs + +MY_P="${PN}${PV}" + +DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac" +HOMEPAGE="http://www.cmbi.kun.nl/~schaft/molden/molden.html" +SRC_URI="ftp://ftp.cmbi.kun.nl/pub/molgraph/${PN}/${MY_P}.tar.gz" + +LICENSE="MOLDEN" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="opengl" + +RDEPEND=" + x11-libs/libXmu + virtual/glu + opengl? ( + media-libs/freeglut + virtual/opengl )" +DEPEND="${RDEPEND} + x11-misc/gccmakedep + app-editors/vim" + # vim provides ex, which the build system uses (surf/Makefile, at least) + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-ambfor.patch \ + "${FILESDIR}"/${P}-overflow.patch \ + "${FILESDIR}"/${P}-ldflags.patch \ + "${FILESDIR}"/${PN}-4.7-implicit-dec.patch + sed \ + -e 's:makedepend:gccmakedep:g' \ + -e "s:/usr/include/sgidefs.h::g" \ + -i surf/Makefile || die + sed 's:shell g77:shell $(FC):g' -i makefile || die +} + +src_compile() { + # Use -mieee on alpha, according to the Makefile + use alpha && append-flags -mieee + + # Honor CC, CFLAGS, FC, and FFLAGS from environment; + # unfortunately a bash bug prevents us from doing typeset and + # assignment on the same line. + typeset -a args + args=( + CC="$(tc-getCC) ${CFLAGS}" \ + FC="$(tc-getFC)" \ + LDR="$(tc-getFC)" \ + FFLAGS="${FFLAGS}" ) + + einfo "Building Molden..." + emake -j1 "${args[@]}" + if use opengl ; then + einfo "Building Molden OpenGL helper..." + emake -j1 "${args[@]}" moldenogl + fi +} + +src_install() { + dobin ${PN} g${PN} + if use opengl ; then + dobin ${PN}ogl + fi + + dodoc HISTORY README REGISTER + cd doc + uncompress * && dodoc * +} diff --git a/sci-chemistry/molden/molden-5.0.ebuild b/sci-chemistry/molden/molden-5.0.ebuild new file mode 100644 index 000000000000..e4ad3b6d802d --- /dev/null +++ b/sci-chemistry/molden/molden-5.0.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 flag-o-matic toolchain-funcs + +MY_P="${PN}${PV}" + +DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac" +HOMEPAGE="http://www.cmbi.kun.nl/~schaft/molden/molden.html" +SRC_URI="ftp://ftp.cmbi.kun.nl/pub/molgraph/${PN}/${MY_P}.tar.gz" + +LICENSE="MOLDEN" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="opengl" + +RDEPEND=" + x11-libs/libXmu + virtual/glu + opengl? ( + media-libs/freeglut + virtual/opengl )" +DEPEND="${RDEPEND} + x11-misc/gccmakedep + app-editors/vim" + # vim provides ex, which the build system uses (surf/Makefile, at least) + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-ambfor.patch \ + "${FILESDIR}"/${P}-overflow.patch \ + "${FILESDIR}"/${PN}-4.8-ldflags.patch \ + "${FILESDIR}"/${PN}-4.7-implicit-dec.patch + sed \ + -e 's:makedepend:gccmakedep:g' \ + -e "s:/usr/include/sgidefs.h::g" \ + -i surf/Makefile || die + sed 's:shell g77:shell $(FC):g' -i makefile || die +} + +src_compile() { + # Use -mieee on alpha, according to the Makefile + use alpha && append-flags -mieee + + # Honor CC, CFLAGS, FC, and FFLAGS from environment; + # unfortunately a bash bug prevents us from doing typeset and + # assignment on the same line. + typeset -a args + args=( + CC="$(tc-getCC) ${CFLAGS}" \ + FC="$(tc-getFC)" \ + LDR="$(tc-getFC)" \ + FFLAGS="${FFLAGS}" ) + + einfo "Building Molden..." + emake -j1 "${args[@]}" + if use opengl ; then + einfo "Building Molden OpenGL helper..." + emake -j1 "${args[@]}" moldenogl + fi +} + +src_install() { + dobin ${PN} g${PN} + if use opengl ; then + dobin ${PN}ogl + fi + + dodoc HISTORY README REGISTER + cd doc + uncompress * && dodoc * +} diff --git a/sci-chemistry/moldy/Manifest b/sci-chemistry/moldy/Manifest new file mode 100644 index 000000000000..9e0e3883fa2f --- /dev/null +++ b/sci-chemistry/moldy/Manifest @@ -0,0 +1 @@ +DIST moldy-2.16e.tar.gz 488410 RMD160 ef9c1c6cf1afa6e28e78a51a6a771d127aac2c83 SHA1 e7984f59170a11b5dab0beae89c5f4cf4da20ad1 SHA256 51abefc5e7de355022f48084382c30e72738cc1f21cd3d67fde7f047f1822ea8 diff --git a/sci-chemistry/moldy/files/2.16e-as-needed.patch b/sci-chemistry/moldy/files/2.16e-as-needed.patch new file mode 100644 index 000000000000..67399e08560e --- /dev/null +++ b/sci-chemistry/moldy/files/2.16e-as-needed.patch @@ -0,0 +1,65 @@ +diff --git a/Makefile.in b/Makefile.in +index 0b02f00..ec588a8 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -115,25 +115,25 @@ VMSBUILD= compile_moldy.com link_moldy.com defcomm.com\ + + DOSBUILD= Makefile.mak OFILES.RSP SHAKOBJS.RSP Makefile.w32 + +-all: moldy utilities Makefile ++all: moldy utilities + + moldy: $(OFILES) $(EXTRA_OBJ) $(HFILES) +- $(CC) -o moldy $(LDFLAGS) $(OFILES) $(EXTRA_OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) -o moldy $(LDFLAGS) $(OFILES) $(EXTRA_OBJ) $(LIBS) + + moldyext: moldyext.c $(LIBOBJS) $(HFILES) +- $(CC) $(CFLAGS) -o moldyext $(OPT) $(DEFS) $(LDFLAGS1) moldyext.c $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o moldyext $(OPT) $(DEFS) $(LDFLAGS1) moldyext.c $(LIBOBJS) $(LIBS) + + manalyze: manalyze.c $(HFILES) +- $(CC) $(CFLAGS) -o manalyze $(OPT) $(DEFS) $(LDFLAGS1) manalyze.c $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o manalyze $(OPT) $(DEFS) $(LDFLAGS1) manalyze.c $(LIBS) + + dumpanal: dumpanal.c xdr.o $(HFILES) +- $(CC) $(CFLAGS) -o dumpanal $(OPT) $(DEFS) $(LDFLAGS1) dumpanal.c xdr.o $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o dumpanal $(OPT) $(DEFS) $(LDFLAGS1) dumpanal.c xdr.o $(LIBS) + + dumpext: dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(HFILES) +- $(CC) $(CFLAGS) -o dumpext $(OPT) $(DEFS) $(LDFLAGS1) dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o dumpext $(OPT) $(DEFS) $(LDFLAGS1) dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(LIBS) + + dumpconv: dumpconv.c xdr.o $(HFILES) +- $(CC) $(CFLAGS) -o dumpconv $(OPT) $(DEFS) $(LDFLAGS1) dumpconv.c xdr.o $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o dumpconv $(OPT) $(DEFS) $(LDFLAGS1) dumpconv.c xdr.o $(LIBS) + + #mdtraj: mdtraj.o $(SHAKOBJS) $(LIBOBJS) + # $(CC) -o mdtraj $(LDFLAGS) mdtraj.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) +@@ -142,21 +142,21 @@ mdshak: mdshak.o $(SHAKOBJS) $(LIBOBJS) + $(CC) -o mdshak $(LDFLAGS) mdshak.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + + msd: msd.o $(SHAKOBJS) $(LIBOBJS) +- $(CC) -o msd $(LDFLAGS1) msd.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o msd $(LDFLAGS1) msd.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + + mdvaf: mdvaf.o $(SHAKOBJS) $(LIBOBJS) +- $(CC) -o mdvaf $(LDFLAGS1) mdvaf.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o mdvaf $(LDFLAGS1) mdvaf.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + mdavpos: mdavpos.o $(SHAKOBJS) $(LIBOBJS) +- $(CC) -o mdavpos $(LDFLAGS1) mdavpos.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o mdavpos $(LDFLAGS1) mdavpos.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + + mdbond: mdbond.o $(SHAKOBJS) $(LIBOBJS) +- $(CC) -o mdbond $(LDFLAGS1) mdbond.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o mdbond $(LDFLAGS1) mdbond.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + + bdist: bdist.c $(HFILES) +- $(CC) $(CFLAGS) -o bdist $(OPT) $(DEFS) $(LDFLAGS1) bdist.c $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o bdist $(OPT) $(DEFS) $(LDFLAGS1) bdist.c $(LIBOBJS) $(LIBS) + + ransub: ransub.o $(SHAKOBJS) $(LIBOBJS) +- $(CC) -o ransub $(LDFLAGS1) ransub.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o ransub $(LDFLAGS1) ransub.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + + utilities: $(UTILS) $(UTILS2) + diff --git a/sci-chemistry/moldy/metadata.xml b/sci-chemistry/moldy/metadata.xml new file mode 100644 index 000000000000..e42d0af60f42 --- /dev/null +++ b/sci-chemistry/moldy/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild new file mode 100644 index 000000000000..27db651f82a3 --- /dev/null +++ b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Molecular dynamics simulations platform" +HOMEPAGE="http://www.ccp5.ac.uk/moldy/moldy.html" +SRC_URI="ftp://ftp.earth.ox.ac.uk/pub/keith/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc examples" + +DEPEND="doc? ( virtual/latex-base )" +RDEPEND="" + +S="${WORKDIR}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-as-needed.patch + sed \ + -e 's:-O2::g' \ + -e 's:-ffast-math::g' \ + -i configure || die +} + +src_configure() { + #Individuals may want to edit the OPT* variables below. + #From the READ.ME: + #You may need to "hand-tune" compiler or optimization options, + #which may be specified by setting the OPT and OPT2 environment + #variables. OPT2 is used to compile only the most performance-critical + #modules and usually will select a very high level of optimization. + #It should be safe to select an optimization which means "treat all + #function arguments as restricted pointers which are not aliased to + #any other object". OPT is used for less preformance-critical modules + #and may be set to a lower level of optimization than OPT2. + + OPT="${CFLAGS}" \ + OPT2="${CFLAGS} ${CFLAGS_OPT}" \ + CC=$(tc-getCC) \ + econf +} + +src_compile() { + emake + # To prevent sandbox violations by metafont + if use doc; then + VARTEXFONTS="${T}"/fonts emake moldy.pdf + fi +} + +src_install() { + dodir /usr/bin + emake prefix="${ED}"/usr install + dodoc BENCHMARK READ.ME RELNOTES + + if use examples; then + rm Makefile.in configure.in config.h.in + insinto /usr/share/${PN}/examples/ + doins *.in *.out control.* || die + fi + if use doc; then + insinto /usr/share/doc/${PF}/pdf + newins moldy.pdf moldy-manual.pdf + fi +} diff --git a/sci-chemistry/molequeue/Manifest b/sci-chemistry/molequeue/Manifest new file mode 100644 index 000000000000..8511144b0f00 --- /dev/null +++ b/sci-chemistry/molequeue/Manifest @@ -0,0 +1 @@ +DIST molequeue-0.7.1.tar.gz 658745 SHA256 cdf184936a73e382b8cbff02768b9a04a3a64fec658d6dde4f6574236a73d3bf SHA512 09bdd45c1b2833be3a4f4cd3a0ade8d51276f8da150b0206d9c4a0d3b4999c58bc6cb3df48b9be70907d47c11bbd22aacc7c8d9ae401aa2f21a43405d6a8e3cd WHIRLPOOL 7ea17582495145b9d616bf1df58fbae3d4a6876c1490d5efdcefae1804cf7d29b08543a112ac7c033e2d2e18aa1537ed73a80f75484c90c7319f52dd469b5812 diff --git a/sci-chemistry/molequeue/metadata.xml b/sci-chemistry/molequeue/metadata.xml new file mode 100644 index 000000000000..e7326743bc35 --- /dev/null +++ b/sci-chemistry/molequeue/metadata.xml @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +MoleQueue is an open-source, cross-platform, system-tray resident desktop +application for abstracting, managing, and coordinating the execution of tasks +both locally and on remote computational resources. It is built and tested and +Linux, Mac OS X, and Windows, with nightly binaries currently available for +Mac OS X and Windows. Users can set up local and remote queues that describe +where the task will be executed. Each queue can have programs, with templates +to facilitate the execution of the program. Input files can be staged, and +output files collected using a standard interface. +</longdescription> + <use> + <flag name="zeromq">Build with <pkg>net-libs/zeromq</pkg> support</flag> + <flag name="client">Build the client application</flag> + <flag name="server">Build the serve application</flag> + </use> + <upstream> + <remote-id type="sourceforge">molequeue</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/molequeue/molequeue-0.7.1.ebuild b/sci-chemistry/molequeue/molequeue-0.7.1.ebuild new file mode 100644 index 000000000000..a7700f58577a --- /dev/null +++ b/sci-chemistry/molequeue/molequeue-0.7.1.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils multilib python-single-r1 versionator virtualx + +DESCRIPTION="Abstract, manage and coordinate execution of tasks" +HOMEPAGE="http://www.openchemistry.org/OpenChemistry/project/molequeue.html" +SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+client doc server test +zeromq" + +REQUIRED_USE="${PYTHON_REQUIRED_USE} + server? ( client ) + test? ( server )" + +RDEPEND="${PYTHON_DEPS} + dev-qt/qtcore:4 + dev-qt/qtgui:4 + zeromq? ( net-libs/cppzmq:0= )" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_enable test TESTING) + $(cmake-utils_use_use zeromq ZERO_MQ) + $(cmake-utils_use_build doc DOCUMENTATION) + $(cmake-utils_use client MoleQueue_BUILD_CLIENT) + $(cmake-utils_use server MoleQueue_BUILD_APPLICATION) + -DINSTALL_LIBRARY_DIR=$(get_libdir) + ) + use zeromq && \ + mycmakeargs+=( -DZeroMQ_ROOT_DIR=\"${EPREFIX}/usr\" ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile all $(usex doc documentation "") +} + +src_test() { + VIRTUALX_COMMAND=cmake-utils_src_test + virtualmake +} + +src_install() { + use doc && HTML_DOCS=( "${BUILD_DIR}"/docs/html/. ) + cmake-utils_src_install +} diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest new file mode 100644 index 000000000000..3b9280e4b834 --- /dev/null +++ b/sci-chemistry/molmol/Manifest @@ -0,0 +1,2 @@ +DIST molmol-2k.2.0-doc.tar.gz 1062297 SHA256 07e1c3fd04ffe7c9e9d91eaefa0bf72e6d0913a981eec3bf0879bfc65537a6be SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe WHIRLPOOL b74f47149c4dce8199722075fda17c9cbe22263eec57b647ef543b15386d53b267ee85d5a2c44a4fda7e533fd6ccdafb82fbbbd71e671ec4e1fd58e07363677c +DIST molmol-2k.2.0-src.tar.gz 1088805 SHA256 1104dcb1b2517581c7d6b1695ff2e92f4076ad34afc48dd896eec38e5acf2287 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b WHIRLPOOL e258ede83ac4a8fe9b4a9274588ced7e1294415d864c909ed83e3e56d36512e1388e6f77e45da614bc19992a265d32b739c54aace7faa28971c61a01bba27541 diff --git a/sci-chemistry/molmol/files/cast.patch b/sci-chemistry/molmol/files/cast.patch new file mode 100644 index 000000000000..16ac411c76e5 --- /dev/null +++ b/sci-chemistry/molmol/files/cast.patch @@ -0,0 +1,21 @@ +diff --git a/src/data/DataDist.c b/src/data/DataDist.c +index 7f7121f..18eef33 100644 +--- a/src/data/DataDist.c ++++ b/src/data/DataDist.c +@@ -27,6 +27,7 @@ + + #include <stdio.h> + #include <stdlib.h> ++#include <stdint.h> + + #include <hashtab.h> + +@@ -89,7 +90,7 @@ hashInter(void *p, unsigned size) + { + TabEntryInter *entryP = p; + +- return ((unsigned) entryP->atom1P + (unsigned) entryP->atom2P) % size; ++ return ((unsigned)(uintptr_t) entryP->atom1P + (unsigned)(uintptr_t) entryP->atom2P) % size; + } + + static int diff --git a/sci-chemistry/molmol/files/ldflags.patch b/sci-chemistry/molmol/files/ldflags.patch new file mode 100644 index 000000000000..ff6e06ef490c --- /dev/null +++ b/sci-chemistry/molmol/files/ldflags.patch @@ -0,0 +1,13 @@ +diff --git a/src/main/Makefile b/src/main/Makefile +index 74530fa..102d1b7 100644 +--- a/src/main/Makefile ++++ b/src/main/Makefile +@@ -22,7 +22,7 @@ SRC = $(OBJ:.o=.c) + default: $(PROGRAM) + + $(PROGRAM): $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) +- $(CC) -o $@ $(CFLAGS) $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) $(SYSLIB) ++ $(CC) $(CFLAGS) ${LDFLAGS} -o $@ $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) $(SYSLIB) + + clean: + rm -f $(OBJ) $(PROGRAM) core *.ps diff --git a/sci-chemistry/molmol/files/libpng15.patch b/sci-chemistry/molmol/files/libpng15.patch new file mode 100644 index 000000000000..cd27e4906608 --- /dev/null +++ b/sci-chemistry/molmol/files/libpng15.patch @@ -0,0 +1,32 @@ +--- src/motogl/MotOGLDump.c ++++ src/motogl/MotOGLDump.c +@@ -248,7 +248,7 @@ + pngErrHand(png_structp pngStrucP, char *errMsg) + { + IORaiseError(errMsg); +- longjmp(pngStrucP->jmpbuf, 1); ++ longjmp(png_jmpbuf(pngStrucP), 1); + } + #endif + +@@ -357,7 +357,7 @@ + return IO_RES_ERR; + } + +- if (setjmp(pngStrucP->jmpbuf)) { ++ if (setjmp(png_jmpbuf(pngStrucP))) { + if (cBuf != NULL) + free(cBuf); + if (fBuf != NULL) +@@ -368,10 +368,7 @@ + + png_init_io(pngStrucP, ImgFileP); + +- pngInfoP->width = imgW; +- pngInfoP->height = imgH; +- pngInfoP->bit_depth = 8; +- pngInfoP->color_type = PNG_COLOR_TYPE_RGB; ++ png_set_IHDR(pngStrucP, pngInfoP, imgW, imgH, 8, PNG_COLOR_TYPE_RGB, 0, PNG_COMPRESSION_TYPE_DEFAULT, PNG_FILTER_TYPE_DEFAULT); + png_write_info(pngStrucP, pngInfoP); + } + #endif diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch b/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch new file mode 100644 index 000000000000..14cc83b63e9e --- /dev/null +++ b/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch @@ -0,0 +1,356 @@ + src/calc/CalcRmsd.c | 8 ++++---- + src/cmdfig/FigUtil.c | 46 +++++++++++++++++++++++----------------------- + src/cmdio/ExWriteSec.c | 6 +++--- + src/data/DataDist.c | 2 +- + src/data/DataHand.c | 8 ++++---- + src/expr/ExprScan.c | 2 +- + src/iodev/IODev.c | 2 -- + src/motif/MotifDial.c | 2 +- + src/motif/MotifMainW.c | 4 ++-- + src/os/GFile.c | 2 +- + src/prim/PrimDraw.c | 2 +- + src/prim/RibbonCalc.c | 12 ++++++------ + src/pudev/PuMainW.c | 2 +- + src/tty/TTY.c | 2 +- + tools/src/IsoSurface.c | 22 +++++++++++----------- + 15 files changed, 60 insertions(+), 62 deletions(-) + +diff --git a/src/calc/CalcRmsd.c b/src/calc/CalcRmsd.c +index 0e4629e..ed99e76 100644 +--- a/src/calc/CalcRmsd.c ++++ b/src/calc/CalcRmsd.c +@@ -1025,10 +1025,10 @@ CalcRmsd(BOOL fitPairs, char *range, char *glob1, char *glob2, + } + + for (propI = 0; propI < 2; propI++) { +- if (groupNo == 0 || propI == 0 && ! calc1) ++ if (groupNo == 0 || (propI == 0 && ! calc1)) + continue; + +- if (groupNo == 0 || propI == 1 && ! calc2) ++ if (groupNo == 0 || (propI == 1 && ! calc2)) + continue; + + Report("\nAverage RMSD, dev., min. and max of "); +@@ -1052,8 +1052,8 @@ CalcRmsd(BOOL fitPairs, char *range, char *glob1, char *glob2, + Report(" "); + + for (groupI2 = 0; groupI2 < groupNo; groupI2++) { +- if (groupI1 < groupI2 && +- groupInfoP[groupI1].membNo != groupInfoP[groupI2].membNo || ++ if (((groupI1 < groupI2) && ++ (groupInfoP[groupI1].membNo != groupInfoP[groupI2].membNo)) || + groupInfoP[groupI1].membNo == 0 || + groupInfoP[groupI2].membNo == 0) { + groupInfoP[groupI2].stat.avg = 0.0f; +diff --git a/src/cmdfig/FigUtil.c b/src/cmdfig/FigUtil.c +index 20d403a..b8dc3a6 100644 +--- a/src/cmdfig/FigUtil.c ++++ b/src/cmdfig/FigUtil.c +@@ -44,29 +44,29 @@ typedef struct { + } TabEntry; + + static TabEntry GreekTab[] = { +- "ALPHA", 'a', +- "BETA", 'b', +- "CHI", 'c', +- "DELTA", 'd', +- "EPSILON", 'e', +- "PHI" , 'f', +- "GAMMA", 'g', +- "ETA", 'h', +- "IOTA", 'i', +- "KAPPA", 'k', +- "LAMBDA", 'l', +- "MU", 'm', +- "NU", 'n', +- "PI", 'p', +- "THETA", 'q', +- "RHO", 'r', +- "SIGMA", 's', +- "TAU", 't', +- "UPSILON", 'u', +- "OMEGA", 'w', +- "XI", 'x', +- "PSI", 'y', +- "ZETA", 'z' ++ {"ALPHA", 'a'}, ++ {"BETA", 'b'}, ++ {"CHI", 'c'}, ++ {"DELTA", 'd'}, ++ {"EPSILON", 'e'}, ++ {"PHI" , 'f'}, ++ {"GAMMA", 'g'}, ++ {"ETA", 'h'}, ++ {"IOTA", 'i'}, ++ {"KAPPA", 'k'}, ++ {"LAMBDA", 'l'}, ++ {"MU", 'm'}, ++ {"NU", 'n'}, ++ {"PI", 'p'}, ++ {"THETA", 'q'}, ++ {"RHO", 'r'}, ++ {"SIGMA", 's'}, ++ {"TAU", 't'}, ++ {"UPSILON", 'u'}, ++ {"OMEGA", 'w'}, ++ {"XI", 'x'}, ++ {"PSI", 'y'}, ++ {"ZETA", 'z'} + }; + + int +diff --git a/src/cmdio/ExWriteSec.c b/src/cmdio/ExWriteSec.c +index 7f705d4..8da8336 100644 +--- a/src/cmdio/ExWriteSec.c ++++ b/src/cmdio/ExWriteSec.c +@@ -250,9 +250,9 @@ writeSecondary(DhResP *resPA, int resNo) + + if (neighLStart != NO_RES) { + if (num != neighLEnd + 1 || +- neighNum != neighREnd + 1 && neighNum != neighREnd - 1 || +- neighREnd > neighRStart && neighNum != neighREnd + 1 || +- neighREnd < neighRStart && neighNum != neighREnd - 1) { ++ (neighNum != neighREnd + 1 && neighNum != neighREnd - 1) || ++ (neighREnd > neighRStart && neighNum != neighREnd + 1) || ++ (neighREnd < neighRStart && neighNum != neighREnd - 1)) { + writeNeigh(neighLStart, neighLEnd, neighRStart, neighREnd); + neighLStart = NO_RES; + } else { +diff --git a/src/data/DataDist.c b/src/data/DataDist.c +index 18eef33..c683f9e 100644 +--- a/src/data/DataDist.c ++++ b/src/data/DataDist.c +@@ -117,7 +117,7 @@ fillIntra(TabEntryIntra *entryP, DhAtomP atom1P, DhAtomP atom2P) + entryP->atom2I = DhAtomGetNumber(atom2P); + + if (entryP->res1I > entryP->res2I || +- entryP->res1I == entryP->res2I && entryP->atom1I > entryP->atom2I) { ++ (entryP->res1I == entryP->res2I && entryP->atom1I > entryP->atom2I)) { + t = entryP->res1I; + entryP->res1I = entryP->res2I; + entryP->res2I = t; +diff --git a/src/data/DataHand.c b/src/data/DataHand.c +index b20e29c..368aad3 100644 +--- a/src/data/DataHand.c ++++ b/src/data/DataHand.c +@@ -2043,8 +2043,8 @@ applyBondList(PropRefP refP, LINLIST bondL, int groupNum, + groupNum1 = getGroupNum(bondAddP->res1P->molP); + groupNum2 = getGroupNum(bondAddP->res2P->molP); + if (atom1P->state == AS_VALID && atom2P->state == AS_VALID && +- (groupNum1 == groupNum && groupNum2 == groupNum || +- groupNum < 0 && groupNum1 != groupNum2)) ++ ((groupNum1 == groupNum && groupNum2 == groupNum) || ++ (groupNum < 0 && groupNum1 != groupNum2))) + applyF(bondP, atom1P, atom2P, clientData); + } + bondAddP = nextBondAddP; +@@ -2367,8 +2367,8 @@ callDistApply(PropRefP refP, DhDistP distP, int groupNum, + groupNum1 = getGroupNum(distP->res1P->molP); + groupNum2 = getGroupNum(distP->res2P->molP); + if (atom1P->state == AS_VALID && atom2P->state == AS_VALID && +- (groupNum1 == groupNum && groupNum2 == groupNum || +- groupNum < 0 && groupNum1 != groupNum2)) ++ ((groupNum1 == groupNum && groupNum2 == groupNum) || ++ (groupNum < 0 && groupNum1 != groupNum2))) + applyF(distP, atom1P, atom2P, clientData); + } + } +diff --git a/src/expr/ExprScan.c b/src/expr/ExprScan.c +index dcef69e..6266b4d 100644 +--- a/src/expr/ExprScan.c ++++ b/src/expr/ExprScan.c +@@ -221,7 +221,7 @@ ExprScanGetSym(void) + for (;;) { + if (isdigit(ch)) { + DStrAppChar(StrVal, ch); +- } else if (ch == '.' && ExprStr[1] != '.' || ++ } else if ((ch == '.' && ExprStr[1] != '.') || + ch == 'e' || ch == 'E') { + DStrAppChar(StrVal, ch); + isFloat = TRUE; +diff --git a/src/iodev/IODev.c b/src/iodev/IODev.c +index 9c04ce8..aa4f9a7 100644 +--- a/src/iodev/IODev.c ++++ b/src/iodev/IODev.c +@@ -44,7 +44,6 @@ extern void IOMotifGLDSetDev(void); + #endif + #ifdef IO_DEV_MOTIF_OGL + extern void IOMotifOGLSetDev(void); +-extern void IOMotifOGLDSetDev(void); + #endif + #ifdef IO_DEV_MOTIF_XGL + extern void IOMotifXGLSetDev(void); +@@ -76,7 +75,6 @@ static DevListEntry DevList[] = { + #endif + #ifdef IO_DEV_MOTIF_OGL + {"Motif/OpenGL", IOMotifOGLSetDev}, +- {"Motif/OpenGLD", IOMotifOGLDSetDev}, + #endif + #ifdef IO_DEV_MOTIF_XGL + {"Motif/XGL", IOMotifXGLSetDev}, +diff --git a/src/motif/MotifDial.c b/src/motif/MotifDial.c +index 2514549..6e3bfd7 100644 +--- a/src/motif/MotifDial.c ++++ b/src/motif/MotifDial.c +@@ -1323,7 +1323,7 @@ PuMotifAddGizmoCB(PuGizmo gizmo, PuGizmoCBType type, + + switch (type) { + case PU_CT_ACTIVATE: +- if (gType == GIZMO_TEXT_FIELD || GIZMO_TEXT) ++ if (gType == (GIZMO_TEXT_FIELD | GIZMO_TEXT)) + XtAddCallback(gizmo, XmNactivateCallback, textActivateCB, infoP); + else if (gType == GIZMO_BUTTON) + XtAddCallback(gizmo, XmNactivateCallback, gizmoGenCB, infoP); +diff --git a/src/motif/MotifMainW.c b/src/motif/MotifMainW.c +index abbb444..77ce8fd 100644 +--- a/src/motif/MotifMainW.c ++++ b/src/motif/MotifMainW.c +@@ -80,8 +80,8 @@ checkPressOrExpose(Display *dpy, XEvent *eventP, XPointer arg) + { + Window *winP = (Window *) arg; + +- return eventP->type == ButtonPress && eventP->xbutton.window == *winP || +- eventP->type == Expose && eventP->xexpose.window == *winP; ++ return (eventP->type == ButtonPress && eventP->xbutton.window == *winP) || ++ (eventP->type == Expose && eventP->xexpose.window == *winP); + } + + static void +diff --git a/src/os/GFile.c b/src/os/GFile.c +index d0d63b6..08d48c7 100644 +--- a/src/os/GFile.c ++++ b/src/os/GFile.c +@@ -385,7 +385,7 @@ GFileEOF(GFile gf) + { + if (gf->format == GF_FORMAT_MEMORY) + return gf->currP == NULL || +- gf->currP->nextP == NULL && gf->currPos == gf->currP->len; ++ (gf->currP->nextP == NULL && gf->currPos == gf->currP->len); + else + return feof(gf->fp); + } +diff --git a/src/prim/PrimDraw.c b/src/prim/PrimDraw.c +index 32bd593..ba89c57 100644 +--- a/src/prim/PrimDraw.c ++++ b/src/prim/PrimDraw.c +@@ -461,7 +461,7 @@ drawRibbon(PrimObjP primP) + } + + if (partP->paint == RP_ATOM || +- partP->paint == RP_ATOM_SMOOTH && partP->polyNo > 0) ++ (partP->paint == RP_ATOM_SMOOTH && partP->polyNo > 0)) + SgSetColor(attrP->colR, attrP->colG, attrP->colB); + + if (partP->paint == RP_ATOM_SMOOTH) +diff --git a/src/prim/RibbonCalc.c b/src/prim/RibbonCalc.c +index 09874cf..0849d03 100644 +--- a/src/prim/RibbonCalc.c ++++ b/src/prim/RibbonCalc.c +@@ -907,7 +907,7 @@ calcStrips(PrimObjP primP, PrimObjP prevP) + getSplinePoints(partP, ribbonP, ePar, partP->endPar, ePNo + 1, + parA + sPNo + mPNo - 1, xA + sPNo + mPNo - 1, dzA + sPNo + mPNo - 1); + +- if (partP->style == RS_ROUND && partP->midRad == 0.0f || ++ if ((partP->style == RS_ROUND && partP->midRad == 0.0f) || + BreakInterrupted()) { + /* draw only one line */ + partP->traceNo = 1; +@@ -1128,15 +1128,15 @@ calcStrips(PrimObjP primP, PrimObjP prevP) + Vec3Copy(partP->traceA[traceI].nvA[pointI], nv); + } + +- if (pointI == 0 && partP->startStyle == RE_SHARP || +- pointI == pointNo - ePNo && partP->endStyle == RE_ARROW) ++ if ((pointI == 0 && partP->startStyle == RE_SHARP) || ++ (pointI == pointNo - ePNo && partP->endStyle == RE_ARROW)) + Vec3Copy(partP->polyA[polyI].xA[traceNo - 1 - traceI], x); + else if (pointI == pointNo - 1 && partP->endStyle == RE_SHARP) + Vec3Copy(partP->polyA[polyI].xA[traceI], x); + } + +- if (pointI == 0 && partP->startStyle == RE_SHARP || +- pointI == pointNo - ePNo && partP->endStyle == RE_ARROW) { ++ if ((pointI == 0 && partP->startStyle == RE_SHARP) || ++ (pointI == pointNo - ePNo && partP->endStyle == RE_ARROW)) { + Vec3Copy(x, dy); + Vec3Cross(x, dx); + Vec3Copy(partP->polyA[polyI].nv, x); +@@ -1327,7 +1327,7 @@ RibbonCalc(PrimObjP primP) + + if (! partP->pointValid || prec != partP->prec || + startRad != partP->startRad || +- partP->style == RS_ROUND && midRad != partP->midRad || ++ (partP->style == RS_ROUND && midRad != partP->midRad) || + endRad != partP->endRad || radChanged) { + for (i = 0; i < partP->traceNo; i++) { + free(partP->traceA[i].xA); +diff --git a/src/pudev/PuMainW.c b/src/pudev/PuMainW.c +index 73d183b..d287345 100644 +--- a/src/pudev/PuMainW.c ++++ b/src/pudev/PuMainW.c +@@ -57,7 +57,7 @@ PuSetTextField(PuTextFieldChoice fieldChoice, char *text) + if (text[0] != LOCK_CHAR) + return; + text++; +- if (text[0] == '\0' || text[0] == ' ' && text[1] == '\0') { ++ if (text[0] == '\0' || (text[0] == ' ' && text[1] == '\0')) { + StatusLocked = FALSE; + text = " "; + } +diff --git a/src/tty/TTY.c b/src/tty/TTY.c +index 0090f75..22adfef 100644 +--- a/src/tty/TTY.c ++++ b/src/tty/TTY.c +@@ -164,7 +164,7 @@ PuTTYSwitchFullscreen(BOOL onOff) + void + PuTTYSetTextField(PuTextFieldChoice fieldChoice, char *text) + { +- if (text[0] == '\0' || text[0] == ' ' && text[1] == '\0') ++ if (text[0] == '\0' || (text[0] == ' ' && text[1] == '\0')) + return; + + switch (fieldChoice) { +diff --git a/tools/src/IsoSurface.c b/tools/src/IsoSurface.c +index 5e11a98..09f89d0 100644 +--- a/tools/src/IsoSurface.c ++++ b/tools/src/IsoSurface.c +@@ -104,19 +104,19 @@ typedef struct { + } Strip; + + static CubeDesc CubeEven = { +- 0, 3, 5, 6, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}, +- 3, 0, 5, 1, {{D_0, 0}, {D_MZ, 4}, {D_MY, 1}, {D_PX, 2}}, +- 0, 3, 6, 2, {{D_0, 0}, {D_MZ, 3}, {D_PY, 2}, {D_MX, 1}}, +- 3, 5, 6, 7, {{D_0, 0}, {D_PX, 3}, {D_PZ, 1}, {D_PY, 4}}, +- 5, 0, 6, 4, {{D_0, 0}, {D_MY, 3}, {D_MX, 4}, {D_PZ, 2}} ++ {{0, 3, 5, 6, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}}, ++ {3, 0, 5, 1, {{D_0, 0}, {D_MZ, 4}, {D_MY, 1}, {D_PX, 2}}}, ++ {0, 3, 6, 2, {{D_0, 0}, {D_MZ, 3}, {D_PY, 2}, {D_MX, 1}}}, ++ {3, 5, 6, 7, {{D_0, 0}, {D_PX, 3}, {D_PZ, 1}, {D_PY, 4}}}, ++ {5, 0, 6, 4, {{D_0, 0}, {D_MY, 3}, {D_MX, 4}, {D_PZ, 2}}}} + }; + + static CubeDesc CubeOdd = { +- 1, 2, 7, 4, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}, +- 2, 1, 7, 3, {{D_0, 0}, {D_MZ, 3}, {D_PX, 2}, {D_PY, 1}}, +- 1, 2, 4, 0, {{D_0, 0}, {D_MZ, 4}, {D_MX, 1}, {D_MY, 2}}, +- 2, 7, 4, 6, {{D_0, 0}, {D_PY, 4}, {D_PZ, 2}, {D_MX, 3}}, +- 7, 1, 4, 5, {{D_0, 0}, {D_PX, 4}, {D_MY, 3}, {D_PZ, 1}} ++ {{1, 2, 7, 4, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}}, ++ {2, 1, 7, 3, {{D_0, 0}, {D_MZ, 3}, {D_PX, 2}, {D_PY, 1}}}, ++ {1, 2, 4, 0, {{D_0, 0}, {D_MZ, 4}, {D_MX, 1}, {D_MY, 2}}}, ++ {2, 7, 4, 6, {{D_0, 0}, {D_PY, 4}, {D_PZ, 2}, {D_MX, 3}}}, ++ {7, 1, 4, 5, {{D_0, 0}, {D_PX, 4}, {D_MY, 3}, {D_PZ, 1}}}} + }; + + static BOOL Initialized = FALSE; +@@ -158,7 +158,7 @@ fillFaces(TetDesc *tetP) + static BOOL + equalPair(int i00, int i01, int i10, int i11) + { +- return i00 == i10 && i01 == i11 || i00 == i11 && i01 == i10; ++ return (i00 == i10 && i01 == i11) || (i00 == i11 && i01 == i10); + } + + static int diff --git a/sci-chemistry/molmol/files/opengl.patch b/sci-chemistry/molmol/files/opengl.patch new file mode 100644 index 000000000000..c1db35d9013d --- /dev/null +++ b/sci-chemistry/molmol/files/opengl.patch @@ -0,0 +1,96 @@ + molmol | 65 +++++++++-------------------------------------------------------- + 1 file changed, 9 insertions(+), 56 deletions(-) + +diff --git a/molmol b/molmol +index 7863225..b6c75ce 100755 +--- a/molmol ++++ b/molmol +@@ -11,55 +11,8 @@ ostype=`uname` + osrel=`uname -r` + osmaj=`echo $osrel | awk -F. '{print $1}'` + osmin=`echo $osrel | awk -F. '{print $2}'` +-localdev= +-glxdev= +- +-if [ $ostype = "IRIX" -o $ostype = "IRIX64" ]; then +- if [ $osmaj -eq 6 -a $osmin -ge 2 -o $osmaj -gt 6 ]; then +- arch=sgi6 +- localdev=Motif/OpenGL +- glxdev=Motif/OpenGL +- elif [ $osmaj -eq 5 -a $osmin -ge 3 -o $osmaj -gt 5 ]; then +- arch=sgi5 +- localdev=Motif/OpenGL +- glxdev=Motif/OpenGL +- else +- arch=sgi4 +- localdev=Motif/GL +- fi +- MONITOR=72HZ; export MONITOR +-elif [ $ostype = "AIX" ]; then +- arch=aix +- localdev=Motif/OpenGL +-elif [ $ostype = "HP-UX" ]; then +- arch=hp +- localdev=Motif/OpenGL +- glxdev=Motif/OpenGL +-elif [ $ostype = "OSF1" ]; then +- arch=dec +- localdev=Motif/OpenGL +-elif [ $ostype = "Linux" ]; then +- arch=lnx +- localdev=Motif/OpenGL +-elif [ $ostype = "SunOS" ]; then +- if [ $osmaj -eq 5 -a $osmin -ge 4 -o $osmaj -gt 5 ]; then +- arch=sol +- localdev=Motif/OpenGL +- else +- arch=sun +- fi +-else +- arch=unknown +-fi +- +-if [ $ostype = "SunOS" ]; then +- xdpy=/usr/openwin/bin/xdpyinfo +-elif [ $ostype = "HP-UX" ]; then +- xdpy=/usr/contrib/bin/X11/xdpyinfo +-else +- xdpy=/usr/bin/X11/xdpyinfo +-fi +- ++localdev=Motif/OpenGL ++glxdev=Motif/OpenGL + printUsage () { + echo "Usage: molmol -ht2as [-o dev] [-r range] [-f macro] files" + echo "" +@@ -121,15 +74,15 @@ done + + magictmp=/tmp/molmol_magic$$ + +-if [ ! -d $HOME/molmol ]; then +- mkdir $HOME/molmol ++if [ ! -d $HOME/.molmol ]; then ++ mkdir $HOME/.molmol + fi +-startmacro=$HOME/molmol/options.mac ++startmacro=$HOME/.molmol/options.mac + cp /dev/null $startmacro + + if [ -n "$*" ]; then +- if [ -f $HOME/molmol/dump ]; then +- mv -f $HOME/molmol/dump $HOME/molmol/dump.old ++ if [ -f $HOME/.molmol/dump ]; then ++ mv -f $HOME/.molmol/dump $HOME/.molmol/dump.old + fi + echo "0 long 0x3b7a12f9 MOLMOL" > $magictmp + echo "0 long 0xf9127a3b MOLMOL" >> $magictmp +@@ -209,7 +162,7 @@ elif [ -x $xdpy ]; then + fi + + if [ "$input" = "-" -o -n "$nograph" ]; then +- $MOLMOLHOME/molmol.$arch $xopt ++ $MOLMOLHOME/molmol $xopt + else +- $MOLMOLHOME/molmol.$arch $xopt < /dev/null ++ $MOLMOLHOME/molmol $xopt < /dev/null + fi diff --git a/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff b/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff new file mode 100644 index 000000000000..0ad57d93e107 --- /dev/null +++ b/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff @@ -0,0 +1,103 @@ +Only in molmol_rh9: makedef +diff -ru molmol_rh9_unpatched/makedef.lnx molmol_rh9/makedef.lnx +--- molmol_rh9_unpatched/makedef.lnx 2003-01-20 16:10:18.000000000 -0500 ++++ molmol_rh9/makedef.lnx 2003-05-06 10:40:08.000000000 -0400 +@@ -1,31 +1,38 @@ + # definitions for Linux + +-MISSFUNC = -Dsqrtf=sqrt -Dexpf=exp -Dlogf=log -Dpowf=pow \ +- -Dsinf=sin -Dcosf=cos -Dtanf=tan \ +- -Dasinf=asin -Dacosf=acos -Datanf=atan -Datan2f=atan2 \ +- -Dfabsf=fabs -Dceilf=ceil +-MCPPFLAGS = $(MISSFUNC) +-MCFLAGS = -O2 +- +-RANLIB = /bin/true +-WAIT = /usr/bin/sleep 2 +-SHELL = /bin/sh +-CPP = /lib/cpp +-CC = /usr/bin/gcc ++#TIFFDIR = $(TOP)/tiff-v3.4/libtiff ++#JPEGDIR = $(TOP)/../libjpeg/jpeg-6a ++#PNGDIR = $(TOP)/../libpng/libpng-0.89c ++#ZLIBDIR = $(TOP)/../libpng/zlib-1.0.2 ++ ++IMGDEF = -DTIFF_SUPPORT -DJPEG_SUPPORT -DPNG_SUPPORT ++IMGLIB = -ltiff -ljpeg -lpng -lz ++IMGINCL = # -I$(TIFFDIR) -I$(JPEGDIR) -I$(PNGDIR) -I$(ZLIBDIR) ++ ++XINCL = -I/usr/X11R6/include ++ ++CC=gcc ++MCPPFLAGS = ++MCFLAGS =-pipe -O3 -ffast-math -march=i686 -mcpu=i686 ++ ++RANLIB = /bin/true ++WAIT = sleep 2 ++SHELL = /bin/sh ++CPP = /lib/cpp + +-SGDEVDIR = x11 no pov rib vrml1 vrml2 ps fm +- +-SGDEVDEF = -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB -DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4 ++SGDEVDIR = ogl x11 no pov rib vrml1 vrml2 ps fm ++SGDEVDEF = -DSG_DEV_OGL -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB -DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4 + + PUDEVDIR = motif tty + PUDEVDEF = -DPU_DEV_MOTIF -DPU_DEV_TTY + +-IODEVDIR = motx11 ttyno +-IODEVDEF = -DIO_DEV_MOTIF_X11 -DIO_DEV_TTY_NO ++IODEVDIR = motogl motx11 ttyno ++IODEVDEF = -DIO_DEV_MOTIF_OGL -DIO_DEV_MOTIF_X11 -DIO_DEV_TTY_NO + ++OPENGLDEF = -DOPENGL_SGI_STEREO + MOTIFDEF = -DFUNCPROTO + +-SYSLIB = -L/usr/X11R6/lib -lXm -lXt -lXpm -lX11 -lm -lc -lieee ++SYSLIB = -lGLw -lGLU -lGL -lXm -lXpm -lXt -lXext -lX11 -lm + + TOOLSDIR = $(TOP)/tools +-SGDIR = $(TOP)/sg ++SGDIR = $(TOP)/sg +diff -ru molmol_rh9_unpatched/src/motogl/MotOGL.c molmol_rh9/src/motogl/MotOGL.c +--- molmol_rh9_unpatched/src/motogl/MotOGL.c 2000-05-29 12:31:51.000000000 -0400 ++++ molmol_rh9/src/motogl/MotOGL.c 2003-05-06 11:51:05.000000000 -0400 +@@ -31,7 +31,7 @@ + #include <Xm/XmStrDefs.h> + + #define BOOL MOTIF_BOOL /* hack to avoid naming conflict */ +-#include <X11/GLw/GLwMDrawA.h> ++#include <GL/GLwMDrawA.h> + #undef BOOL + + #include <sg.h> +diff -ru molmol_rh9_unpatched/src/os/GFile.c molmol_rh9/src/os/GFile.c +--- molmol_rh9_unpatched/src/os/GFile.c 2001-06-17 14:59:17.000000000 -0400 ++++ molmol_rh9/src/os/GFile.c 2003-05-06 12:34:34.000000000 -0400 +@@ -30,6 +30,7 @@ + #include <string.h> + #include <memory.h> + #include <ctype.h> ++#include <errno.h> + + #include <linlist.h> + +@@ -38,7 +39,7 @@ + const INT32 GFMagic = 0x3b7a12f9; + + #ifndef __linux__ +-extern char *sys_errlist[]; ++extern char *strerror(); + #endif + extern int errno; + +@@ -81,7 +82,7 @@ + { + if (msg == NULL) { + if (NextMsg == NULL) +- msg = sys_errlist[errno]; ++ msg = strerror(errno); + else + msg = NextMsg; + } diff --git a/sci-chemistry/molmol/files/prefix.patch b/sci-chemistry/molmol/files/prefix.patch new file mode 100644 index 000000000000..89f17b2e984e --- /dev/null +++ b/sci-chemistry/molmol/files/prefix.patch @@ -0,0 +1,22 @@ +diff --git a/molmol b/molmol +index e774abf..9f10558 100755 +--- a/molmol ++++ b/molmol +@@ -57,7 +57,7 @@ if [ $ostype = "SunOS" ]; then + elif [ $ostype = "HP-UX" ]; then + xdpy=/usr/contrib/bin/X11/xdpyinfo + else +- xdpy=/usr/bin/X11/xdpyinfo ++ xdpy=@GENTOO_PORTAGE_EPREFIX@/usr/bin/xdpyinfo + fi + + printUsage () { +@@ -119,7 +119,7 @@ while [ -n "$*" ]; do + esac + done + +-magictmp=/tmp/molmol_magic$$ ++magictmp=@GENTOO_PORTAGE_EPREFIX@/tmp/molmol_magic$$ + + if [ ! -d $HOME/molmol ]; then + mkdir $HOME/molmol diff --git a/sci-chemistry/molmol/files/wild.patch b/sci-chemistry/molmol/files/wild.patch new file mode 100644 index 000000000000..8be9baf92203 --- /dev/null +++ b/sci-chemistry/molmol/files/wild.patch @@ -0,0 +1,1866 @@ + include/cmd_dial.h | 1 + + include/cmd_io.h | 7 +- + include/cmd_struc.h | 1 + + include/curr_dir.h | 1 + + include/data_hand.h | 6 + + src/cip/cmd_tab.h | 3 + + src/cmddial/ExDialColor.c | 314 +++++++++++++++++++++++++++++++----------- + src/cmddial/ExDialRes.c | 340 ++++++++++++++++++++++++++++++++++++++++++++++ + src/cmddial/Makefile | 2 +- + src/cmdio/ExPdb.c | 70 +++++++++- + src/cmdstruc/ExBuild.c | 123 +++++++++++++++++ + src/data/DataHand.c | 114 +++++++++++++++- + src/iodev/IODev.c | 2 + + src/main/MolInit.c | 5 +- + src/main/MolMol.c | 2 +- + src/motif/MotifDial.c | 32 ++--- + src/motogl/MotOGLDump.c | 2 +- + src/os/CurrDir.c | 46 ++----- + src/os/ProgDir.c | 25 +++- + src/win/WinDial.c | 255 +++++++++++++++++----------------- + src/winogl/WinOGLDump.c | 7 +- + 21 files changed, 1073 insertions(+), 285 deletions(-) + +diff --git a/include/cmd_dial.h b/include/cmd_dial.h +index f60e918..47fb8f8 100644 +--- a/include/cmd_dial.h ++++ b/include/cmd_dial.h +@@ -29,6 +29,7 @@ extern ErrCode ExUserInterface(char *); + + extern ErrCode ExDialColor(char *); + extern ErrCode ExDialMol(char *); ++extern ErrCode ExDialRes(char *); + extern ErrCode ExDialMeasure(char *); + extern ErrCode ExDialRmsd(char *); + extern ErrCode ExDialSelect(char *); +diff --git a/include/cmd_io.h b/include/cmd_io.h +index 79b173c..9a7b12c 100644 +--- a/include/cmd_io.h ++++ b/include/cmd_io.h +@@ -30,15 +30,16 @@ extern ErrCode ExReadAng(char *); + extern ErrCode ExReadDg(char *); + extern ErrCode ExReadDump(char *); + extern ErrCode ExReadLib(char *); +-extern ErrCode ExReadPdb(char *); +-extern ErrCode ExReadSeq(char *); +-extern ErrCode ExReadShift(char *); + extern ErrCode ExReadLimit(char *); + extern ErrCode ExReadListAng(char *); + extern ErrCode ExReadListDg(char *); + extern ErrCode ExReadListPdb(char *); ++extern ErrCode ExReadOldPdb(char *); + extern ErrCode ExReadOmap(char *); ++extern ErrCode ExReadPdb(char *); + extern ErrCode ExReadPot(char *); ++extern ErrCode ExReadSeq(char *); ++extern ErrCode ExReadShift(char *); + extern ErrCode ExReadSybyl(char *); + extern ErrCode ExReadXyz(char *); + extern ErrCode ExWriteAng(char *); +diff --git a/include/cmd_struc.h b/include/cmd_struc.h +index e0d729f..f4950b9 100644 +--- a/include/cmd_struc.h ++++ b/include/cmd_struc.h +@@ -33,6 +33,7 @@ extern ErrCode ExAddDist(char *); + extern ErrCode ExAddLimit(char *); + extern ErrCode ExAddPseudo(char *); + extern ErrCode ExAddRes(char *); ++extern ErrCode ExMakeMolCyclic(char *); + extern ErrCode ExChangeRes(char *); + extern ErrCode ExFirstMol(char *); + extern ErrCode ExFlipAtom(char *); +diff --git a/include/curr_dir.h b/include/curr_dir.h +index c7895c4..04e404d 100644 +--- a/include/curr_dir.h ++++ b/include/curr_dir.h +@@ -26,6 +26,7 @@ + #ifndef _CURR_DIR_H_ + #define _CURR_DIR_H_ + ++extern void CurrDirSet(char *dir); + extern char *CurrDirGet(void); + + #endif /* _CURR_DIR_H_ */ +diff --git a/include/data_hand.h b/include/data_hand.h +index 4462328..74a716a 100644 +--- a/include/data_hand.h ++++ b/include/data_hand.h +@@ -112,6 +112,7 @@ extern void DhMolMoveFirst(DhMolP); + extern void DhMolDestroy(DhMolP); + + extern DhResP DhResNew(DhMolP, DhResDefP, DhSeqPos); ++extern DhResP DhResNewCyclic(DhMolP, DhResDefP, DhSeqPos); + extern void DhResMutate(DhResP, DhResDefP, DhMutationKind); + extern void DhResSetNeigh(DhResP, DhNeighChoice, DhResP); + extern BOOL DhResDestroy(DhResP); +@@ -287,6 +288,7 @@ extern void DhMolGetTransVect(DhMolP, Vec3); + extern MolAttrP DhMolGetAttr(DhMolP); + + extern DSTR DhResGetName(DhResP); ++extern DhAtomP DhResGetAtomA(DhResP); + extern int DhResGetNumber(DhResP); + + extern DSTR DhAtomGetName(DhAtomP); +@@ -335,6 +337,10 @@ extern void DhResAnglesChanged(DhResP); + extern void DhResDockPrev(DhResP); + extern void DhResDockNext(DhResP); + extern void DhResCalcAtom(DhResP, DSTR); ++extern DhResP DhResPrev(DhResP resP); ++extern DhResP DhResNext(DhResP resP); ++extern DhResP DhResFirst(DhMolP molP); ++extern DhResP DhResLast(DhMolP molP); + + /* dump/undump */ + +diff --git a/src/cip/cmd_tab.h b/src/cip/cmd_tab.h +index 0b73f65..cf7bc2a 100644 +--- a/src/cip/cmd_tab.h ++++ b/src/cip/cmd_tab.h +@@ -108,6 +108,7 @@ static CmdTabEntry BuiltinCmdTab[] = { + {"DialColor", ExDialColor, US_NONE}, + {"DialMeasure", ExDialMeasure, US_NONE}, + {"DialMol", ExDialMol, US_NONE}, ++ {"DialRes", ExDialRes, US_NONE}, + {"DialRmsd", ExDialRmsd, US_NONE}, + {"DialSelect", ExDialSelect, US_NONE}, + {"DialStyle", ExDialStyle, US_NONE}, +@@ -164,6 +165,7 @@ static CmdTabEntry BuiltinCmdTab[] = { + {"ListSelectedDist", ExListSelected, US_NONE}, + {"ListSelectedMol", ExListSelected, US_NONE}, + {"ListSelectedRes", ExListSelected, US_NONE}, ++ {"MakeMolCyclic", ExMakeMolCyclic, US_ALL}, + {"MaterialAtom", ExMaterial, US_ALL}, + {"MaterialBond", ExMaterial, US_ALL}, + {"MaterialDist", ExMaterial, US_ALL}, +@@ -213,6 +215,7 @@ static CmdTabEntry BuiltinCmdTab[] = { + {"ReadListDg", ExReadListDg, US_ALL}, + {"ReadListPdb", ExReadListPdb, US_ALL}, + {"ReadLol", ExReadLimit, US_ALL}, ++ {"ReadOldPdb", ExReadOldPdb, US_ALL}, + {"ReadOmap", ExReadOmap, US_ALL}, + {"ReadPdb", ExReadPdb, US_ALL}, + {"ReadPot", ExReadPot, US_ALL}, +diff --git a/src/cmddial/ExDialColor.c b/src/cmddial/ExDialColor.c +index f960e1d..e827c4f 100644 +--- a/src/cmddial/ExDialColor.c ++++ b/src/cmddial/ExDialColor.c +@@ -43,6 +43,9 @@ + #define NAME_LEN 100 + #define NUM_LEN 6 + #define CMD_NO 7 ++#define MAXRGBVALUE 255 ++#define ICOLOR(c) (int) ((float)c * (float)MAXRGBVALUE) ++#define FCOLOR(c) (float) ((float)c / (float)MAXRGBVALUE) + + #define EPS ((float) 1.0e-5) + +@@ -56,8 +59,8 @@ typedef struct { + static ColorDesc *ColorList; + static int ColorNo = 0; + static BOOL DialOn = FALSE; +-static PuGizmo DialGizmo = NULL, NameGizmo, RGizmo, GGizmo, BGizmo, ColGizmo; +-static DSTR NameStr = NULL, RStr, GStr, BStr; ++static PuGizmo DialGizmo = NULL, NameGizmo, RGizmo, GGizmo, BGizmo, ColGizmo, rGizmo, gGizmo, bGizmo; ++static DSTR NameStr = NULL, RStr, GStr, BStr, rStr, gStr, bStr; + + static char *LabelList[] = { + "Back", +@@ -136,22 +139,50 @@ editCB(PuGizmo g, char *name, void *clientData, void *callData) + char *field = clientData; + PuTextCBStruc *callP = callData; + +- if (field[0] == 'N') ++ if (field[0] == 'N') { + DStrAssignStr(NameStr, callP->newText); +- else if (field[0] == 'R') ++ } ++ else if (field[0] == 'R') { + DStrAssignStr(RStr, callP->newText); +- else if (field[0] == 'G') ++ } ++ else if (field[0] == 'G') { + DStrAssignStr(GStr, callP->newText); +- else ++ } ++ else if (field[0] == 'B') { + DStrAssignStr(BStr, callP->newText); ++ } ++ else if (field[0] == 'r') { ++ DStrAssignStr(rStr, callP->newText); ++ } ++ else if (field[0] == 'g') { ++ DStrAssignStr(gStr, callP->newText); ++ } ++ else if (field[0] == 'b') { ++ DStrAssignStr(bStr, callP->newText); ++ } + } + + static void + updateFields(int colorI) + { ++ char buf[10]; ++ float f; ++ + PuSetStr(RGizmo, PU_SC_TEXT, ColorList[colorI].r); + PuSetStr(GGizmo, PU_SC_TEXT, ColorList[colorI].g); + PuSetStr(BGizmo, PU_SC_TEXT, ColorList[colorI].b); ++ ++ f = atof(ColorList[colorI].r); ++ (void) sprintf(buf, "%i", ICOLOR(f)); ++ PuSetStr(rGizmo, PU_SC_TEXT, buf); ++ ++ f = atof(ColorList[colorI].g); ++ (void) sprintf(buf, "%i", ICOLOR(f)); ++ PuSetStr(gGizmo, PU_SC_TEXT, buf); ++ ++ f = atof(ColorList[colorI].b); ++ (void) sprintf(buf, "%i", ICOLOR(f)); ++ PuSetStr(bGizmo, PU_SC_TEXT, buf); + } + + static void +@@ -190,17 +221,96 @@ activateCB(PuGizmo g, char *name, void *clientData, void *callData) + { + char *field = clientData; + int i; ++ float f; ++ char buf[10]; + + if (field[0] == 'N') { + for (i = 0; i < ColorNo; i++) + if (strcmp(ColorList[i].name, DStrToStr(NameStr)) == 0) { +- updateFields(i); +- break; ++ updateFields(i); ++ break; + } + } else { ++ if (field[0] == 'R') { ++ f = atof(DStrToStr(RStr)); ++ if (f>1.0) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(RStr, buf); ++ PuSetStr(RGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(rStr, buf); ++ PuSetStr(rGizmo, PU_SC_TEXT, buf); ++ } ++ else if (field[0] == 'G') { ++ f = atof(DStrToStr(GStr)); ++ if (f>1.0) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(GStr, buf); ++ PuSetStr(GGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(gStr, buf); ++ PuSetStr(gGizmo, PU_SC_TEXT, buf); ++ } ++ else if (field[0] == 'B') { ++ f = atof(DStrToStr(BStr)); ++ if (f>1.0) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(BStr, buf); ++ PuSetStr(BGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(bStr, buf); ++ PuSetStr(bGizmo, PU_SC_TEXT, buf); ++ } ++ else if (field[0] == 'r') { ++ i = atoi(DStrToStr(rStr)); ++ if (i>MAXRGBVALUE) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(rStr, buf); ++ PuSetStr(rGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(RStr, buf); ++ PuSetStr(RGizmo, PU_SC_TEXT, buf); ++ } ++ else if (field[0] == 'g') { ++ i = atoi(DStrToStr(gStr)); ++ if (i>MAXRGBVALUE) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(gStr, buf); ++ PuSetStr(gGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(GStr, buf); ++ PuSetStr(GGizmo, PU_SC_TEXT, buf); ++ } ++ else if (field[0] == 'b') { ++ i = atoi(DStrToStr(bStr)); ++ if (i>MAXRGBVALUE) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(bStr, buf); ++ PuSetStr(bGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(BStr, buf); ++ PuSetStr(BGizmo, PU_SC_TEXT, buf); ++ } + showName(); + } +- + showColor(); + } + +@@ -258,13 +368,20 @@ showAttr(AttrP attrP) + { + char buf[10]; + +- (void) sprintf(buf, "%5.3f", attrP->colR); ++ (void) sprintf(buf, "%1.3f", attrP->colR); + PuSetStr(RGizmo, PU_SC_TEXT, buf); +- (void) sprintf(buf, "%5.3f", attrP->colG); ++ (void) sprintf(buf, "%1.3f", attrP->colG); + PuSetStr(GGizmo, PU_SC_TEXT, buf); +- (void) sprintf(buf, "%5.3f", attrP->colB); ++ (void) sprintf(buf, "%1.3f", attrP->colB); + PuSetStr(BGizmo, PU_SC_TEXT, buf); + ++ (void) sprintf(buf, "%i", ICOLOR(attrP->colR)); ++ PuSetStr(rGizmo, PU_SC_TEXT, buf); ++ (void) sprintf(buf, "%i", ICOLOR(attrP->colG)); ++ PuSetStr(gGizmo, PU_SC_TEXT, buf); ++ (void) sprintf(buf, "%i", ICOLOR(attrP->colB)); ++ PuSetStr(bGizmo, PU_SC_TEXT, buf); ++ + showName(); + showColor(); + } +@@ -315,107 +432,152 @@ buildDial(void) + PuGizmo g; + PuConstraints con; + int i; +- +- DialGizmo = PuCreateDialog("Color Dialog", 7, 5); +- PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE); +- +- con.x = 0; +- con.w = 1; +- con.h = 1; +- +- g = PuCreateLabel(DialGizmo, "Name"); +- con.y = 0; +- PuSetConstraints(g, con); +- PuSwitchGizmo(g, TRUE); +- +- g = PuCreateLabel(DialGizmo, "Red"); +- con.y = 1; +- PuSetConstraints(g, con); +- PuSwitchGizmo(g, TRUE); +- +- g = PuCreateLabel(DialGizmo, "Green"); +- con.y = 2; +- PuSetConstraints(g, con); +- PuSwitchGizmo(g, TRUE); +- +- g = PuCreateLabel(DialGizmo, "Blue"); +- con.y = 3; +- PuSetConstraints(g, con); +- PuSwitchGizmo(g, TRUE); +- +- con.x = 1; +- con.w = 2; +- con.h = 1; +- + NameStr = DStrNew(); ++ + RStr = DStrNew(); + GStr = DStrNew(); + BStr = DStrNew(); ++ rStr = DStrNew(); ++ gStr = DStrNew(); ++ bStr = DStrNew(); ++ + DStrAssignStr(RStr, "0.0"); + DStrAssignStr(GStr, "0.0"); + DStrAssignStr(BStr, "0.0"); ++ DStrAssignStr(rStr, "0"); ++ DStrAssignStr(gStr, "0"); ++ DStrAssignStr(bStr, "0"); + ++ DialGizmo = PuCreateDialog("Color Dialog", 3, 20); ++ PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE); ++ ++ con.x = 1; ++ con.y = 0; ++ con.w = 2; ++ con.h = 3; ++ ColGizmo = PuCreateColorField(DialGizmo, "Color"); ++ PuSetConstraints(ColGizmo, con); ++ PuSetConstraints(ColGizmo, con); ++ showColor(); ++ PuSwitchGizmo(ColGizmo, TRUE); ++ ++ con.x = 0; ++ con.y = 4; ++ con.w = 1; ++ con.h = 1; ++ g = PuCreateLabel(DialGizmo, "Name"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ con.x = 1; ++ con.w = 2; ++ con.h = 1; + NameGizmo = PuCreateTextField(DialGizmo, "Name", DStrToStr(NameStr)); +- con.y = 0; + PuSetConstraints(NameGizmo, con); +- PuSetInt(NameGizmo, PU_IC_TEXT_WIDTH, 13); ++ PuSetInt(NameGizmo, PU_IC_TEXT_WIDTH, 10); + PuAddGizmoCB(NameGizmo, PU_CT_MODIFY, editCB, "N", NULL); + PuAddGizmoCB(NameGizmo, PU_CT_ACTIVATE, activateCB, "N", NULL); + showName(); + PuSwitchGizmo(NameGizmo, TRUE); + +- RGizmo = PuCreateTextField(DialGizmo, "Red", DStrToStr(RStr)); +- con.y = 1; ++ con.x = 1; ++ con.y = 5; ++ con.w = 2; ++ con.h = 5; ++ g = PuCreateList(DialGizmo, "Color List"); ++ for (i = 0; i < ColorNo; i++) ++ PuAddListEntry(g, ColorList[i].name, FALSE); ++ PuSetConstraints(g, con); ++ PuSetBool(g, PU_BC_AUTO_DESEL, TRUE); ++ PuAddGizmoCB(g, PU_CT_SELECT, selectCB, NULL, NULL); ++ PuSwitchGizmo(g, TRUE); ++ ++ con.x = 1; ++ con.y = 11; ++ con.w = 1; ++ con.h = 1; ++ g = PuCreateLabel(DialGizmo, "Float"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ con.x = 2; ++ con.y = 11; ++ g = PuCreateLabel(DialGizmo, "RGB"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ ++ con.x = 0; ++ con.y = 12; ++ con.w = 1; ++ con.h = 1; ++ g = PuCreateLabel(DialGizmo, "Red"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ con.x = 1; ++ RGizmo = PuCreateTextField(DialGizmo, "RED", DStrToStr(RStr)); + PuSetConstraints(RGizmo, con); + PuSetInt(RGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); + PuAddGizmoCB(RGizmo, PU_CT_MODIFY, editCB, "R", NULL); + PuAddGizmoCB(RGizmo, PU_CT_ACTIVATE, activateCB, "R", NULL); + PuSwitchGizmo(RGizmo, TRUE); ++ con.x = 2; ++ rGizmo = PuCreateTextField(DialGizmo, "red", DStrToStr(rStr)); ++ PuSetConstraints(rGizmo, con); ++ PuSetInt(rGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); ++ PuAddGizmoCB(rGizmo, PU_CT_MODIFY, editCB, "r", NULL); ++ PuAddGizmoCB(rGizmo, PU_CT_ACTIVATE, activateCB, "r", NULL); ++ PuSwitchGizmo(rGizmo, TRUE); + +- GGizmo = PuCreateTextField(DialGizmo, "Green", DStrToStr(GStr)); +- con.y = 2; ++ con.x = 0; ++ con.y = 13; ++ con.w = 1; ++ con.h = 1; ++ g = PuCreateLabel(DialGizmo, "Green"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ con.x = 1; ++ GGizmo = PuCreateTextField(DialGizmo, "GREEN", DStrToStr(GStr)); + PuSetConstraints(GGizmo, con); + PuSetInt(GGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); + PuAddGizmoCB(GGizmo, PU_CT_MODIFY, editCB, "G", NULL); + PuAddGizmoCB(GGizmo, PU_CT_ACTIVATE, activateCB, "G", NULL); + PuSwitchGizmo(GGizmo, TRUE); ++ con.x = 2; ++ gGizmo = PuCreateTextField(DialGizmo, "green", DStrToStr(gStr)); ++ PuSetConstraints(gGizmo, con); ++ PuSetInt(gGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); ++ PuAddGizmoCB(gGizmo, PU_CT_MODIFY, editCB, "g", NULL); ++ PuAddGizmoCB(gGizmo, PU_CT_ACTIVATE, activateCB, "g", NULL); ++ PuSwitchGizmo(gGizmo, TRUE); + +- BGizmo = PuCreateTextField(DialGizmo, "Blue", DStrToStr(BStr)); +- con.y = 3; ++ con.x = 0; ++ con.y = 14; ++ con.w = 1; ++ con.h = 1; ++ g = PuCreateLabel(DialGizmo, "Blue"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ con.x = 1; ++ BGizmo = PuCreateTextField(DialGizmo, "BLUE", DStrToStr(BStr)); + PuSetConstraints(BGizmo, con); + PuSetInt(BGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); + PuAddGizmoCB(BGizmo, PU_CT_MODIFY, editCB, "B", NULL); + PuAddGizmoCB(BGizmo, PU_CT_ACTIVATE, activateCB, "B", NULL); + PuSwitchGizmo(BGizmo, TRUE); ++ con.x = 2; ++ bGizmo = PuCreateTextField(DialGizmo, "blue", DStrToStr(bStr)); ++ PuSetConstraints(bGizmo, con); ++ PuSetInt(bGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); ++ PuAddGizmoCB(bGizmo, PU_CT_MODIFY, editCB, "b", NULL); ++ PuAddGizmoCB(bGizmo, PU_CT_ACTIVATE, activateCB, "b", NULL); ++ PuSwitchGizmo(bGizmo, TRUE); + +- ColGizmo = PuCreateColorField(DialGizmo, "Color"); +- con.x = 3; +- con.y = 0; +- con.w = 2; +- con.h = 4; +- PuSetConstraints(ColGizmo, con); +- showColor(); +- PuSwitchGizmo(ColGizmo, TRUE); +- +- g = PuCreateList(DialGizmo, "Color List"); +- for (i = 0; i < ColorNo; i++) +- PuAddListEntry(g, ColorList[i].name, FALSE); +- con.x = 5; +- con.y = 0; +- con.w = 2; +- con.h = 4; +- PuSetConstraints(g, con); +- PuSetBool(g, PU_BC_AUTO_DESEL, TRUE); +- PuAddGizmoCB(g, PU_CT_SELECT, selectCB, NULL, NULL); +- PuSwitchGizmo(g, TRUE); +- +- con.y = 4; ++ con.x = 0; ++ con.y = 15; + con.w = 1; + con.h = 1; +- + for (i = 0; i < CMD_NO; i++) { + g = PuCreateButton(DialGizmo, LabelList[i]); +- con.x = i; ++ con.x = i%3; ++ if (i%3 == 0) con.y++; + PuSetConstraints(g, con); + PuAddGizmoCB(g, PU_CT_ACTIVATE, cmdCB, NULL, NULL); + PuSwitchGizmo(g, TRUE); +diff --git a/src/cmddial/ExDialRes.c b/src/cmddial/ExDialRes.c +new file mode 100644 +index 0000000..06925ff +--- /dev/null ++++ b/src/cmddial/ExDialRes.c +@@ -0,0 +1,340 @@ ++/* ++************************************************************************ ++* ++* ExDialMol.c - DialMol command ++* ++* Copyright (c) 1994-98 ++* ++* ETH Zuerich ++* Institut fuer Molekularbiologie und Biophysik ++* ETH-Hoenggerberg ++* CH-8093 Zuerich ++* ++* SPECTROSPIN AG ++* Industriestr. 26 ++* CH-8117 Faellanden ++* ++* All Rights Reserved ++* ++* Date of last modification : 98/08/17 ++* Pathname of SCCS file : /tmp_mnt/net/sn/homeb/rkoradi/molmol-master/src/cmddial/SCCS/s.ExDialMol.c ++* SCCS identification : 1.10 ++* ++************************************************************************ ++*/ ++ ++#include <cmd_dial.h> ++ ++#include <stdio.h> ++#include <string.h> ++#include <stdlib.h> ++ ++#include <break.h> ++#include <pu.h> ++#include <arg.h> ++#include <cip.h> ++#include <data_hand.h> ++ ++#define PROP_NO 3 ++ ++typedef struct { ++ char *label; ++ char *propName; ++ char *cmd; ++} PropDesc; ++typedef struct { ++ char *name; ++ BOOL active; ++} Residue; ++ ++static BOOL DialOn = FALSE; ++static PuGizmo DialGizmo = NULL, ListGizmo; ++static int CurrProp; ++static PropRefP CurrRefP; ++static int MolNo, MolI; ++static BOOL *MolStateA; ++static BOOL SuppressUpdate = FALSE; ++static PropDesc PropTab[] = { ++ {"sel", PROP_SELECTED, "SelectRes"}, ++ {"disp", PROP_DISPLAYED, "DefPropRes 'displayed'"}, ++ {"move", PROP_MOVABLE, "DefProRes 'movable'"} ++}; ++static Residue ResidueTab[] = { ++ {"ARG", FALSE}, ++ {"CYS", FALSE}, ++ {"PRO", FALSE}, ++ {"ASP", FALSE}, ++ {"PHE", FALSE}, ++ {"LEU", FALSE}, ++ {"GLU", FALSE}, ++ {"PRO", FALSE}, ++ {"TYR", FALSE}, ++ {"GLY", FALSE}, ++ {"ASN", FALSE}, ++ {"ALA", FALSE}, ++ {"SER", FALSE}, ++ {"THR", FALSE}, ++ {"LYS", FALSE}, ++ {"ILE", FALSE} ++}; ++ ++static void ++countMol(DhResP molP, void *clientData) ++{ ++ MolNo++; ++} ++ ++ ++ ++static void ++addMol(DhResP molP, void *clientData) ++{ ++ ++ ++ DSTR name; ++ DSTR residue; ++ char buf[10]; ++ char buf2[5]; ++ BOOL propVal; ++ int j; ++ name = DStrNew(); ++ residue = DStrNew(); ++ ++ ++ j= DhResGetNumber(molP); ++ (void) sprintf(buf, "%5d " , j); ++ ++ DStrAssignStr(name, buf); ++ DStrAssignStr(residue, buf2); ++ DStrAppStr(name, " "); ++ ++ DStrAppDStr(residue, DhResGetName(molP)); ++ DStrAppDStr(name, DhResGetName(molP)); ++ propVal = DhResGetProp(CurrRefP, molP); ++ ++ ++ ++ if (! BreakCheck(10)){ ++ PuAddListEntry(ListGizmo, DStrToStr(name), propVal); ++ ++ } ++ ++ ++ ++ MolStateA[MolI] = propVal; ++ ++ DStrFree(name); ++ ++ MolI++; ++} ++ ++static void ++selectMolCB(PuGizmo g, char *name, void *clientData, void *callData) ++{ ++ PuSelectCBStruc *callP = callData; ++ DSTR cmd; ++ BOOL isFirst; ++ char buf[10]; ++ int num, startI, i; ++ ++ (void) sscanf(name, "%d", &num); ++ MolStateA[num - 1] = callP->onOff; ++ ++ if (! callP->last) ++ return; ++ ++ cmd = DStrNew(); ++ DStrAssignStr(cmd, PropTab[CurrProp].cmd); ++ isFirst = TRUE; ++ ++ for (i = 0; i < MolNo; i++) { ++ if (i == 0 || ! MolStateA[i - 1]) ++ startI = i; ++ if (MolStateA[i] && (i == MolNo - 1 || ! MolStateA[i + 1])) { ++ if (isFirst) ++ DStrAppStr(cmd, " 'num = "); ++ else ++ DStrAppStr(cmd, ","); ++ (void) sprintf(buf, "%d", startI + 1); ++ DStrAppStr(cmd, buf); ++ if (i > startI) { ++ DStrAppStr(cmd, ".."); ++ (void) sprintf(buf, "%d", i + 1); ++ DStrAppStr(cmd, buf); ++ } ++ ++ isFirst = FALSE; ++ } ++ } ++ ++ if (isFirst) ++ DStrAppStr(cmd, " '0'"); ++ else ++ DStrAppStr(cmd, "'"); ++ ++ SuppressUpdate = TRUE; ++ CipExecCmd(DStrToStr(cmd)); ++ SuppressUpdate = FALSE; ++ ++ DStrFree(cmd); ++} ++ ++static void ++buildList(void) ++{ ++ int lineNo; ++ ++ MolNo = 0; ++ DhApplyRes(PropGetRef(PROP_ALL, FALSE), countMol, NULL); ++ if (MolNo > 0) { ++ if (MolStateA == NULL) ++ MolStateA = malloc(MolNo * sizeof(*MolStateA)); ++ else ++ MolStateA = realloc(MolStateA, MolNo * sizeof(*MolStateA)); ++ lineNo = MolNo; ++ if (lineNo > 40) ++ lineNo = 40; ++ } else { ++ lineNo = 1; ++ } ++ ++ PuSetInt(ListGizmo, PU_IC_ENTRY_NO, lineNo); ++ ++ MolI = 0; ++ BreakActivate(TRUE); ++ DhApplyRes(PropGetRef(PROP_ALL, FALSE), addMol, NULL); ++ BreakActivate(FALSE); ++ ++ PuSwitchGizmo(ListGizmo, TRUE); ++} ++ ++static void ++updateList(void) ++{ ++ if (SuppressUpdate) ++ return; ++ ++ PuSwitchGizmo(ListGizmo, FALSE); ++ PuRemoveListEntries(ListGizmo, 0, MolNo); ++ buildList(); ++} ++ ++static void ++selectPropCB(PuGizmo g, char *name, void *clientData, void *callData) ++{ ++ PuSelectCBStruc *callP = callData; ++ PropRefP newPropP; ++ int i; ++ ++ if (! callP->onOff) ++ return; ++ ++ for (i = 0; i < PROP_NO; i++) ++ if (strcmp(name, PropTab[i].label) == 0) ++ break; ++ ++ newPropP = PropGetRef(PropTab[i].propName, FALSE); ++ ++ if (newPropP != CurrRefP) { ++ CurrRefP = newPropP; ++ CurrProp = i; ++ updateList(); ++ } ++} ++ ++static void ++popdownCB(PuGizmo g, char *name, void *clientData, void *callData) ++{ ++ PuSwitchGizmo(DialGizmo, FALSE); ++ DialOn = FALSE; ++} ++ ++static void ++listCB(void *clientData) ++{ ++ updateList(); ++} ++ ++static void ++helpCB(PuGizmo g, char *name, void *clientData, void *callData) ++{ ++ CipShowHelpFile(DialGizmo, "DialMol"); ++} ++ ++static void ++buildDial(void) ++{ ++ ++ PuGizmo g; ++ int i; ++ ++ CurrProp = 0; ++ CurrRefP = PropGetRef(PropTab[CurrProp].propName, FALSE); ++ ++ DialGizmo = PuCreateDialog("Residue Dialog", 0, 0); ++ PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE); ++ ++ g = PuCreateRadioBox(DialGizmo, "Property"); ++ for (i = 0; i < PROP_NO; i++) ++ PuAddToggle(g, PropTab[i].label, i == 0); ++ PuAddGizmoCB(g, PU_CT_SELECT, selectPropCB, NULL, NULL); ++ PuSwitchGizmo(g, TRUE); ++ ++ ListGizmo = PuCreateList(DialGizmo, "Molecules"); ++ PuAddGizmoCB(ListGizmo, PU_CT_SELECT, selectMolCB, NULL, NULL); ++ PuSetBool(ListGizmo, PU_BC_MULT_SEL, TRUE); ++ buildList(); ++ ++ PuAddGizmoCB(DialGizmo, PU_CT_CLOSE, popdownCB, NULL, NULL); ++ PuAddGizmoCB(DialGizmo, PU_CT_HELP, helpCB, NULL, NULL); ++ ++} ++ ++ErrCode ++ExDialRes(char *cmd) ++{ ++ ArgDescr arg; ++ EnumEntryDescr enumEntry[2]; ++ ErrCode errCode; ++ ++ arg.type = AT_ENUM; ++ ++ ArgInit(&arg, 1); ++ ++ arg.prompt = "Residue Dialog"; ++ arg.u.enumD.entryP = enumEntry; ++ arg.u.enumD.n = 2; ++ ++ enumEntry[0].str = "off"; ++ enumEntry[1].str = "on"; ++ ++ enumEntry[0].onOff = DialOn; ++ enumEntry[1].onOff = ! DialOn; ++ if (DialOn) ++ arg.v.intVal = 0; ++ else ++ arg.v.intVal = 1; ++ ++ errCode = ArgGet(&arg, 1); ++ if (errCode != EC_OK) { ++ ArgCleanup(&arg, 1); ++ return errCode; ++ } ++ ++ DialOn = (arg.v.intVal == 1); ++ ++ ArgCleanup(&arg, 1); ++ ++ if (DialOn) { ++ if (DialGizmo == NULL) { ++ buildDial(); ++ DhAddMolListCB(listCB, NULL); ++ } ++ PuSwitchGizmo(DialGizmo, TRUE); ++ } else { ++ if (DialGizmo != NULL) ++ PuSwitchGizmo(DialGizmo, FALSE); ++ } ++ ++ return EC_OK; ++} +\ No newline at end of file +diff --git a/src/cmddial/Makefile b/src/cmddial/Makefile +index d94609d..66fdea9 100644 +--- a/src/cmddial/Makefile ++++ b/src/cmddial/Makefile +@@ -8,7 +8,7 @@ CPPFLAGS = $(INCLUDES) $(MCPPFLAGS) + CFLAGS = $(CPPFLAGS) $(MCFLAGS) + + OBJ = ExDialColor.o ExDialSelect.o ExDialStyle.o ExDialMol.o ExDialMeas.o \ +- ExDialRmsd.o ExUserInterf.o ExRecordMac.o ++ ExDialRes.o ExDialRmsd.o ExUserInterf.o ExRecordMac.o + SRC = $(OBJ:.o=.c) + + default: $(LIBDIR)/libcmd.a +diff --git a/src/cmdio/ExPdb.c b/src/cmdio/ExPdb.c +index 8447c4c..fde9c73 100644 +--- a/src/cmdio/ExPdb.c ++++ b/src/cmdio/ExPdb.c +@@ -1,7 +1,7 @@ + /* + ************************************************************************ + * +-* ExPdb.c - ReadPdb, ReadListPdb and WritePdb commands ++* ExPdb.c - ReadPdb, ReadOldPdb, ReadListPdb and WritePdb commands + * + * Copyright (c) 1994-98 + * +@@ -105,7 +105,7 @@ compFunc(void *p1, void *p2) + } + + static void +-readTransTab(BOOL pdbToIntern) ++readTransTab(BOOL pdbToIntern, BOOL isNewNomenclature) + { + GFile gf; + GFileRes res; +@@ -114,7 +114,7 @@ readTransTab(BOOL pdbToIntern) + + TransTab = TreeOpen(sizeof(TransTabEntry), compFunc); + gf = SetupOpen(PN_PDB_ATOMS, "PdbAtoms", FALSE); +- if (gf == NULL) ++ if (gf == NULL || isNewNomenclature) + return; + + if (pdbToIntern) { +@@ -675,7 +675,7 @@ ExReadPdb(char *cmd) + return errCode; + } + +- readTransTab(TRUE); ++ readTransTab(TRUE, TRUE); + UnknownErrInit(); + + if (replace) { +@@ -755,7 +755,7 @@ ExReadListPdb(char *cmd) + + FileNamePath(fileName); + +- readTransTab(TRUE); ++ readTransTab(TRUE,TRUE); + UnknownErrInit(); + inName = DStrNew(); + pdbName = DStrNew(); +@@ -932,7 +932,7 @@ ExWritePdb(char *cmd) + if (gf == NULL) + return EC_ERROR; + +- readTransTab(FALSE); ++ readTransTab(FALSE,TRUE); + + CHECK_RES(GFileWriteStr(gf, "HEADER Structure from")); + CHECK_RES(GFileWriteStr(gf, PROG_NAME)); +@@ -987,3 +987,61 @@ ExWritePdb(char *cmd) + + return EC_OK; + } ++ ++ErrCode ++ExReadOldPdb(char *cmd) ++{ ++ BOOL replace; ++ DSTR name; ++ int molNo, readNo; ++ DhMolP *molPA; ++ ErrCode errCode; ++ DSTR errStr; ++ ++ replace = (strncmp(cmd, "Replace", 7) == 0); ++ ++ name = DStrNew(); ++ errCode = ArgGetFilename(name, CurrDirGet(), "*.pdb", TRUE); ++ if (errCode != EC_OK) { ++ DStrFree(name); ++ return errCode; ++ } ++ ++ readTransTab(TRUE, FALSE); ++ UnknownErrInit(); ++ ++ if (replace) { ++ molNo = SelMolGet(NULL, 0); ++ if (molNo > 0) { ++ molPA = malloc(molNo * sizeof(*molPA)); ++ (void) SelMolGet(molPA, molNo); ++ } ++ } else { ++ molNo = 0; ++ molPA = NULL; ++ } ++ ++ BreakActivate(TRUE); ++ errCode = readFile(molPA, molNo, name, &readNo); ++ BreakActivate(FALSE); ++ ++ DStrFree(name); ++ TreeClose(TransTab); ++ if (molNo > 0) ++ free(molPA); ++ ++ if (errCode != EC_OK) ++ return EC_ERROR; ++ ++ if (replace) ++ GraphMolChanged(PROP_SELECTED); ++ ++ errStr = UnknownErrGet(); ++ if (errStr != NULL) { ++ CipSetError(DStrToStr(errStr)); ++ DStrFree(errStr); ++ return EC_WARNING; ++ } ++ ++ return EC_OK; ++} +diff --git a/src/cmdstruc/ExBuild.c b/src/cmdstruc/ExBuild.c +index 32bc650..7f003b2 100644 +--- a/src/cmdstruc/ExBuild.c ++++ b/src/cmdstruc/ExBuild.c +@@ -31,11 +31,16 @@ + #include <data_hand.h> + #include <data_sel.h> + #include <graph_draw.h> ++#include <pu.h> + + #define ARG_NUM 1 + + static int CurrPos = 1; + static int CurrKind = 0; ++static PuTextWindow TextW; ++static DhMolP LastMolP=NULL; ++static BOOL messageWindowCreated=FALSE; ++static BOOL cyclicResidueFound=FALSE; + + ErrCode + ExNewMol(char *cmd) +@@ -206,3 +211,121 @@ ExChangeRes(char *cmd) + + return EC_OK; + } ++ ++static void ++writeInt(int num) ++{ ++ char buf[10]; ++ (void) sprintf(buf, "%5d ", num); ++ PuWriteStr(TextW, buf); ++} ++ ++static void ++checkMolCyclic(DhMolP molP, void *clientData) ++{ ++ DhResP resP; ++ DSTR resName = DStrNew(); ++ DStrAssignStr(resName, "XXX"); ++ ++ resP = DhResFirst(molP); ++ while (resP != NULL) { ++ if (DStrCmp(resName, DhResGetName(resP)) == 0) { ++ cyclicResidueFound=TRUE; ++ } ++ resP = DhResNext(resP); ++ } ++ ++ if (cyclicResidueFound && !messageWindowCreated) { ++ TextW = PuCreateTextWindow("MakeMolCyclic"); ++ PuWriteStr(TextW, "--------------------------------------------------\n"); ++ messageWindowCreated=TRUE; ++ } ++ if (cyclicResidueFound) { ++ PuWriteStr(TextW, "Error -"); ++ writeInt(DhMolGetNumber(molP) + 1); ++ PuWriteStr(TextW, DStrToStr(DhMolGetName(molP))); ++ PuWriteStr(TextW, " already made cyclic!\n"); ++ } ++} ++ ++static void ++makeMolCyclic(DhMolP molP, void *clientData) ++{ ++ DhResP xResP, yResP; ++ Vec3 firstCoord, lastCoord, midCoord; ++ DhResP firstResP, lastResP; ++ DhAtomP caAtomP; ++ DSTR atomName = DStrNew(); ++ DhResDefP resDefP = (DhResDefP) clientData; ++ ++ DStrAssignStr(atomName, "CA"); ++ ++ xResP = DhResNewCyclic(molP, resDefP, SP_FIRST); ++ DhResInit(xResP); ++ yResP = DhResNewCyclic(molP, resDefP, SP_LAST); ++ DhResInit(yResP); ++ ++ xResP = DhResFirst(molP); ++ ++ firstResP = DhResNext(xResP); ++ caAtomP = NULL; ++ while (caAtomP == NULL && firstResP != NULL) { ++ caAtomP = DhAtomFindName(firstResP, atomName, FALSE); ++ firstResP = DhResNext(firstResP); ++ } ++ if (caAtomP == NULL) { ++ return; ++ } ++ DhAtomGetCoord(caAtomP, firstCoord); ++ ++ yResP = DhResLast(molP); ++ lastResP = DhResPrev(yResP); ++ caAtomP = NULL; ++ while (caAtomP == NULL && lastResP != NULL) { ++ caAtomP = DhAtomFindName(lastResP, atomName, FALSE); ++ lastResP = DhResPrev(lastResP); ++ } ++ if (caAtomP == NULL) { ++ return; ++ } ++ ++ DhAtomGetCoord(caAtomP, lastCoord); ++ ++ midCoord[0] = (firstCoord[0]+lastCoord[0])/2; ++ midCoord[1] = (firstCoord[1]+lastCoord[1])/2; ++ midCoord[2] = (firstCoord[2]+lastCoord[2])/2; ++ ++ DhAtomSetCoord(DhResGetAtomA(xResP), midCoord); ++ DhAtomSetCoord(DhResGetAtomA(yResP), midCoord); ++} ++ ++ErrCode ++ExMakeMolCyclic(char *cmd) ++{ ++ int ind=0; ++ DhResDefP resDefP; ++ DSTR resName = DStrNew(); ++ ++ messageWindowCreated=FALSE; ++ cyclicResidueFound=FALSE; ++ DhApplyMol(PropGetRef(PROP_SELECTED, FALSE), checkMolCyclic, NULL); ++ if (cyclicResidueFound) { ++ DSTR msg = DStrNew(); ++ DStrAssignStr(msg, "Error cyclic molecules selected"); ++ PuSetTextField(PU_TF_STATUS, DStrToStr(msg)); ++ DStrFree(msg); ++ return EC_OK; ++ } ++ ++ DStrAssignStr(resName, "XXX"); ++ resDefP = DhResDefGet(resName); ++ if (resDefP == NULL) { ++ CipSetError("error cyclic marker residue 'XXX' not found in residue library"); ++ return EC_ERROR; ++ } ++ ++ DhApplyMol(PropGetRef(PROP_SELECTED, FALSE), makeMolCyclic, resDefP); ++ GraphMolChanged(PROP_SELECTED); ++ GraphRedrawNeeded(); ++ return EC_OK; ++} +diff --git a/src/data/DataHand.c b/src/data/DataHand.c +index 368aad3..d020c20 100644 +--- a/src/data/DataHand.c ++++ b/src/data/DataHand.c +@@ -994,9 +994,11 @@ BOOL + DhResDestroy(DhResP resP) + { + /* can only destroy first or last residue of molecule! */ ++ DhMolP molP; + if (resP == ListFirst(resP->molP->resL)) { ++ molP = resP->molP; + ListRemove(resP->molP->resL, resP); +- setEquivI(ListFirst(resP->molP->resL), NULL); ++ setEquivI((DhResP)ListFirst(molP->resL), NULL); + return TRUE; + } else if (resP == ListLast(resP->molP->resL)) { + ListRemove(resP->molP->resL, resP); +@@ -2842,6 +2844,18 @@ DhResGetName(DhResP resP) + return resP->defP->name; + } + ++DhAtomP ++DhResGetAtomA(DhResP resP) ++{ ++ return resP->atomA; ++} ++ ++DhResDefP ++DhResGetDefP(DhResP resP) ++{ ++ return resP->defP; ++} ++ + int + DhResGetNumber(DhResP resP) + { +@@ -3313,3 +3327,101 @@ DhAltCoordListGet(void) + { + return AltCoordList; + } ++ ++static void ++initResCyclic(DhResP resP) ++{ ++ DhResDefP defP; ++ DhResP prevResP, nextResP; ++ DhAtomP atomP, equivAtomP; ++ int i; ++ ++ defP = resP->defP; ++ ++ resP->neighLeftP = NULL; ++ resP->neighRightP = NULL; ++ ++ resP->atomA = malloc(defP->atomNo * sizeof(*resP->atomA)); ++ resP->bondA = malloc(defP->bondNo * sizeof(*resP->bondA)); ++ resP->angleA = malloc(defP->angleNo * sizeof(*resP->angleA)); ++ ++ for (i = 0; i < defP->atomNo; i++) ++ initAtom(resP->atomA + i, resP); ++ ++ for (i = defP->firstBondI; i <= defP->lastBondI; i++) ++ initBond(resP->bondA + i, resP); ++ ++ for (i = 0; i < defP->angleNo; i++) { ++ resP->angleA[i].resP = resP; ++ resP->angleA[i].val = 0.0f; ++ resP->angleA[i].minVal = DH_ANGLE_MIN; ++ resP->angleA[i].maxVal = DH_ANGLE_MAX; ++ resP->angleA[i].changed = FALSE; ++ resP->angleA[i].propTab = PropNewTab(FALSE); ++ } ++ ++ resP->propTab = PropNewTab(FALSE); ++ ++ for (i = 0; i < EQUIV_NO; i++) { ++ resP->equivI[i] = -1; ++ } ++ ++ prevResP = ListPrev(resP->molP->resL, resP); ++ nextResP = ListNext(resP->molP->resL, resP); ++} ++ ++DhResP ++DhResNewCyclic(DhMolP molP, DhResDefP defP, DhSeqPos pos) ++{ ++ struct DhResS resS; ++ DhResP resP, prevResP, nextResP; ++ ++ resS.molP = molP; ++ resS.defP = defP; ++ ++ if (pos == SP_FIRST) { ++ nextResP = ListFirst(molP->resL); ++ if (nextResP == NULL) ++ resS.num = 1; ++ else ++ resS.num = nextResP->num - 1; ++ ++ resP = ListInsertFirst(molP->resL, &resS); ++ } else { ++ prevResP = ListLast(molP->resL); ++ if (prevResP == NULL) ++ resS.num = 1; ++ else ++ resS.num = prevResP->num + 1; ++ ++ resP = ListInsertLast(molP->resL, &resS); ++ } ++ ++ initResCyclic(resP); ++ ++ return resP; ++} ++ ++DhResP ++DhResPrev(DhResP resP) ++{ ++ return (DhResP) ListPrev(resP->molP->resL, resP); ++} ++ ++DhResP ++DhResNext(DhResP resP) ++{ ++ return (DhResP) ListNext(resP->molP->resL, resP); ++} ++ ++DhResP ++DhResFirst(DhMolP molP) ++{ ++ return (DhResP) ListFirst(molP->resL); ++} ++ ++DhResP ++DhResLast(DhMolP molP) ++{ ++ return (DhResP) ListLast(molP->resL); ++} +diff --git a/src/iodev/IODev.c b/src/iodev/IODev.c +index aa4f9a7..9c04ce8 100644 +--- a/src/iodev/IODev.c ++++ b/src/iodev/IODev.c +@@ -44,6 +44,7 @@ extern void IOMotifGLDSetDev(void); + #endif + #ifdef IO_DEV_MOTIF_OGL + extern void IOMotifOGLSetDev(void); ++extern void IOMotifOGLDSetDev(void); + #endif + #ifdef IO_DEV_MOTIF_XGL + extern void IOMotifXGLSetDev(void); +@@ -75,6 +76,7 @@ static DevListEntry DevList[] = { + #endif + #ifdef IO_DEV_MOTIF_OGL + {"Motif/OpenGL", IOMotifOGLSetDev}, ++ {"Motif/OpenGLD", IOMotifOGLDSetDev}, + #endif + #ifdef IO_DEV_MOTIF_XGL + {"Motif/XGL", IOMotifXGLSetDev}, +diff --git a/src/main/MolInit.c b/src/main/MolInit.c +index a7c467a..fccccd3 100644 +--- a/src/main/MolInit.c ++++ b/src/main/MolInit.c +@@ -313,8 +313,9 @@ MolInit(char *defaultDev, int argc, char *argv[], char *macroName) + + SgSetDoubleBuffer(TRUE); + +- ProgDirSet("MOLMOLHOME", "/usr/molmol"); ++ ProgDirSet("MOLMOLHOME", argv[0]); + SetupSetDir("setup"); ++ CurrDirSet(getenv("HOME")); +- UserFileSetDir(CurrDirGet(), "molmol"); ++ UserFileSetDir(CurrDirGet(), ".molmol"); + GFileSetErrorHandler(handleFileError); + +@@ -326,7 +327,7 @@ MolInit(char *defaultDev, int argc, char *argv[], char *macroName) + IOSetErrorHandler(handleIOError); + + PuSetTextField(PU_TF_TITLE, +- "MOLMOL - MOLecule analysis and MOLecule display"); ++ "MOLMOL - MOLecule analysis and MOLecule display - JCU V1.0.8"); + + gf = UserFileOpenRead("par"); + if (gf != NULL) { +diff --git a/src/main/MolMol.c b/src/main/MolMol.c +index 6f825e8..902b50a 100644 +--- a/src/main/MolMol.c ++++ b/src/main/MolMol.c +@@ -30,5 +30,5 @@ + int + main(int argc, char *argv[]) + { +- return MolInit("Motif/X11", argc, argv, NULL); ++ return MolInit("Motif/OpenGL", argc, argv, NULL); + } +diff --git a/src/motif/MotifDial.c b/src/motif/MotifDial.c +index 6e3bfd7..8fe0c5a 100644 +--- a/src/motif/MotifDial.c ++++ b/src/motif/MotifDial.c +@@ -1115,26 +1115,24 @@ PuMotifSetStr(PuGizmo gizmo, PuStrChoice choice, char *val) + void + PuMotifSetColor(PuGizmo gizmo, float r, float g, float b) + { +- Display *dpy; +- int screen; +- Pixel pix; +- XColor col; ++ Display *display; ++ Pixel pixel; ++ XColor color; ++ Colormap colormap; + +- dpy = XtDisplay(gizmo); +- screen = DefaultScreen(dpy); +- XtVaGetValues(gizmo, +- XmNbackground, &pix, +- NULL); ++ display = XtDisplay(gizmo); ++ XtVaGetValues(gizmo, XmNbackground, &pixel, NULL); ++ colormap = DefaultColormapOfScreen(XtScreen(gizmo)); + +- if (pix == BlackPixel(dpy, screen)) +- return; ++ color.pixel = pixel; ++ color.red = FLOAT2SHORT(r); ++ color.green = FLOAT2SHORT(g); ++ color.blue = FLOAT2SHORT(b); ++ color.flags = DoRed | DoGreen | DoBlue; + +- col.pixel = pix; +- col.red = FLOAT2SHORT(r); +- col.green = FLOAT2SHORT(g); +- col.blue = FLOAT2SHORT(b); +- col.flags = DoRed | DoGreen | DoBlue; +- XStoreColor(dpy, DefaultColormap(dpy, screen), &col); ++ XFreeColors(display, colormap, &pixel, 1, 0); ++ XAllocColor(display, colormap, &color); ++ XtVaSetValues(gizmo, XmNbackground, color.pixel, NULL); + } + + void +diff --git a/src/motogl/MotOGLDump.c b/src/motogl/MotOGLDump.c +index 54a4222..3bc25cc 100644 +--- a/src/motogl/MotOGLDump.c ++++ b/src/motogl/MotOGLDump.c +@@ -302,7 +302,7 @@ writeImg(void) + TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, 8); + + if (Quality < 100) +- TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_PACKBITS); ++ TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_LZW); + else + TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_NONE); + +diff --git a/src/os/CurrDir.c b/src/os/CurrDir.c +index edee778..7d2b242 100644 +--- a/src/os/CurrDir.c ++++ b/src/os/CurrDir.c +@@ -26,9 +26,9 @@ + #include <curr_dir.h> + + #include <stdlib.h> +-#ifdef WIN32 +-#include <direct.h> + #include <string.h> ++#ifdef WIN32 ++#include <direct.h> + #else + #include <unistd.h> + #include <errno.h> +@@ -36,43 +36,15 @@ + + static char *CurrDir = NULL; + ++void ++CurrDirSet(char *dir) ++{ ++ CurrDir = malloc(strlen(dir) + 1); ++ (void) strcpy(CurrDir, dir); ++} ++ + char * + CurrDirGet(void) + { +-#ifdef WIN32 +- int len, i; +-#else +- int size = 10; +-#endif +- +- if (CurrDir != NULL) +- return CurrDir; +- +-#ifdef WIN32 +- CurrDir = _getcwd(NULL, 0); +- if (CurrDir != NULL) { +- len = strlen(CurrDir); +- for (i = 0; i < len; i++) +- if (CurrDir[i] == '\\') +- CurrDir[i] = '/'; +- return CurrDir; +- } +-#else +- CurrDir = malloc(size); +- for (;;) { +- if (getcwd(CurrDir, size) != NULL) +- return CurrDir; +- if (errno != ERANGE) +- break; +- size *= 2; +- CurrDir = realloc(CurrDir, size); +- } +-#endif +- +- /* cannot get current directory, return root directory */ +- CurrDir = realloc(CurrDir, 2); +- CurrDir[0] = '/'; +- CurrDir[1] = '\0'; +- + return CurrDir; + } +diff --git a/src/os/ProgDir.c b/src/os/ProgDir.c +index 7abb08d..79ede45 100644 +--- a/src/os/ProgDir.c ++++ b/src/os/ProgDir.c +@@ -45,10 +45,6 @@ ProgDirSet(char *envVar, char *defVal) + dir = getenv(envVar); + if (dir == NULL) { + len = GetModuleFileName(NULL, exePath, sizeof(exePath)); +- if (len == 0) { +- ProgDir = defVal; +- return; +- } + len--; + while (len > 0 && exePath[len] != '\\') + len--; +@@ -65,9 +61,24 @@ ProgDirSet(char *envVar, char *defVal) + if (ProgDir[i] == '\\') + ProgDir[i] = '/'; + #else +- ProgDir = getenv(envVar); +- if (ProgDir == NULL) +- ProgDir = defVal; ++ char *dir; ++ char *exePath; ++ int len; ++ dir = getenv(envVar); ++ if (dir == NULL) { ++ exePath = defVal; ++ len = strlen(exePath); ++ len--; ++ while (len > 0 && exePath[len] != '/') ++ len--; ++ dir = exePath; ++ } else { ++ len = strlen(dir); ++ } ++ ++ ProgDir = malloc(len + 1); ++ (void) strncpy(ProgDir, dir, len); ++ + #endif + } + +diff --git a/src/win/WinDial.c b/src/win/WinDial.c +index 61d6432..e880559 100644 +--- a/src/win/WinDial.c ++++ b/src/win/WinDial.c +@@ -1072,148 +1072,143 @@ dialProc(HWND w, UINT msgKind, WPARAM wParam, LPARAM lParam) + childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); + + switch (notifyCode) { +- case BN_CLICKED: +- if (childId < infoP->u.dial.childNo) { ++ case BN_CLICKED: ++ if (childId < infoP->u.dial.childNo) { + childP = (GizmoInfo *) GetWindowLong(GetFocus(), GWL_USERDATA); +- if (childP->type == GIZMO_TOGGLE) { +- boxP = childP->u.toggle.boxP; +- if (boxP->type == GIZMO_RADIO_BOX) { +- for (i = 0; i < infoP->u.dial.childNo; i++) { +- cP = infoP->u.dial.childPA[i]; +- if (cP->type != GIZMO_TOGGLE) +- continue; +- if (cP->u.toggle.boxP != boxP) +- continue; +- onOff = SendMessage(cP->w, BM_GETCHECK, 0, 0); +- if (onOff && cP != childP) { +- cP->u.toggle.onOff = FALSE; +- SendMessage(cP->w, BM_SETCHECK, FALSE, 0); +- selectStruc.onOff = FALSE; +- callCB(boxP, PU_CT_SELECT, cP->name, &selectStruc); +- break; +- } +- } +- if (cP != childP) { +- childP->u.toggle.onOff = TRUE; +- SendMessage(childP->w, BM_SETCHECK, TRUE, 0); +- selectStruc.onOff = TRUE; +- callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); +- } +- } else { +- onOff = ! SendMessage(childP->w, BM_GETCHECK, 0, 0); +- childP->u.toggle.onOff = onOff; +- SendMessage(childP->w, BM_SETCHECK, onOff, 0); +- selectStruc.onOff = onOff; +- callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); +- } +- } else { +- callCB(childP, PU_CT_ACTIVATE, childP->name, NULL); +- if (childP->type == GIZMO_TEXT_FIELD && +- childP->u.text.historySize > 0) +- childP->u.text.firstMod = TRUE; +- } +- } else { +- buttonI = childId - infoP->u.dial.childNo; +- callCB(infoP, BUTTON_FIRST + buttonI, ButtonLabelA[buttonI], NULL); +- } ++ if (childP->type == GIZMO_TOGGLE) { ++ boxP = childP->u.toggle.boxP; ++ if (boxP->type == GIZMO_RADIO_BOX) { ++ for (i = 0; i < infoP->u.dial.childNo; i++) { ++ cP = infoP->u.dial.childPA[i]; ++ if (cP->type != GIZMO_TOGGLE) continue; ++ if (cP->u.toggle.boxP != boxP) continue; ++ onOff = SendMessage(cP->w, BM_GETCHECK, 0, 0); ++ if (onOff && cP != childP) { ++ cP->u.toggle.onOff = FALSE; ++ SendMessage(cP->w, BM_SETCHECK, FALSE, 0); ++ selectStruc.onOff = FALSE; ++ callCB(boxP, PU_CT_SELECT, cP->name, &selectStruc); ++ break; ++ } ++ } ++ if (cP != childP) { ++ childP->u.toggle.onOff = TRUE; ++ SendMessage(childP->w, BM_SETCHECK, TRUE, 0); ++ selectStruc.onOff = TRUE; ++ callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); ++ } ++ } else { ++ onOff = ! SendMessage(childP->w, BM_GETCHECK, 0, 0); ++ childP->u.toggle.onOff = onOff; ++ SendMessage(childP->w, BM_SETCHECK, onOff, 0); ++ selectStruc.onOff = onOff; ++ callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); ++ } ++ } else { ++ callCB(childP, PU_CT_ACTIVATE, childP->name, NULL); ++ if (childP->type == GIZMO_TEXT_FIELD && childP->u.text.historySize > 0) childP->u.text.firstMod = TRUE; ++ } ++ } else { ++ buttonI = childId - infoP->u.dial.childNo; ++ callCB(infoP, BUTTON_FIRST + buttonI, ButtonLabelA[buttonI], NULL); ++ } + return TRUE; +- case EN_UPDATE: +- textEdit(childP); +- return TRUE; +- case LBN_SELCHANGE: +- for (i = 0; i < childP->u.list.entryNo; i++) +- if (SendMessage(childW, LB_GETSEL, i, 0) != +- childP->u.list.entryA[i].onOff) +- lastI = i; + +- for (i = 0; i < childP->u.list.entryNo; i++) { +- onOff = SendMessage(childW, LB_GETSEL, i, 0); +- if (onOff != childP->u.list.entryA[i].onOff) { +- if (! childP->u.list.autoDesel) ++ case EN_UPDATE: ++ textEdit(childP); ++ return TRUE; ++ ++ case LBN_SELCHANGE: ++ for (i = 0; i < childP->u.list.entryNo; i++) ++ if (SendMessage(childW, LB_GETSEL, i, 0) != childP->u.list.entryA[i].onOff) ++ lastI = i; ++ ++ for (i = 0; i < childP->u.list.entryNo; i++) { ++ onOff = SendMessage(childW, LB_GETSEL, i, 0); ++ if (onOff != childP->u.list.entryA[i].onOff) { ++ if (! childP->u.list.autoDesel) + childP->u.list.entryA[i].onOff = onOff; +- selectStruc.onOff = onOff; +- selectStruc.last = (i == lastI); +- callCB(childP, PU_CT_SELECT, +- childP->u.list.entryA[i].str, &selectStruc); +- } +- } +- +- if (childP->u.list.autoDesel) +- SendMessage(childW, LB_SETCURSEL, -1, 0); +- +- return TRUE; ++ selectStruc.onOff = onOff; ++ selectStruc.last = (i == lastI); ++ callCB(childP, PU_CT_SELECT, ++ childP->u.list.entryA[i].str, &selectStruc); ++ } ++ } ++ if (childP->u.list.autoDesel) ++ SendMessage(childW, LB_SETCURSEL, -1, 0); ++ return TRUE; + } ++ break; + +- break; +- case WM_VSCROLL: +- childW = (HWND) lParam; +- childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); +- scrollCode = LOWORD(wParam); ++ case WM_VSCROLL: ++ childW = (HWND) lParam; ++ childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); ++ scrollCode = LOWORD(wParam); + +- if (scrollCode == SB_LINEUP) { +- upHistory(childP->u.scroll.textP); +- } else if (scrollCode == SB_LINEDOWN) { +- downHistory(childP->u.scroll.textP); +- } else { +- return FALSE; +- } +- return TRUE; +- case WM_HSCROLL: +- scrollCode = LOWORD(wParam); +- if (scrollCode != SB_THUMBPOSITION && scrollCode != SB_THUMBTRACK) +- return FALSE; ++ if (scrollCode == SB_LINEUP) { ++ upHistory(childP->u.scroll.textP); ++ } else if (scrollCode == SB_LINEDOWN) { ++ downHistory(childP->u.scroll.textP); ++ } else { ++ return FALSE; ++ } ++ return TRUE; ++ case WM_HSCROLL: ++ scrollCode = LOWORD(wParam); ++ if (scrollCode != SB_THUMBPOSITION && scrollCode != SB_THUMBTRACK) ++ return FALSE; + +- scrollPos = (int)(short)HIWORD(wParam); +- childW = (HWND) lParam; +- childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); ++ scrollPos = (int)(short)HIWORD(wParam); ++ childW = (HWND) lParam; ++ childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); + +- floatStruc.oldVal = childP->u.slider.val; +- childP->u.slider.val = scrollPos / childP->u.slider.factor; +- SetScrollPos(childW, SB_CTL, +- (int) (childP->u.slider.val * childP->u.slider.factor), +- TRUE); ++ floatStruc.oldVal = childP->u.slider.val; ++ childP->u.slider.val = scrollPos / childP->u.slider.factor; ++ SetScrollPos(childW, SB_CTL, ++ (int) (childP->u.slider.val * childP->u.slider.factor), TRUE); + +- if (childP->u.slider.valuatorCB == NULL) { +- floatStruc.newVal = childP->u.slider.val; +- callCB(childP, PU_CT_MODIFY, childP->name, &floatStruc); +- } else { +- valStruc.act = PU_MA_ACTIVATE; +- valStruc.name = childP->name; +- valStruc.val = childP->u.slider.val; +- childP->u.slider.valuatorCB(childP, childP->u.slider.clientData, &valStruc); +- } ++ if (childP->u.slider.valuatorCB == NULL) { ++ floatStruc.newVal = childP->u.slider.val; ++ callCB(childP, PU_CT_MODIFY, childP->name, &floatStruc); ++ } else { ++ valStruc.act = PU_MA_ACTIVATE; ++ valStruc.name = childP->name; ++ valStruc.val = childP->u.slider.val; ++ childP->u.slider.valuatorCB(childP, childP->u.slider.clientData, &valStruc); ++ } ++ return TRUE; + +- return TRUE; +- case WM_PAINT: +- for (childId = 0; childId < infoP->u.dial.childNo; childId++) { +- childP = infoP->u.dial.childPA[childId]; +- if (childP->type == GIZMO_COLOR_FIELD) +- paintColor(childP->w, +- childP->u.color.r, childP->u.color.g, childP->u.color.b); +- } +- break; +- case WM_MOVE: +- if (infoP->u.dial.outside) { +- WinPlaceChanged(infoP->w); +- return TRUE; +- } +- break; +- case WM_CLOSE: +- buttonNo = 0; +- for (i = 0; i < BUTTON_NO; i++) +- if (infoP->u.dial.buttonSwitchA[i]) +- buttonNo++; +- if (buttonNo == 0) +- ShowWindow(infoP->w, SW_HIDE); +- return TRUE; +- case WM_DESTROY: +- WinRemoveDialog(w); +- for (childId = 0; childId < infoP->u.dial.childNo; childId++) +- freeInfo(infoP->u.dial.childPA[childId]); +- freeInfo(infoP); +- return TRUE; +- } ++ case WM_PAINT: ++ for (childId = 0; childId < infoP->u.dial.childNo; childId++) { ++ childP = infoP->u.dial.childPA[childId]; ++ if (childP->type == GIZMO_COLOR_FIELD) ++ paintColor(childP->w, ++ childP->u.color.r, childP->u.color.g, childP->u.color.b); ++ } ++ break; + ++ case WM_MOVE: ++ if (infoP->u.dial.outside) { ++ WinPlaceChanged(infoP->w); ++ return TRUE; ++ } ++ break; ++ case WM_CLOSE: ++ buttonNo = 0; ++ for (i = 0; i < BUTTON_NO; i++) { ++ if (infoP->u.dial.buttonSwitchA[i]) buttonNo++; ++ if (buttonNo == 0) { ++ ShowWindow(infoP->w, SW_HIDE); ++ } ++ } ++ return TRUE; ++ case WM_DESTROY: ++ WinRemoveDialog(w); ++ for (childId = 0; childId < infoP->u.dial.childNo; childId++) ++ freeInfo(infoP->u.dial.childPA[childId]); ++ freeInfo(infoP); ++ return TRUE; ++ } + return FALSE; + } + +diff --git a/src/winogl/WinOGLDump.c b/src/winogl/WinOGLDump.c +index 0a7d61a..a8ce850 100644 +--- a/src/winogl/WinOGLDump.c ++++ b/src/winogl/WinOGLDump.c +@@ -44,6 +44,7 @@ + #endif + #ifdef PNG_SUPPORT + #include <png.h> ++#include <pngpriv.h> + #endif + + #include "winogl_int.h" +@@ -251,7 +252,7 @@ static void + pngErrHand(png_structp pngStrucP, char *errMsg) + { + IORaiseError(errMsg); +- longjmp(pngStrucP->jmpbuf, 1); ++ longjmp(pngStrucP->longjmp_buffer, 1); + } + #endif + +@@ -314,7 +315,7 @@ writeImg(void) + TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, 8); + + if (Quality < 100) +- TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_PACKBITS); ++ TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_LZW); + else + TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_NONE); + +@@ -369,7 +370,7 @@ writeImg(void) + return IO_RES_ERR; + } + +- if (setjmp(pngStrucP->jmpbuf)) { ++ if (setjmp(pngStrucP->longjmp_buffer)) { + if (cBuf != NULL) + free(cBuf); + if (fBuf != NULL) diff --git a/sci-chemistry/molmol/metadata.xml b/sci-chemistry/molmol/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/molmol/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild new file mode 100644 index 000000000000..a8658310e612 --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils multilib prefix toolchain-funcs + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" +HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + || ( + ( media-libs/mesa + x11-libs/libGLw ) + media-libs/mesa[motif] ) + media-libs/libpng:0 + media-libs/tiff:0 + sys-libs/zlib + virtual/glu + virtual/jpeg + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +MAKEOPTS="${MAKEOPTS} -j1" + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" +} + +src_prepare() { + rm -rf tiff* + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + + epatch "${FILESDIR}"/prefix.patch + eprefixify molmol + + epatch "${FILESDIR}"/ldflags.patch + + ln -s makedef.lnx "${S}"/makedef || die + + sed \ + -e "s:/bin/ksh:${EPREFIX}/bin/sh:" \ + -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \ + -i "${S}"/molmol || die + sed \ + -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -i "${S}"/makedef || die + + epatch "${FILESDIR}"/cast.patch + epatch "${FILESDIR}"/libpng15.patch +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + newexe src/main/molmol molmol.lnx + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + dodoc HISTORY README +} diff --git a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild new file mode 100644 index 000000000000..366d41a75bd9 --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils multilib prefix toolchain-funcs + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" +HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + || ( + ( media-libs/mesa + x11-libs/libGLw ) + media-libs/mesa[motif] ) + media-libs/libpng:0 + media-libs/tiff:0 + sys-libs/zlib + virtual/glu + virtual/jpeg + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +MAKEOPTS="${MAKEOPTS} -j1" + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" +} + +src_prepare() { + rm -rf tiff* + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + + epatch "${FILESDIR}"/prefix.patch + eprefixify molmol + + epatch "${FILESDIR}"/ldflags.patch + + ln -s makedef.lnx "${S}"/makedef || die + + sed \ + -e "s:/bin/ksh:${EPREFIX}/bin/sh:" \ + -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \ + -i "${S}"/molmol || die + sed \ + -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -i "${S}"/makedef || die + + epatch "${FILESDIR}"/cast.patch + epatch "${FILESDIR}"/libpng15.patch + + # patch from fink + # fixes numerous bad bracings and hopefully the OGL bug 429974 + epatch "${FILESDIR}"/${P}-fink.patch +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + newexe src/main/molmol molmol.lnx + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + dodoc HISTORY README +} diff --git a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild new file mode 100644 index 000000000000..e463ff241d06 --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild @@ -0,0 +1,86 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils multilib prefix toolchain-funcs + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" +HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + || ( + ( media-libs/mesa + x11-libs/libGLw ) + media-libs/mesa[motif] ) + media-libs/libpng:0 + media-libs/tiff:0 + sys-libs/zlib + virtual/glu + virtual/jpeg + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +MAKEOPTS="${MAKEOPTS} -j1" + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" +} + +src_prepare() { + rm -rf tiff* + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + + epatch "${FILESDIR}"/prefix.patch + eprefixify molmol + + epatch "${FILESDIR}"/ldflags.patch + + ln -s makedef.lnx "${S}"/makedef || die + + sed \ + -e "s:/bin/ksh:${EPREFIX}/bin/sh:" \ + -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \ + -i "${S}"/molmol || die + sed \ + -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -i "${S}"/makedef || die + + epatch "${FILESDIR}"/cast.patch + epatch "${FILESDIR}"/libpng15.patch + + # patch from fink + # fixes numerous bad bracings and hopefully the OGL bug 429974 + epatch "${FILESDIR}"/${P}-fink.patch + + tc-export AR +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + newexe src/main/molmol molmol.lnx + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + dodoc HISTORY README +} diff --git a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild new file mode 100644 index 000000000000..8def42023aac --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild @@ -0,0 +1,85 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils multilib prefix toolchain-funcs + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" +HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + || ( + ( media-libs/mesa + x11-libs/libGLw ) + media-libs/mesa[motif] ) + media-libs/libpng:0 + media-libs/tiff:0 + sys-libs/zlib + virtual/glu + virtual/jpeg + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +MAKEOPTS="${MAKEOPTS} -j1" + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" +} + +src_prepare() { + rm -rf tiff* + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + + epatch "${FILESDIR}"/ldflags.patch + epatch "${FILESDIR}"/opengl.patch + + ln -s makedef.lnx "${S}"/makedef || die + + sed \ + -e "s:ksh:sh:" \ + -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR};MOLMOLDEV=\"Motif/OpenGL\":" \ + -i "${S}"/molmol || die + sed \ + -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -i "${S}"/makedef || die + + epatch "${FILESDIR}"/cast.patch + epatch "${FILESDIR}"/libpng15.patch + + # patch from fink + # fixes numerous bad bracings and hopefully the OGL bug 429974 + epatch "${FILESDIR}"/${P}-fink.patch + + epatch "${FILESDIR}"/wild.patch + tc-export AR +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + doexe src/main/molmol + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + dodoc HISTORY README +} diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest new file mode 100644 index 000000000000..7206bd5555b8 --- /dev/null +++ b/sci-chemistry/molrep/Manifest @@ -0,0 +1,2 @@ +DIST molrep-11.0.02.tar.gz 3594084 SHA256 6acb00bc91ad76027461ce6055eda72c8de34e5243449a31d5ede9e537e9adce +DIST molrep-11.0.03.tar.gz 3643087 SHA256 f4c317713b0dddf0ca883734f0bfe27600b50f8d4dd354ea8ae8245e21ce4392 SHA512 d9ff351e3754871d100c41aa9b8af48e3588768320f5ed92e536fac5e24114ca5df6497103d0b077455fc4e30e2d3d085aeb63854eb88dc8e74259b4e1683dc8 WHIRLPOOL b16e128e3ca7f1734ca79f70decab3e262d47b6a37c49e46c4c7d51f3fd8093cd3a0f20e487caeb5e9aa0a37a9fd050588cad3e99ad46e1866d05ff4a8ed0bb6 diff --git a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch new file mode 100644 index 000000000000..d81ec793b510 --- /dev/null +++ b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch @@ -0,0 +1,61 @@ +--- src/makefile 2009-02-27 16:51:46.492890717 +0100 ++++ src/makefile.new 2009-02-27 16:52:18.295619642 +0100 +@@ -5,8 +5,8 @@ + + BIN = $(MOLREP)/bin + +-OBJS = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym.o molrep_unix.o +-OBJSL = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym.o molrep_unix.o ++OBJS = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym_ccp4.o molrep_unix_ccp4.o ++OBJSL = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym_ccp4.o molrep_unix_ccp4.o + + + all: molrep +@@ -19,31 +19,31 @@ + # ----------------------------- + + molrep.o: molrep.f +- $(MR_FORT) -c molrep.f ++ $(MR_FORT) $(FFLAGS) -c molrep.f + molrep1.o: molrep1.f +- $(MR_FORT) -c molrep1.f ++ $(MR_FORT) $(FFLAGS) -c molrep1.f + molrep2.o: molrep2.f +- $(MR_FORT) -c molrep2.f ++ $(MR_FORT) $(FFLAGS) -c molrep2.f + molrep3.o: molrep3.f +- $(MR_FORT) -c molrep3.f ++ $(MR_FORT) $(FFLAGS) -c molrep3.f + molrep_prog.o: molrep_prog.f +- $(MR_FORT) -c molrep_prog.f ++ $(MR_FORT) $(FFLAGS) -c molrep_prog.f + molrep_prog1.o: molrep_prog1.f +- $(MR_FORT) -c molrep_prog1.f ++ $(MR_FORT) $(FFLAGS) -c molrep_prog1.f + molrep_prog2.o: molrep_prog2.f +- $(MR_FORT) -c molrep_prog2.f ++ $(MR_FORT) $(FFLAGS) -c molrep_prog2.f + molrep_subr.o: molrep_subr.f +- $(MR_FORT) -c molrep_subr.f +-molrep_sym.o: molrep_sym.f +- $(MR_FORT) -c molrep_sym.f ++ $(MR_FORT) $(FFLAGS) -c molrep_subr.f ++molrep_sym_ccp4.o: molrep_sym.f ++ $(MR_FORT) $(FFLAGS) -c molrep_sym_ccp4.f + main_molrep_mtz.o: main_molrep_mtz.f molrep_version.fh molrep_keywords.fh +- $(MR_FORT) -c main_molrep_mtz.f +-molrep_unix.o: molrep_unix.f +- $(MR_FORT) -c molrep_unix.f ++ $(MR_FORT) $(FFLAGS) -c main_molrep_mtz.f ++molrep_unix_ccp4.o: molrep_unix.f ++ $(MR_FORT) $(FFLAGS) -c molrep_unix_ccp4.f + molrep_dummy.o: molrep_dummy.f +- $(MR_FORT) -c molrep_dummy.f ++ $(MR_FORT) $(FFLAGS) -c molrep_dummy.f + + molrep: $(OBJS) +- $(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) ++ $(MR_FORT) $(FFLAGS) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) + + # -------------------------------- + diff --git a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch new file mode 100644 index 000000000000..c18b9a1e3f0d --- /dev/null +++ b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch @@ -0,0 +1,12 @@ +diff --git a/src/makefile b/src/makefile +index 30d0de7..10dd68f 100755 +--- a/src/makefile ++++ b/src/makefile +@@ -46,6 +46,6 @@ molrep_dummy.o: molrep_dummy.f + $(MR_FORT) -c molrep_dummy.f + + molrep: $(OBJS) +- $(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) ++ $(MR_FORT) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) + + # -------------------------------- diff --git a/sci-chemistry/molrep/files/11.0.00-test.patch b/sci-chemistry/molrep/files/11.0.00-test.patch new file mode 100644 index 000000000000..d90cfb8c7b35 --- /dev/null +++ b/sci-chemistry/molrep/files/11.0.00-test.patch @@ -0,0 +1,191 @@ +diff --git a/molrep_check/em.bat b/molrep_check/em.bat +index 2f0f992..96ddd75 100755 +--- a/molrep_check/em.bat ++++ b/molrep_check/em.bat +@@ -8,6 +8,8 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop + # -------------------------------- + _NMON 6 + stop ++echo $? ++[[ $? ]] || exit 1 + # -------------------------------- + # + # 2. Atomic model --> EM map +@@ -20,6 +22,7 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop + _NMON 6 + _prf y + stop ++[[ $? ]] || exit 1 + # -------------------------------- + # + # 3. Atomic model --> EM map +@@ -36,6 +39,7 @@ _ncs 322 + _centre 0.500 0.490 0.490 + _angles 0.0 0.0 90.0 + stop ++[[ $? ]] || exit 1 + # -------------------------------- + # + cp out/molrep.pdb hexamer.pdb +@@ -52,6 +56,7 @@ $MR_TEST/molrep -mx hexamer.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop + # -------------------------------- + _DOM s + stop ++[[ $? ]] || exit 1 + # -------------------------------- + # + # 5. EM --> X-ray +@@ -60,6 +65,7 @@ stop + $MR_TEST/molrep -f ../em/p2.cif -m ../em/pel.map -po out/ -ps scr/ -i <<stop + # -------------------------------- + stop ++[[ $? ]] || exit 1 + # -------------------------------- + # + # 6. Placing the model to a particular orientation and position. +@@ -72,4 +78,5 @@ $MR_TEST/molrep -f ../em/p2.cif -m ../em/pel.map -po out/ -ps scr/ -i <<stop + _fun s + _file_t ../em/tab + stop ++[[ $? ]] || exit 1 + #========================================== +diff --git a/molrep_check/mr.bat b/molrep_check/mr.bat +index 284a4cd..6e00695 100755 +--- a/molrep_check/mr.bat ++++ b/molrep_check/mr.bat +@@ -10,6 +10,7 @@ + $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i <<stop + # -------------------------------- + stop ++[[ $? ]] || exit 1 + # + # ================================================================= + # +@@ -26,6 +27,7 @@ _nmon 2 + _COMPL .5 + _SIM .7 + stop ++[[ $? ]] || exit 1 + # + # ================================================================= + # +@@ -46,6 +48,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -mx ../data/test_mod + # -------------------------------- + _NP 3 + stop ++[[ $? ]] || exit 1 + # + # ================================================================= + # +@@ -67,6 +70,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -po out/ -ps scr/ -i + _NMON 2 + _NP 3 + stop ++[[ $? ]] || exit 1 + # + # ================================================================= + # +@@ -85,6 +89,7 @@ _NPT 3 + _NPTD 3 + _DYAD D + stop ++[[ $? ]] || exit 1 + # + # ================================================================= + # +@@ -103,6 +108,7 @@ _NP 3 + _NPT 10 + _NMR 3 + stop ++[[ $? ]] || exit 1 + # + # ================================================================= + # +@@ -118,6 +124,7 @@ _PRF Y + _compl 1. + _sim .2 + stop ++[[ $? ]] || exit 1 + # + # ================================================================= + # +@@ -136,6 +143,7 @@ _ph PH + _fom FOM + # + stop ++[[ $? ]] || exit 1 + # ================================================================= + # + # 9. use sequence +@@ -145,6 +153,7 @@ stop + $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -s ../data/s100.seq -po out/ -ps scr/ -i <<stop + # -------------------------------- + stop ++[[ $? ]] || exit 1 + # ================================================================= + # + # 10. Locked RF +@@ -157,6 +166,7 @@ _lock y + _file_tsrf ../data/srf.tab + _nsrf 1 + stop ++[[ $? ]] || exit 1 + # ================================================================= + # + # 11. Multi-monomer search using NCS, SELF = 'A' means to compute Self RF and +@@ -169,6 +179,7 @@ $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -m2 ../data/monomer.p + _self a + _nsrf 1 + stop ++[[ $? ]] || exit 1 + # ================================================================= + # + # 12. use pst +@@ -179,6 +190,7 @@ $MR_TEST/molrep -f ../data/pst.mtz -m ../data/model_pst.pdb -po out/ -ps scr/ -i + # -------------------------------- + # + stop ++[[ $? ]] || exit 1 + # ================================================================= + # + # 13. space group check +@@ -189,7 +201,8 @@ $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i + # -------------------------------- + _sg all + # +-stop ++s[[ $? ]] || exit 1 ++top + # ========================================================== + # + # 14. Example for finding HA position by MR solution. +@@ -206,6 +219,7 @@ _SIGFD SIGFD3 + # + _FUN d + stop ++[[ $? ]] || exit 1 + # ========================================================== + # + # 15. Example for HA search by multi-copy search +@@ -225,6 +239,7 @@ _diff h + _dyad y + _nmon 4 + stop ++[[ $? ]] || exit 1 + # ========================================================== + # + # 16. Example HA for search by translation function +@@ -242,6 +257,7 @@ _FUN t + _diff h + _nmon 4 + stop ++[[ $? ]] || exit 1 + # ========================================================== + # + # 17. Example for Self RF for Heavy Atom structure in derivative. +@@ -258,4 +274,5 @@ _SIGFD SIGFD3 + _FUN r + _diff h + stop ++[[ $? ]] || exit 1 + # ========================================================== diff --git a/sci-chemistry/molrep/files/11.0.03-EOR.patch b/sci-chemistry/molrep/files/11.0.03-EOR.patch new file mode 100644 index 000000000000..430629e8dcc1 --- /dev/null +++ b/sci-chemistry/molrep/files/11.0.03-EOR.patch @@ -0,0 +1,16 @@ + src/molrep.f | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/src/molrep.f b/src/molrep.f +index eac0cfc..94f74c6 100755 +--- a/src/molrep.f ++++ b/src/molrep.f +@@ -1257,7 +1257,7 @@ C CHECK_DENS_FILE( 2 ) + LEN1 = 1 + IF(LEN.GT.60) LEN1 = LEN - 59 + WRITE(LINE,'(''Input MODEL_2(fixed)_file:'',A)') +- * NAME2(LEN11:LEN) ++ * NAME2(LEN1:LEN) + CALL MSGDOC(MDoc,LINE) + + ENDIF diff --git a/sci-chemistry/molrep/metadata.xml b/sci-chemistry/molrep/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/molrep/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/molrep/molrep-11.0.02.ebuild b/sci-chemistry/molrep/molrep-11.0.02.ebuild new file mode 100644 index 000000000000..51ff6cb26524 --- /dev/null +++ b/sci-chemistry/molrep/molrep-11.0.02.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 multilib toolchain-funcs + +DESCRIPTION="molecular replacement program" +HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html" +SRC_URI="mirror://gentoo/${P}.tar.gz" + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-libs/ccp4-libs-6.1.3 + sci-libs/mmdb + virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}" + +src_prepare() { + epatch \ + "${FILESDIR}"/11.0.00-respect-FLAGS.patch \ + "${FILESDIR}"/11.0.00-test.patch +} + +src_compile() { + cd "${S}"/src + emake clean + emake \ + MR_FORT="$(tc-getFC) ${FFLAGS}" \ + FFLAGS="${FFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm" +} + +src_test() { + export MR_TEST="${S}/bin/" + cd "${S}"/molrep_check/work + mkdir out scr + cp ../*.bat . + bash em.bat || die + bash mr.bat || die +} + +src_install() { + exeinto /usr/libexec/ccp4/bin/ + doexe bin/${PN} + dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} + dodoc readme doc/${PN}.rtf +} diff --git a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild new file mode 100644 index 000000000000..3a0d7538b481 --- /dev/null +++ b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs + +DESCRIPTION="molecular replacement program" +HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz" + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-libs/ccp4-libs-6.1.3 + sci-libs/mmdb + virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}" + +src_prepare() { + epatch \ + "${FILESDIR}"/11.0.00-respect-FLAGS.patch \ + "${FILESDIR}"/11.0.00-test.patch \ + "${FILESDIR}"/${PV}-EOR.patch + [[ $(tc-getFC) =~ gfortran ]] && append-fflags -fno-second-underscore +} + +src_compile() { + cd "${S}"/src + emake clean + emake \ + MR_FORT="$(tc-getFC) ${FFLAGS}" \ + FFLAGS="${FFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm" +} + +src_test() { + export MR_TEST="${S}/bin/" + cd "${S}"/molrep_check/work + mkdir out scr + cp ../*.bat . + bash em.bat || die + bash mr.bat || die +} + +src_install() { + exeinto /usr/libexec/ccp4/bin/ + doexe bin/${PN} + dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} + dodoc readme doc/${PN}.rtf +} diff --git a/sci-chemistry/molscript/Manifest b/sci-chemistry/molscript/Manifest new file mode 100644 index 000000000000..d1fa0a225a02 --- /dev/null +++ b/sci-chemistry/molscript/Manifest @@ -0,0 +1 @@ +DIST molscript-2.1.2.tar.gz 412497 SHA256 01252931f5a3542d5659ddaa4ebceaed2e75becb8ed150dfa14b59da9a63ca01 SHA512 0f82936da3123770c0fdb703094dbb5289cc39e9f9ffd034d8dba563f8d615788f67040d38158ac2f203b480c5838a7d8e71ca07bc5098181c1e3cfea26703a4 WHIRLPOOL 1588f4dd47117f8da797a8bf62a2eba071106b1faca4f79b06e3093fe76092cae54476f1a0be995e3637173561ae6003fded264dd6d3a424d235488f95085a75 diff --git a/sci-chemistry/molscript/files/2.1.2-ldflags.patch b/sci-chemistry/molscript/files/2.1.2-ldflags.patch new file mode 100644 index 000000000000..8867bc10a6b5 --- /dev/null +++ b/sci-chemistry/molscript/files/2.1.2-ldflags.patch @@ -0,0 +1,22 @@ +diff --git a/Makefile.complete b/Makefile.complete +index 4ad535a..b565266 100644 +--- a/Makefile.complete ++++ b/Makefile.complete +@@ -91,7 +91,7 @@ clean: + + #------------------------------------------------------------ + molscript: $(OBJ) clib/clib.a +- $(CC) -o molscript $(COPT) $(OBJ) $(YLIB) clib/clib.a \ ++ $(CC) $(LDFLAGS) -o molscript $(COPT) $(OBJ) $(YLIB) clib/clib.a \ + $(GLUTLINK) $(JPEGLINK) $(PNGLINK) $(GIFLINK) $(ZLIBLINK) -lm + + molscript.tab.o: molscript.tab.c molscript.tab.h +@@ -147,7 +147,7 @@ gif_img.o: gif_img.c gif_img.h global.h graphics.h image.h opengl.h + + #------------------------------------------------------------ + molauto: molauto.o clib/clib.a +- $(CC) -o molauto molauto.o clib/clib.a -lm ++ $(CC) $(LDFLAGS) -o molauto molauto.o clib/clib.a -lm + + molauto.o: molauto.c + diff --git a/sci-chemistry/molscript/files/2.1.2-libpng15.patch b/sci-chemistry/molscript/files/2.1.2-libpng15.patch new file mode 100644 index 000000000000..9ed1b85909e8 --- /dev/null +++ b/sci-chemistry/molscript/files/2.1.2-libpng15.patch @@ -0,0 +1,19 @@ +--- png_img.c ++++ png_img.c +@@ -18,6 +18,7 @@ + + #include <GL/gl.h> + ++#include <zlib.h> + #include <png.h> + + #include "clib/str_utils.h" +@@ -69,7 +70,7 @@ + info_ptr = png_create_info_struct (png_ptr); + if (info_ptr == NULL) + yyerror ("png_img: could not create PNG info structure"); +- if (setjmp (png_ptr->jmpbuf)) yyerror ("png_img: could not setjmp"); ++ if (setjmp (png_jmpbuf(png_ptr))) yyerror ("png_img: could not setjmp"); + + png_init_io (png_ptr, outfile); + png_set_compression_level (png_ptr, compression_level); diff --git a/sci-chemistry/molscript/files/2.1.2-prll.patch b/sci-chemistry/molscript/files/2.1.2-prll.patch new file mode 100644 index 000000000000..e4c972a10533 --- /dev/null +++ b/sci-chemistry/molscript/files/2.1.2-prll.patch @@ -0,0 +1,10 @@ +diff --git a/Makefile.complete b/Makefile.complete +index 92ef20a..e3f68e3 100644 +--- a/Makefile.complete ++++ b/Makefile.complete +@@ -153,4 +153,4 @@ molauto.o: molauto.c + + #------------------------------------------------------------ + clib/clib.a: +- cd clib; make clib.a CFLAGS="-I. $(CFLAGS)" OPENGLCLIBOBJ="$(OPENGLCLIBOBJ)" ++ $(MAKE) -C clib clib.a CFLAGS="-I. $(CFLAGS)" OPENGLCLIBOBJ="$(OPENGLCLIBOBJ)" diff --git a/sci-chemistry/molscript/files/fix-makefile-shared.patch b/sci-chemistry/molscript/files/fix-makefile-shared.patch new file mode 100644 index 000000000000..a9947a61a665 --- /dev/null +++ b/sci-chemistry/molscript/files/fix-makefile-shared.patch @@ -0,0 +1,62 @@ +diff -urN molscript-2.1.2.orig/Makefile.complete molscript-2.1.2/Makefile.complete +--- molscript-2.1.2.orig/Makefile.complete 1998-11-25 01:04:39.000000000 -0800 ++++ molscript-2.1.2/Makefile.complete 2005-11-21 12:28:06.000000000 -0800 +@@ -23,9 +23,9 @@ + + # OpenGL and GLUT for X (UNIX). + # Must be modified for Windows 95/NT. <--- +-GLUTDIR = $(FREEWAREDIR)/glut +-GLUTLINK = $(GLUTDIR)/lib/glut/libglut.a -lGLU -lGL -lXmu -lXext -lX11 +-OPENGLFLAG = -DOPENGL_SUPPORT -I$(GLUTDIR)/include ++GLUTDIR = $(FREEWAREDIR) ++GLUTLINK = -lglut -lGLU -lGL -lXmu -lXext -lX11 ++OPENGLFLAG = -DOPENGL_SUPPORT -I$(GLUTDIR)/include/GL + OPENGLOBJ = opengl.o + OPENGLCLIBOBJ = ogl_utils.o ogl_body.o ogl_bitmap_character.o + +@@ -35,25 +35,25 @@ + + # JPEG image file format; requires the JPEG library. + # Comment out these lines if the JPEG library is not available. <--- +-JPEGDIR = $(FREEWAREDIR)/jpeg +-JPEGLINK = $(JPEGDIR)/libjpeg.a +-JPEGFLAG = -DJPEG_SUPPORT -I$(JPEGDIR) ++JPEGDIR = $(FREEWAREDIR) ++JPEGLINK = -ljpeg ++JPEGFLAG = -DJPEG_SUPPORT + JPEGOBJ = jpeg_img.o + + # PNG image file format; requires the PNG library and the zlib library. + # Comment out these lines if the PNG and zlib libraries are not available. <--- +-ZLIBDIR = $(FREEWAREDIR)/zlib +-ZLIBLINK = $(ZLIBDIR)/libz.a +-PNGDIR = $(FREEWAREDIR)/libpng +-PNGLINK = $(PNGDIR)/libpng.a +-PNGFLAG = -DPNG_SUPPORT -I$(PNGDIR) -I$(ZLIBDIR) ++ZLIBDIR = $(FREEWAREDIR) ++ZLIBLINK = -lz ++PNGDIR = $(FREEWAREDIR) ++PNGLINK = -lpng ++PNGFLAG = -DPNG_SUPPORT + PNGOBJ = png_img.o + + # GIF image file format; requires the gd 1.3 library. + # Comment out these lines if the gd 1.3 library is not available. <--- +-GIFDIR = $(FREEWAREDIR)/gd +-GIFLINK = $(GIFDIR)/libgd.a +-GIFFLAG = -DGIF_SUPPORT -I$(GIFDIR) ++GIFDIR = $(FREEWAREDIR) ++GIFLINK = -lgd ++GIFFLAG = -DGIF_SUPPORT + GIFOBJ = gif_img.o + + # SGI IRIX's C compiler. +@@ -62,7 +62,7 @@ + COPT = -O1 + # Correctness flags: + #CCHECK = -ansi -fullwarn -g -DSELECT_DEBUG +-CCHECK = -ansi -fullwarn ++CCHECK = -ansi + #CCHECK = -ansi -fullwarn -DNDEBUG + + # General cc compile flags. diff --git a/sci-chemistry/molscript/files/glutbitmap.h b/sci-chemistry/molscript/files/glutbitmap.h new file mode 100644 index 000000000000..9584bb129daa --- /dev/null +++ b/sci-chemistry/molscript/files/glutbitmap.h @@ -0,0 +1,32 @@ +#ifndef __glutbitmap_h__ +#define __glutbitmap_h__ + +/* Copyright (c) Mark J. Kilgard, 1994, 1998. */ + +/* This program is freely distributable without licensing fees + and is provided without guarantee or warrantee expressed or + implied. This program is -not- in the public domain. */ + +#define GLUT_NO_LIB_PRAGMA /* Avoid auto library linking when building + the GLUT library itself. */ +#include <GL/glut.h> + +typedef struct { + const GLsizei width; + const GLsizei height; + const GLfloat xorig; + const GLfloat yorig; + const GLfloat advance; + const GLubyte *bitmap; +} BitmapCharRec, *BitmapCharPtr; + +typedef struct { + const char *name; + const int num_chars; + const int first; + const BitmapCharRec * const *ch; +} BitmapFontRec, *BitmapFontPtr; + +typedef void *GLUTbitmapFont; + +#endif /* __glutbitmap_h__ */ diff --git a/sci-chemistry/molscript/metadata.xml b/sci-chemistry/molscript/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/molscript/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild b/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild new file mode 100644 index 000000000000..9440dce9820c --- /dev/null +++ b/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Display molecular 3D structures, such as proteins, in both schematic and detailed representations" +HOMEPAGE="http://www.avatar.se/molscript/" +SRC_URI="${P}.tar.gz" + +LICENSE="glut molscript" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + media-libs/freeglut + media-libs/gd:2= + media-libs/libpng:0= + virtual/jpeg:0= + || ( + x11-libs/libXmu + x11-libs/libXext + x11-libs/libX11 + )" +RDEPEND="${DEPEND}" + +RESTRICT="fetch" + +pkg_nofetch() { + elog "Please visit ${HOMEPAGE}" + elog "and get ${A}." + elog "Place it in ${DISTDIR}" +} + +src_prepare() { + epatch \ + "${FILESDIR}"/fix-makefile-shared.patch \ + "${FILESDIR}"/${PV}-ldflags.patch \ + "${FILESDIR}"/${PV}-prll.patch \ + "${FILESDIR}"/${PV}-libpng15.patch + + # Provide glutbitmap.h, because freeglut doesn't have it + cp "${FILESDIR}"/glutbitmap.h "${S}"/clib/ || die + + # Stop an incredibly hacky include + sed \ + -e 's:<../lib/glut/glutbitmap.h>:"glutbitmap.h":g' \ + -i "${S}"/clib/ogl_bitmap_character.c || die +} + +src_compile() { + # Prefix of programs it links with + export FREEWAREDIR="${EPREFIX}/usr" + + ln -s Makefile.complete Makefile || die + + emake \ + CC="$(tc-getCC)" \ + COPT="${CFLAGS}" +} + +src_install() { + dobin molscript molauto + dohtml "${S}"/doc/*.html +} diff --git a/sci-chemistry/molsketch/Manifest b/sci-chemistry/molsketch/Manifest new file mode 100644 index 000000000000..28ee7103bdb4 --- /dev/null +++ b/sci-chemistry/molsketch/Manifest @@ -0,0 +1,2 @@ +DIST Molsketch-0.2.0-Source.tar.gz 276809 SHA256 05e058bf71fc99e5dda56ef1779a82c8885b2001d1af5dce92d959bf56d8a5d0 SHA512 e72c3b2103d70964ada8bd57cc40c16ae30d0a7c2c45521ca3c7a4c4586270e06707e5d662983a2d0f214b16b12afbfa439b58568873537f70f8ac735aa28d26 WHIRLPOOL 1711ef1e45aa09eda1b6dfa44589b0f235ac533914b343b3802d44faae1f658b668e418014d81a5a797f06132c0c72085eb64b9e8c1f7e22650d4655783cca46 +DIST Molsketch-0.3.0-src.tar.gz 337388 SHA256 078b05bfd591930430bc1e5df802af27bdf40718b9218ba6435eadc209d4d1bc SHA512 405553c9d84f0ce9d70a237834f8273dd5010b95868434f9b1b9042fd626e2782c5d3da7d17d9485946210e48e86d0c2de8385d80667018dbc833c3928d076d4 WHIRLPOOL 659717039bf294072117a8e7dc1cb590c6804d3dbde625aa16451bfdb6371933c71f6241fee1e38cec696bdb89e19111c30cf6ed17810daf09b75272080fbb31 diff --git a/sci-chemistry/molsketch/files/molsketch-0.2.0-openbabel-231.patch b/sci-chemistry/molsketch/files/molsketch-0.2.0-openbabel-231.patch new file mode 100644 index 000000000000..41ddf01df5f8 --- /dev/null +++ b/sci-chemistry/molsketch/files/molsketch-0.2.0-openbabel-231.patch @@ -0,0 +1,54 @@ + CMakeLists.txt | 12 ++++++------ + libmolsketch/src/stereocenteritem.cpp | 2 +- + 2 files changed, 7 insertions(+), 7 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index a4b5d29..f472b40 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -12,10 +12,10 @@ set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake/modules) + # compiler issues are fixed and more warnings are issued. # + ########################################################### + if (CMAKE_COMPILER_IS_GNUCXX) +- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-long-long -std=iso9899:1990 -Wundef -Wcast-align") +- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Werror-implicit-function-declaration -Wchar-subscripts") +- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -W -Wpointer-arith -Wwrite-strings -Wformat-security") +- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wmissing-format-attribute -fno-common") ++# set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-long-long -std=iso9899:1990 -Wundef -Wcast-align") ++# set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Werror-implicit-function-declaration -Wchar-subscripts") ++# set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -W -Wpointer-arith -Wwrite-strings -Wformat-security") ++# set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wmissing-format-attribute -fno-common") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wnon-virtual-dtor -Wno-long-long -ansi -Wundef -Wcast-align") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wchar-subscripts -Wall -W -Wpointer-arith -Wformat-security") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-exceptions -fno-check-new -fno-common") +@@ -32,7 +32,7 @@ set(CPACK_SOURCE_IGNORE_FILES "/build;/.git") + include(CPack) + + # Unit testing, mainly useful for developers and so defaults to off +-option(ENABLE_TESTS "Enable unit testing" ON) ++option(ENABLE_TESTS "Enable unit testing" OFF) + if(ENABLE_TESTS) + set(QT_USE_QTTEST TRUE) + enable_testing() +@@ -48,7 +48,7 @@ configure_file("${CMAKE_MODULE_PATH}/cmake_uninstall.cmake.in" + add_custom_target(uninstall "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake") + + # Enabling debugging symbols +-set(CMAKE_BUILD_TYPE Debug) ++# set(CMAKE_BUILD_TYPE Debug) + + # Enabling shared libraries + set(BUILD_SHARED_LIBS OFF) +diff --git a/libmolsketch/src/stereocenteritem.cpp b/libmolsketch/src/stereocenteritem.cpp +index 44a8015..20f2a4a 100644 +--- a/libmolsketch/src/stereocenteritem.cpp ++++ b/libmolsketch/src/stereocenteritem.cpp +@@ -63,7 +63,7 @@ namespace Molsketch { + graphsym.GetSymmetry(symmetry_classes); + + //std::vector<unsigned long> atomIds = FindTetrahedralAtoms(obmol, symmetry_classes); +- std::vector<OpenBabel::StereogenicUnit> units = FindStereogenicUnits(obmol, symmetry_classes); ++ OpenBabel::OBStereoUnitSet units = FindStereogenicUnits(obmol, symmetry_classes); + + for (unsigned int i = 0; i < units.size(); ++i) { + if (units.at(i).type == OpenBabel::OBStereo::Tetrahedral) { diff --git a/sci-chemistry/molsketch/files/molsketch-0.3.0-_DEFAULT_SOURCE.patch b/sci-chemistry/molsketch/files/molsketch-0.3.0-_DEFAULT_SOURCE.patch new file mode 100644 index 000000000000..af3b5ceedac6 --- /dev/null +++ b/sci-chemistry/molsketch/files/molsketch-0.3.0-_DEFAULT_SOURCE.patch @@ -0,0 +1,16 @@ + CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index e3cd0fe..64c18a2 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -19,7 +19,7 @@ if (CMAKE_COMPILER_IS_GNUCXX) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wnon-virtual-dtor -Wno-long-long -ansi -Wundef -Wcast-align") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wchar-subscripts -Wall -W -Wpointer-arith -Wformat-security") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-exceptions -fno-check-new -fno-common") +- add_definitions(-D_BSD_SOURCE) ++ add_definitions(-D_DEFAULT_SOURCE) + endif (CMAKE_COMPILER_IS_GNUCXX) + + # Enable CPack diff --git a/sci-chemistry/molsketch/files/molsketch-0.3.0-desktop.patch b/sci-chemistry/molsketch/files/molsketch-0.3.0-desktop.patch new file mode 100644 index 000000000000..fd44e88c7870 --- /dev/null +++ b/sci-chemistry/molsketch/files/molsketch-0.3.0-desktop.patch @@ -0,0 +1,19 @@ + molsketch/src/molsketch.desktop | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/molsketch/src/molsketch.desktop b/molsketch/src/molsketch.desktop +index a4a5418..4e0a2ef 100644 +--- a/molsketch/src/molsketch.desktop ++++ b/molsketch/src/molsketch.desktop +@@ -5,9 +5,9 @@ Type=Application + Name=molsKetch + TryExec=molsketch + Exec=molsketch +-Icon=molsketch.png ++Icon=molsketch + DocPath=molsketch/index.html +-MimeType=chemical/x-cml ++MimeType=chemical/x-cml; + Terminal=false + Categories=Qt;Education;Science; + GenericName=2D molecular structures editor diff --git a/sci-chemistry/molsketch/files/molsketch-0.3.0-no-quotes.patch b/sci-chemistry/molsketch/files/molsketch-0.3.0-no-quotes.patch new file mode 100644 index 000000000000..db7be800e385 --- /dev/null +++ b/sci-chemistry/molsketch/files/molsketch-0.3.0-no-quotes.patch @@ -0,0 +1,16 @@ + CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 64c18a2..75c2fb7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -97,7 +97,7 @@ endif(Qt5Core_FOUND AND Qt5Widgets_FOUND AND Qt5Gui_FOUND AND Qt5PrintSupport_FO + if(FORCEQt4) + add_definitions(-DQTVERSIONSUFFIX="") + else(FORCEQt4) +- add_definitions(-DQTVERSIONSUFFIX="\\\"-qt5\\\"") ++ add_definitions(-DQTVERSIONSUFFIX="-qt5") + endif(FORCEQt4) + + # and OpenBabel2 diff --git a/sci-chemistry/molsketch/metadata.xml b/sci-chemistry/molsketch/metadata.xml new file mode 100644 index 000000000000..58bc5230b1ab --- /dev/null +++ b/sci-chemistry/molsketch/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription lang="en"> + Molsketch is a 2D molecular editing tool. Its goal is to help you draw + molecules quick and easily. Of course you're creation can be exported + afterwards in high quality in a number of vector and bitmap formats. +</longdescription> + <upstream> + <remote-id type="sourceforge">molsketch</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/molsketch/molsketch-0.2.0-r1.ebuild b/sci-chemistry/molsketch/molsketch-0.2.0-r1.ebuild new file mode 100644 index 000000000000..f3184d8d27fd --- /dev/null +++ b/sci-chemistry/molsketch/molsketch-0.2.0-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils multilib + +MY_P=${P/m/M}-Source + +DESCRIPTION="A drawing tool for 2D molecular structures" +HOMEPAGE="http://molsketch.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + >=sci-chemistry/openbabel-2.2 + dev-qt/qtcore:4 + dev-qt/qtgui:4 + dev-qt/qttest:4 + >=dev-qt/qthelp-4.7.0:4[compat]" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${MY_P} + +PATCHES=( + "${FILESDIR}"/${P}-openbabel-231.patch + ) + +src_prepare() { + sed -e "/LIBRARY DESTINATION/ s/lib/$(get_libdir)/g" \ + -i libmolsketch/src/CMakeLists.txt || die #351246 + sed -e "s:doc/molsketch:doc/${PF}:g" \ + -i molsketch/src/{CMakeLists.txt,mainwindow.cpp} || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DOPENBABEL2_INCLUDE_DIR="${EPREFIX}/usr/include/openbabel-2.0" + -DCMAKE_DISABLE_FIND_PACKAGE_KDE4=ON + ) + cmake-utils_src_configure +} diff --git a/sci-chemistry/molsketch/molsketch-0.3.0.ebuild b/sci-chemistry/molsketch/molsketch-0.3.0.ebuild new file mode 100644 index 000000000000..3fec18fd5362 --- /dev/null +++ b/sci-chemistry/molsketch/molsketch-0.3.0.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +CMAKE_MAKEFILE_GENERATOR=ninja + +inherit cmake-utils multilib qmake-utils + +MY_P=${P/m/M}-src + +DESCRIPTION="A drawing tool for 2D molecular structures" +HOMEPAGE="http://molsketch.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/${PN}/Molsketch/Lithium%20${PV}/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +DEPEND=" + >=sci-chemistry/openbabel-2.2 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtprintsupport:5 + dev-qt/qtsvg:5 + dev-qt/qtwidgets:5 + " +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${MY_P%%-src} + +PATCHES=( + "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch + "${FILESDIR}"/${P}-desktop.patch + "${FILESDIR}"/${P}-no-quotes.patch + ) + +src_prepare() { + sed -e "/LIBRARY DESTINATION/ s/lib/$(get_libdir)/g" \ + -i {obabeliface,libmolsketch/src}/CMakeLists.txt || die #351246 + sed -e "s:doc/molsketch:doc/${PF}:g" \ + -i molsketch/src/{CMakeLists.txt,mainwindow.cpp} || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DOPENBABEL2_INCLUDE_DIR="${EPREFIX}/usr/include/openbabel-2.0" + -DCMAKE_DISABLE_FIND_PACKAGE_KDE4=ON + -DENABLE_TESTS=$(usex test "ON" "OFF") + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + dosym ${PN}-qt5 /usr/bin/${PN} +} diff --git a/sci-chemistry/mongochem/Manifest b/sci-chemistry/mongochem/Manifest new file mode 100644 index 000000000000..480c14f5f8a7 --- /dev/null +++ b/sci-chemistry/mongochem/Manifest @@ -0,0 +1 @@ +DIST mongochem-0.7.0.tar.gz 448002 SHA256 a93f53e8d945f2e3b97efac8187cfaeae0a7e491265cd65d66d25e34577cf883 SHA512 076f79c9dbed372cc760c972d5529fc3a10ea23ba2a58bf1034b736c5394a9283223562c0d6d14a135cdf87786a222991ca613765484d5a36c31f65c2ccccb05 WHIRLPOOL 4b044e00e44b1333e3faec04e15eaf46e7b17eecd4c155099fc5f06dc9c62bde70adc8bb8a9793df9b305efc89f5e44bdea77eeaac1da3554c002cba117fe8c1 diff --git a/sci-chemistry/mongochem/metadata.xml b/sci-chemistry/mongochem/metadata.xml new file mode 100644 index 000000000000..411a151f03ae --- /dev/null +++ b/sci-chemistry/mongochem/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <upstream> + <remote-id type="github">OpenChemistry/mongochem</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/mongochem/mongochem-0.7.0.ebuild b/sci-chemistry/mongochem/mongochem-0.7.0.ebuild new file mode 100644 index 000000000000..5e6b2b642692 --- /dev/null +++ b/sci-chemistry/mongochem/mongochem-0.7.0.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils vcs-snapshot + +DESCRIPTION="Application for managing large collections of chemical data" +HOMEPAGE="http://www.openchemistry.org/" +#SRC_URI="http://openchemistry.org/files/v0.5/${P}.tar.gz" +SRC_URI="https://github.com/OpenChemistry/mongochem/archive/df36ebce92024dd4fd1c70eb37eb84e4c51120ff.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-db/mongodb[sharedclient] + dev-libs/boost[threads] + sci-libs/avogadrolibs[qt4] + sci-libs/chemkit + sci-libs/vtk[qt4,rendering] + sci-chemistry/molequeue +" +DEPEND="${RDEPEND}" diff --git a/sci-chemistry/mopac7/Manifest b/sci-chemistry/mopac7/Manifest new file mode 100644 index 000000000000..d352d6ff544a --- /dev/null +++ b/sci-chemistry/mopac7/Manifest @@ -0,0 +1,3 @@ +DIST dcart.f 11044 SHA256 cdc4082b6b3811eca25eaf674e9345fcd37f58dfbdca3c5d72e9c4e88c47dec9 SHA512 788a184fd8419ff742e49c1a652d5ea093f9114dbe4f272665b8fb9eeac2afb7f7042628c288f2b81d0f54d8a7ef2f400490cd3aff39dda59a6d70a0deab5b80 WHIRLPOOL 399d7cf92d6fd27bb785c3f81eb24ec9615144b3e8605779d1f1f645ea16644a858428d8dfce44c102a495f984e1ae158fe7743ad0bef2b957ea10adc94ccb73 +DIST gmxmop.f 38956 SHA256 918bfac91b1dab65f7a8f759c3fd49e40be19bbddb6869d95f8e345830b93b67 SHA512 38bb2e5749c4d3c8c24f15682f72e40cb4edb6517c7916cecee1d21675b1870c0fe331ba2ec40312408dec473141e7742d1e155d4b64f1c2a25bfa4e11885194 WHIRLPOOL a0adaf3df1167d9675197f71ae2cd5a9a583eef4523b9a074d39291032dbfe0428349ebf78fabd88ed7e1deb5af093be319c9f19cab019deb52f0fb6e3924998 +DIST mopac7-1.15.tar.gz 764547 SHA256 6d7ac5d78522db70f7794fd816cea32829cfa9e93774202fe80ba5a54375fbaa SHA512 e0ccd643caa6dbd7e156867530d79e50e10243f5e3b5f8bc57781e68e1daf26f2a0e6987fff00afe07eb0fcb98cbd9f01e4cfa5d20acc0d8ab3cca632968636e WHIRLPOOL fe4d71e3900b8fe09697275c25bc239e8f94e97d2a570bf6df03c5bd59a3b2ab80bc7f255f739f09c0fc54037e9739b38cec205590ad3cb31ad58fe2067562d2 diff --git a/sci-chemistry/mopac7/files/Makefile b/sci-chemistry/mopac7/files/Makefile new file mode 100644 index 000000000000..50370b3c2784 --- /dev/null +++ b/sci-chemistry/mopac7/files/Makefile @@ -0,0 +1,23 @@ +VERSION = GENTOOVERSION +MAJOR = 1 + +LIBS = -lgfortran -lf2c + +objects := $(patsubst %.f,%.o,$(wildcard *.f)) + +all: libgmxmopac7 + +clean: + rm -f moldat.*f deriv.* mopac7*.* compfg.* dcart.* + +%.o: %.f + $(FC) $(FFLAGS) -fPIC -c $< + +libgmxmopac7: $(objects) + $(FC) -shared $(LDFLAGS) -Wl,-soname,libgmxmopac7.so.$(MAJOR) -o $@.so.$(VERSION) $^ $(LIBS) + ln -sf $@.so.$(VERSION) libgmxmopac7.so + +static: $(objects) + ar rcv libgmxmopac7.a *.o + ranlib libgmxmopac7.a + diff --git a/sci-chemistry/mopac7/metadata.xml b/sci-chemistry/mopac7/metadata.xml new file mode 100644 index 000000000000..839734dd5d8b --- /dev/null +++ b/sci-chemistry/mopac7/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <use> + <flag name="gmxmopac7">Add support library for gromacs</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild new file mode 100644 index 000000000000..ce0c326678ec --- /dev/null +++ b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit autotools fortran-2 flag-o-matic toolchain-funcs + +DESCRIPTION="Autotooled, updated version of a powerful, fast semi-empirical package" +HOMEPAGE="http://sourceforge.net/projects/mopac7/" +SRC_URI=" + http://www.bioinformatics.org/ghemical/download/current/${P}.tar.gz + http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/dcart.f + http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/gmxmop.f" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux" +IUSE="gmxmopac7 static-libs" + +DEPEND="dev-libs/libf2c" +RDEPEND="${DEPEND}" + +src_prepare() { + # Install the executable + sed -i \ + -e "s:noinst_PROGRAMS = mopac7:bin_PROGRAMS = mopac7:g" \ + fortran/Makefile.am \ + || die "sed failed: install mopac7" + # Install the script to run the executable + sed -i \ + -e "s:EXTRA_DIST = autogen.sh run_mopac7:bin_SCRIPTS = run_mopac7:g" \ + Makefile.am \ + || die "sed failed: install run_mopac7" + + eautoreconf + append-fflags -std=legacy -fno-automatic +} + +src_compile() { + emake + if use gmxmopac7; then + einfo "Making mopac7 lib for gromacs" + mkdir "${S}"/fortran/libgmxmopac7 && cd "${S}"/fortran/libgmxmopac7 + cp -f ../SIZES ../*.f "${FILESDIR}"/Makefile . || die + emake clean + cp -f "${DISTDIR}"/gmxmop.f "${DISTDIR}"/dcart.f . || die + sed "s:GENTOOVERSION:${PV}:g" -i Makefile + emake FC=$(tc-getFC) + use static-libs && emake static + fi +} + +src_install() { + # A correct fix would have a run_mopac7.in with @bindir@ that gets + # replaced by configure, and run_mopac7 added to AC_OUTPUT in configure.ac + sed -i "s:./fortran/mopac7:mopac7:g" run_mopac7 || die + + default + + if use gmxmopac7; then + cd "${S}"/fortran/libgmxmopac7 + dolib.so libgmxmopac7.so* + use static-libs && dolib.a libgmxmopac7.a + fi +} diff --git a/sci-chemistry/mopac7/mopac7-1.15.ebuild b/sci-chemistry/mopac7/mopac7-1.15.ebuild new file mode 100644 index 000000000000..167561f7ed96 --- /dev/null +++ b/sci-chemistry/mopac7/mopac7-1.15.ebuild @@ -0,0 +1,75 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools fortran-2 toolchain-funcs + +DESCRIPTION="Autotooled, updated version of a powerful, fast semi-empirical package" +HOMEPAGE="http://sourceforge.net/projects/mopac7/" +SRC_URI=" + http://www.bioinformatics.org/ghemical/download/current/${P}.tar.gz + http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/dcart.f + http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/gmxmop.f" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux" +IUSE="gmxmopac7 static-libs" + +DEPEND="dev-libs/libf2c" +RDEPEND="${DEPEND}" + +src_prepare() { + # Install the executable + sed -i \ + -e "s:noinst_PROGRAMS = mopac7:bin_PROGRAMS = mopac7:g" \ + fortran/Makefile.am \ + || die "sed failed: install mopac7" + # Install the script to run the executable + sed -i \ + -e "s:EXTRA_DIST = autogen.sh run_mopac7:bin_SCRIPTS = run_mopac7:g" \ + Makefile.am \ + || die "sed failed: install run_mopac7" + + eautoreconf +} + +src_configure() { + #set -std=legacy -fno-automatic according to + #http://www.bioinformatics.org/pipermail/ghemical-devel/2008-August/000763.html + FFLAGS="${FFLAGS} -std=legacy -fno-automatic" econf +} + +src_compile() { + emake + if use gmxmopac7; then + einfo "Making mopac7 lib for gromacs" + mkdir "${S}"/fortran/libgmxmopac7 && cd "${S}"/fortran/libgmxmopac7 + cp -f ../SIZES ../*.f "${FILESDIR}"/Makefile . || die + emake clean + cp -f "${DISTDIR}"/gmxmop.f "${DISTDIR}"/dcart.f . || die + sed "s:GENTOOVERSION:${PV}:g" -i Makefile + emake FC=$(tc-getFC) + if use static-libs; then + emake static + fi + fi +} + +src_install() { + # A correct fix would have a run_mopac7.in with @bindir@ that gets + # replaced by configure, and run_mopac7 added to AC_OUTPUT in configure.ac + sed -i "s:./fortran/mopac7:mopac7:g" run_mopac7 + + make DESTDIR="${D}" install || die + dodoc AUTHORS README ChangeLog + if use gmxmopac7; then + cd "${S}"/fortran/libgmxmopac7 + dolib.so libgmxmopac7.so* + if use static-libs; then + dolib.a libgmxmopac7.a + fi + fi +} diff --git a/sci-chemistry/mosflm/Manifest b/sci-chemistry/mosflm/Manifest new file mode 100644 index 000000000000..80df134c833e --- /dev/null +++ b/sci-chemistry/mosflm/Manifest @@ -0,0 +1 @@ +DIST mosflm709.tgz 3324010 SHA256 d22b05211f274b50c284d4c14fcb456c52b13344e2a48d5f45855fe87f82f6d1 SHA512 aa85f8459f280e0e1d2d54041029ef072346ecef3ffcc7724eb524469e1b77dfbd95aac8b46f2b9682d605a4e5931d9c13f1162d5f3bcff08644db7e79a6316c WHIRLPOOL b3a82858a8d2a3162bc0fcfb3bf7fb7b01cfc6bca80b34643e7c6caae54b1ef1e2b24a58617ffe2b0423ca6626d51e31b49c0dba6a82ed5c61fa10d044e0d3b8 diff --git a/sci-chemistry/mosflm/files/7.0.6-Makefile.patch b/sci-chemistry/mosflm/files/7.0.6-Makefile.patch new file mode 100644 index 000000000000..a35232f6e8c0 --- /dev/null +++ b/sci-chemistry/mosflm/files/7.0.6-Makefile.patch @@ -0,0 +1,13 @@ +--- Makefile 2008-10-17 16:15:30.000000000 +0200 ++++ Makefile.new 2009-02-20 21:52:34.000000000 +0100 +@@ -22,7 +22,7 @@ + CBFLIBS = cbf/lib/libcbf.a + JPGLIBS = jpg/libjpeg.a + +-all: $(DPSLIBS) $(CBFLIBS) $(JPGLIBS) +- cd mosflm ; make ++all: dpslibs cbflibs ++ +make -C mosflm + + ########################################################################## + diff --git a/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch b/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch new file mode 100644 index 000000000000..da393eb93fe6 --- /dev/null +++ b/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch @@ -0,0 +1,36 @@ +diff --git a/mosflm/bravais_fortran.c b/mosflm/bravais_fortran.c +index 3d68cad..800bd0e 100644 +--- a/mosflm/bravais_fortran.c ++++ b/mosflm/bravais_fortran.c +@@ -2,6 +2,7 @@ + #include <stdlib.h> + #include <math.h> + #include "../util/util.h" ++#include "../util/bravais.h" + + /* bravais_fortran_(): This routine converts array from FORTRAN program + to structure for call to bravais +diff --git a/mosflm/chelp.c b/mosflm/chelp.c +index b2aaefc..fa44ab0 100644 +--- a/mosflm/chelp.c ++++ b/mosflm/chelp.c +@@ -5,6 +5,7 @@ + /* modified for Linux by Joachim Meyer jmeyer@embl-heidelberg.de 1998.05.19 */ + + #include "chelp.h" ++#include <stdio.h> + + #if CALL_LIKE_HPUX + void chelp () +diff --git a/mosflm/pck.c b/mosflm/pck.c +index ec094fc..288671d 100644 +--- a/mosflm/pck.c ++++ b/mosflm/pck.c +@@ -17,6 +17,7 @@ + #include <math.h> + #include <ctype.h> + #include <string.h> ++#include <unistd.h> + + #define BYTE char + #define WORD short int diff --git a/sci-chemistry/mosflm/files/7.0.6-parallel.patch b/sci-chemistry/mosflm/files/7.0.6-parallel.patch new file mode 100644 index 000000000000..f735c7ce5cf7 --- /dev/null +++ b/sci-chemistry/mosflm/files/7.0.6-parallel.patch @@ -0,0 +1,28 @@ +--- cbf/Makefile 2009-08-31 09:35:06.000000000 +0200 ++++ cbf/Makefile.new 2009-08-31 10:44:46.000000000 +0200 +@@ -362,6 +362,8 @@ + $(EXAMPLES)/img.h \ + $(INCLUDE)/md5.h + ++OBJ = $(subst .c,.o,$(SOURCE)) ++ + # + # Compile the library and examples + # +@@ -379,11 +381,14 @@ + $(LIB): + mkdir $(LIB) + ++ ++.c.o: $(SOURCE) $(HEADERS) ++ $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $< ++ + # + # CBF library + # +-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) +- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) ++$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP) + $(AR) cr $@ *.o + rm *.o + if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi diff --git a/sci-chemistry/mosflm/files/7.0.7-parallel.patch b/sci-chemistry/mosflm/files/7.0.7-parallel.patch new file mode 100644 index 000000000000..df0a8b63273a --- /dev/null +++ b/sci-chemistry/mosflm/files/7.0.7-parallel.patch @@ -0,0 +1,92 @@ + Makefile | 21 ++++++++++----------- + cbf/Makefile | 9 +++++++-- + 2 files changed, 17 insertions(+), 13 deletions(-) + +diff --git a/Makefile b/Makefile +index 37f4c7e..51d4164 100644 +--- a/Makefile ++++ b/Makefile +@@ -22,8 +22,8 @@ DPSLIBS = lib/DPSLIB.a + CBFLIBS = cbf/lib/libcbf.a + JPGLIBS = jpg/libjpeg.a + +-all: $(DPSLIBS) $(CBFLIBS) $(JPGLIBS) +- cd mosflm ; make ++all: $(DPSLIBS) ++ $(MAKE) -C mosflm + + ########################################################################## + # # +@@ -47,22 +47,21 @@ dpslibs: + + cbflibs: + rm -f `find ./cbf -name "*.a" -print` +- cd cbf ; make all ; if [ -f $(RANLIB) ]; \ +- then $(RANLIB) lib/libcbf.a; fi ++ $(MAKE) -C cbf all + + jpglibs: +- cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; make libjpeg.a ++ cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; $(MAKE) libjpeg.a + + ${DPSLIBS}: +- make dpslibs ++ $(MAKE) dpslibs + + ${CBFLIBS}: +- make cbflibs ++ $(MAKE) cbflibs + + ${JPGLIBS}: +- make jpglibs ++ $(MAKE) jpglibs + +-libs: ${DPSLIBS} ${CBFLIBS} ${JPGLIBS} ++libs: ${DPSLIBS} ${CBFLIBS} + @echo "****************************************************************" + @echo " Making libraries for system ${HOSTTYPE}" + @echo "****************************************************************" +@@ -71,11 +70,11 @@ ipmosflm: libs + @echo "****************************************************************" + @echo " Making IPMOSFLM for system ${HOSTTYPE}" + @echo "****************************************************************" +- cd mosflm ; make ipmosflm ++ $(MAKE) -C mosflm ipmosflm + + force: + rm bin/ipmosflm +- make ipmosflm ++ $(MAKE) ipmosflm + + install: + @echo "the executable is in ${MOSHOME}/bin/ipmosflm" +diff --git a/cbf/Makefile b/cbf/Makefile +index e61497c..c3c94ac 100644 +--- a/cbf/Makefile ++++ b/cbf/Makefile +@@ -362,6 +362,8 @@ HEADERS = $(INCLUDE)/cbf.h \ + $(EXAMPLES)/img.h \ + $(INCLUDE)/md5.h + ++OBJ = $(subst .c,.o,$(SOURCE)) ++ + # + # Compile the library and examples + # +@@ -379,11 +381,14 @@ $(INSTALLDIR): + $(LIB): + mkdir $(LIB) + ++ ++.c.o: $(SOURCE) $(HEADERS) ++ $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $< ++ + # + # CBF library + # +-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) +- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) ++$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP) + $(AR) cr $@ *.o + rm *.o + if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi diff --git a/sci-chemistry/mosflm/files/7.0.9-parallel.patch b/sci-chemistry/mosflm/files/7.0.9-parallel.patch new file mode 100644 index 000000000000..38c6fc45a5c0 --- /dev/null +++ b/sci-chemistry/mosflm/files/7.0.9-parallel.patch @@ -0,0 +1,92 @@ + Makefile | 21 ++++++++++----------- + cbf/Makefile | 9 +++++++-- + 2 files changed, 17 insertions(+), 13 deletions(-) + +diff --git a/Makefile b/Makefile +index 3d2f543..2219d8d 100644 +--- a/Makefile ++++ b/Makefile +@@ -22,8 +22,8 @@ DPSLIBS = lib/DPSLIB.a + CBFLIBS = cbf/lib/libcbf.a + JPGLIBS = jpg/libjpeg.a + +-all: $(DPSLIBS) $(CBFLIBS) $(JPGLIBS) +- cd mosflm ; make ++all: $(DPSLIBS) ++ $(MAKE) -C mosflm + + dpslibs: + @-find . -name "*a" -delete +@@ -32,22 +32,21 @@ dpslibs: + + cbflibs: + @-find ./cbf -name "*.a" -delete +- cd cbf ; make all ; if [ -f $(RANLIB) ]; \ +- then $(RANLIB) lib/libcbf.a; fi ++ $(MAKE) -C cbf all + + jpglibs: +- cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; make libjpeg.a ++ cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; $(MAKE) libjpeg.a + + ${DPSLIBS}: +- make dpslibs ++ $(MAKE) dpslibs + + ${CBFLIBS}: +- make cbflibs ++ $(MAKE) cbflibs + + ${JPGLIBS}: +- make jpglibs ++ $(MAKE) jpglibs + +-libs: ${DPSLIBS} ${CBFLIBS} ${JPGLIBS} ++libs: ${DPSLIBS} ${CBFLIBS} + @echo "****************************************************************" + @echo " Making libraries for system ${HOSTTYPE}" + @echo "****************************************************************" +@@ -56,11 +55,11 @@ ipmosflm: libs + @echo "****************************************************************" + @echo " Making IPMOSFLM for system ${HOSTTYPE}" + @echo "****************************************************************" +- cd mosflm ; make ipmosflm ++ $(MAKE) -C mosflm ipmosflm + + force: + @-rm -f bin/ipmosflm +- make ipmosflm ++ $(MAKE) ipmosflm + + install: + @echo "the executable is in ${MOSHOME}/bin/ipmosflm" +diff --git a/cbf/Makefile b/cbf/Makefile +index e61497c..c3c94ac 100644 +--- a/cbf/Makefile ++++ b/cbf/Makefile +@@ -362,6 +362,8 @@ HEADERS = $(INCLUDE)/cbf.h \ + $(EXAMPLES)/img.h \ + $(INCLUDE)/md5.h + ++OBJ = $(subst .c,.o,$(SOURCE)) ++ + # + # Compile the library and examples + # +@@ -379,11 +381,14 @@ $(INSTALLDIR): + $(LIB): + mkdir $(LIB) + ++ ++.c.o: $(SOURCE) $(HEADERS) ++ $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $< ++ + # + # CBF library + # +-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) +- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) ++$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP) + $(AR) cr $@ *.o + rm *.o + if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch new file mode 100644 index 000000000000..90158eb458d5 --- /dev/null +++ b/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch @@ -0,0 +1,16 @@ + mosflm/pilatus_c.c | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c +index 1eaae26..cce5a02 100644 +--- a/mosflm/pilatus_c.c ++++ b/mosflm/pilatus_c.c +@@ -34,7 +34,7 @@ delete them later */ + int cbf_int[16]; + long cbf_int4[16]; + double cbf_double[16]; +- char cbf_char[16][24]; ++ char cbf_char[16][32]; + /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll + delete them later */ + int id, index, iindex; diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch new file mode 100644 index 000000000000..32f251f8e00c --- /dev/null +++ b/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch @@ -0,0 +1,29 @@ + mosflm/mosflm_jpeg.c | 1 + + src/dps/index/ind_gen_direct.c | 2 ++ + 2 files changed, 3 insertions(+), 0 deletions(-) + +diff --git a/mosflm/mosflm_jpeg.c b/mosflm/mosflm_jpeg.c +index 2b32b2e..54684d0 100644 +--- a/mosflm/mosflm_jpeg.c ++++ b/mosflm/mosflm_jpeg.c +@@ -76,6 +76,7 @@ G. Winter + #include <fcntl.h> + #include <stdio.h> + #include <stdlib.h> ++#include <string.h> + #if (defined _MSC_VER) + /* no need to do this for __MINGW_ (Mingw gcc) this is just about unique!*/ + #define S_IRWXU S_IREAD|S_IWRITE|S_IEXEC +diff --git a/src/dps/index/ind_gen_direct.c b/src/dps/index/ind_gen_direct.c +index 6e143df..2eea61b 100644 +--- a/src/dps/index/ind_gen_direct.c ++++ b/src/dps/index/ind_gen_direct.c +@@ -41,6 +41,8 @@ + /* #include <malloc.h> */ + #include "util.h" + #include "ind_gen_direct.h" ++#include "ind_help.h" ++#include "ind_sort_merge.h" + /* char *strcat( char *, const char *); */ + + diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch new file mode 100644 index 000000000000..bb4a16bf30fc --- /dev/null +++ b/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch @@ -0,0 +1,16 @@ + mosflm/pilatus_c.c | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c +index 4a85b26..9893e0c 100644 +--- a/mosflm/pilatus_c.c ++++ b/mosflm/pilatus_c.c +@@ -34,7 +34,7 @@ delete them later */ + int cbf_int[16] = {0}; + long cbf_int4[16] = {0}; + double cbf_double[16] = {0}; +- char cbf_char[16][24] = {' '}; ++ char cbf_char[16][32] = {' '}; + /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll + delete them later */ + int id, index, iindex; diff --git a/sci-chemistry/mosflm/metadata.xml b/sci-chemistry/mosflm/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/mosflm/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/mosflm/mosflm-7.0.9.ebuild b/sci-chemistry/mosflm/mosflm-7.0.9.ebuild new file mode 100644 index 000000000000..3aa74ced3d94 --- /dev/null +++ b/sci-chemistry/mosflm/mosflm-7.0.9.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs versionator + +MY_PV="$(delete_all_version_separators)" +MY_P="${PN}${MY_PV}" + +DESCRIPTION="A program for integrating single crystal diffraction data from area detectors" +HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/mosflm/" +SRC_URI="${HOMEPAGE}ver${MY_PV}/build-it-yourself/${MY_P}.tgz" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + app-shells/tcsh + sci-libs/cbflib + sci-libs/ccp4-libs + sys-libs/ncurses + virtual/jpeg:0= + x11-libs/libxdl_view" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed \ + -e "s:../cbf/lib/libcbf.a:-lcbf -limg:g" \ + -e "s:../jpg/libjpeg.a:-ljpeg:g" \ + -i ${PN}/Makefile || die + + sed \ + -e '/jinclude.h/d' \ + -i mosflm/mosflm_jpeg.c || die + + cp DATETIME.C mosflm/datetime.c || die + + epatch \ + "${FILESDIR}"/${PV}-parallel.patch \ + "${FILESDIR}"/7.0.6-impl-dec.patch \ + "${FILESDIR}"/${P}-buffer-overflow.patch \ + "${FILESDIR}"/${PN}-7.0.7-impl-dec.patch + + rm -rf test.f {cbf,jpg}/*.{h,c} || die +} + +src_compile() { + emake \ + MOSHOME="${S}" \ + DPS="${S}" \ + FC=$(tc-getFC) \ + FLINK=$(tc-getFC) \ + CC=$(tc-getCC) \ + AR_FLAGS=vru \ + MOSLIBS="-lccp4f -lccp4c -lxdl_view $($(tc-getPKG_CONFIG) --libs ncurses) -lXt -lmmdb -lccif -lstdc++" \ + MCFLAGS="-O0 -fno-second-underscore" \ + MOSFLAGS="${FFLAGS} -fno-second-underscore" \ + FFLAGS="${FFLAGS} -fno-second-underscore" \ + CFLAGS="${CFLAGS}" \ + MOSCFLAGS="${CFLAGS}" \ + LFLAGS="${LDFLAGS}" +} + +src_install() { + exeinto /usr/libexec/ccp4/bin/ + doexe bin/ipmosflm + dosym ../libexec/ccp4/bin/ip${PN} /usr/bin/ip${PN} +} diff --git a/sci-chemistry/mpqc/Manifest b/sci-chemistry/mpqc/Manifest new file mode 100644 index 000000000000..4f7c28d17b0f --- /dev/null +++ b/sci-chemistry/mpqc/Manifest @@ -0,0 +1 @@ +DIST mpqc-2.3.1.tar.bz2 2521392 SHA256 18f162ca9cb8b3b05372b0ec3d02b4b8a4a7aabfc7b2abead350ddef8f048ecc SHA512 34f24f72c6c0024e72d47c7fd17927ca2a88020b30d22a791954fbc933f67ed6dd6741ee8a80ddd4fdb007f1a357b5f5ea7fc284cab85474bf60e9f29aaaa747 WHIRLPOOL 504e5be36673b85494866b8a09588964dd9b352208c4d08a1365cbc06b39dfe91dc6050a0e16cbd713b43b3e92d86cbe40f53a44a644f224e84340dd065e54ab diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-as-needed.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-as-needed.patch new file mode 100644 index 000000000000..a917c0aaff70 --- /dev/null +++ b/sci-chemistry/mpqc/files/mpqc-2.3.1-as-needed.patch @@ -0,0 +1,163 @@ +--- mpqc-2.3.1.orig/src/lib/chemistry/molecule/Makefile 2005-05-26 08:00:29.000000000 +0200 ++++ mpqc-2.3.1/src/lib/chemistry/molecule/Makefile 2010-02-13 14:28:46.514285918 +0100 +@@ -66,6 +66,12 @@ + interface:: $(DEPENDINCLUDE) + + LIBS = $(shell $(LISTLIBS) $(INCLUDE) $(SRCDIR)/LIBS.h) ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCcontainer.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCclass.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCkeyval.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCoptimize.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCscmat.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCsymmetry.la + + LD = $(CXX) + +--- mpqc-2.3.1.orig/src/lib/chemistry/qc/wfn/Makefile 2004-06-12 06:50:35.000000000 +0200 ++++ mpqc-2.3.1/src/lib/chemistry/qc/wfn/Makefile 2010-02-13 14:20:06.911896080 +0100 +@@ -48,6 +48,12 @@ + + LIBS = $(shell $(LISTLIBS) $(INCLUDE) $(SRCDIR)/../dft/LIBS.h) + ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCisosurf.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCsolvent.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCbasis.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCdft.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCintv3.la ++ + wfntest:: wfntest.$(OBJSUF) $(LIBS) + $(LTLINK) $(CXX) $(LDFLAGS) -o wfntest $^ $(SYSLIBS) $(LTLINKBINOPTS) + +--- mpqc-2.3.1.orig/src/lib/chemistry/qc/intv3/Makefile 2002-04-04 01:08:04.000000000 +0200 ++++ mpqc-2.3.1/src/lib/chemistry/qc/intv3/Makefile 2010-02-13 14:04:15.393432311 +0100 +@@ -52,6 +52,8 @@ + LIBOBJ = $(LIBSRC:%.c=%.$(OBJSUF)) + LIBOBJ := $(LIBOBJ:%.cc=%.$(OBJSUF)) + ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCoint3.la ++ + DISTFILES = $(TESTCSRC) $(INC) atoms.sgen Makefile LIBS.h + + DEPENDINCLUDE = $(INC) $(GENINC) $(SGENINC) +--- mpqc-2.3.1.orig/src/lib/chemistry/qc/mbpt/Makefile 2005-07-07 17:54:05.000000000 +0200 ++++ mpqc-2.3.1/src/lib/chemistry/qc/mbpt/Makefile 2010-02-13 14:12:38.975370147 +0100 +@@ -44,6 +44,7 @@ + CSRCS = bzerofast.c + + LIBOBJ= $(CXXSRCS:%.cc=%.$(OBJSUF)) $(CSRCS:%.c=%.$(OBJSUF)) ++LIBADD= $(SRCDIR)/$(TOPDIR)/lib/libSCsymmetry.la + + default:: $(DEPENDINCLUDE) + +--- mpqc-2.3.1.orig/src/lib/chemistry/qc/basis/Makefile 2004-02-11 01:24:43.000000000 +0100 ++++ mpqc-2.3.1/src/lib/chemistry/qc/basis/Makefile 2010-02-13 14:04:15.395432868 +0100 +@@ -59,6 +59,7 @@ + DISTFILES = $(CXXSRC) $(INC) Makefile $(TESTSRC) $(TESTFILES) + + LIBOBJ= $(CXXSRC:%.cc=%.$(OBJSUF)) ++LIBADD = $(SYSLIBS) + + default:: $(DEPENDINCLUDE) + +--- mpqc-2.3.1.orig/src/lib/math/scmat/Makefile 2003-09-16 17:07:03.000000000 +0200 ++++ mpqc-2.3.1/src/lib/math/scmat/Makefile 2010-02-13 14:27:36.028370446 +0100 +@@ -75,6 +75,8 @@ + DISTFILES = $(CXXSRC) $(INC) scmat.h $(WEBSRC) Makefile LIBS.h \ + $(TESTSRC) $(TESTFILES) + ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCgroup.la $(SYSLIBS) ++ + LIBS = $(shell $(LISTLIBS) $(INCLUDE) $(SRCDIR)/LIBS.h) + + matrixtest: +--- mpqc-2.3.1.orig/src/lib/util/class/Makefile 2005-05-26 08:00:49.000000000 +0200 ++++ mpqc-2.3.1/src/lib/util/class/Makefile 2010-02-13 14:04:15.396433004 +0100 +@@ -41,6 +41,7 @@ + + BIN_OR_LIB = LIB + TARGET_TO_MAKE = libSCclass ++LIBADD = $(SYSLIBS) + + TESTCXXSRC = classtest.cc scextest.cc + DISTFILES = $(CXXSRC) $(INC) Makefile LIBS.h $(TESTCXXSRC) +--- mpqc-2.3.1.orig/src/lib/util/state/Makefile 2005-05-26 08:00:51.000000000 +0200 ++++ mpqc-2.3.1/src/lib/util/state/Makefile 2010-02-13 14:22:06.302369965 +0100 +@@ -50,6 +50,7 @@ + + BIN_OR_LIB = LIB + TARGET_TO_MAKE = libSCstate ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCkeyval.la + + default:: $(DEPENDINCLUDE) + +--- mpqc-2.3.1.orig/src/lib/util/group/Makefile 2005-07-30 02:30:18.000000000 +0200 ++++ mpqc-2.3.1/src/lib/util/group/Makefile 2010-02-13 14:21:38.582370124 +0100 +@@ -61,6 +61,7 @@ + + BIN_OR_LIB = LIB + TARGET_TO_MAKE = libSCgroup ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCkeyval.la + + TESTCXXSRC = pooltest.cc messtest.cc rnglocktest.cc thrtest.cc prttest.cc + DISTFILES = $(REQUIREDCXXSRC) $(OPTIONALCXXSRC) $(INC) \ +--- mpqc-2.3.1.orig/src/lib/util/Makefile 2001-08-07 00:29:56.000000000 +0200 ++++ mpqc-2.3.1/src/lib/util/Makefile 2010-02-13 14:40:23.611369920 +0100 +@@ -5,7 +5,7 @@ + + include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile + +-SUBDIRS = options ref container class state misc keyval group render ++SUBDIRS = options keyval ref container class state misc group render + + include $(SRCDIR)/$(TOPDIR)/lib/GlobalSubDirs + +--- mpqc-2.3.1.orig/lib/GlobalRules 2010-02-13 19:47:19.019432588 +0100 ++++ mpqc-2.3.1/lib/GlobalRules 2010-02-13 19:47:57.760370198 +0100 +@@ -75,7 +75,7 @@ + $(RANLIB) $@ + + $(TOPDIR)/lib/$(TARGET_TO_MAKE).la: $(LIBOBJ) +- $(LTLINK) $(CXX) -o $@ $^ $(wildcard $(TMPLREPO)/*.o) $(LTLINKLIBOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(wildcard $(TMPLREPO)/*.o) $(LTLINKLIBOPTS) $(LIBADD) + + else + +@@ -104,7 +104,7 @@ + endif + + $(TOPDIR)/lib/$(TARGET_TO_MAKE).la: $(LIBOBJ) +- $(LTLINK) $(CXX) -o $@ $^ $(LTLINKLIBOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(LTLINKLIBOPTS) $(LIBADD) + + endif + +--- mpqc-2.3.1.orig/doc/devsamp/Makefile 2004-04-28 22:45:14.000000000 +0200 ++++ mpqc-2.3.1/doc/devsamp/Makefile 2010-02-13 19:58:56.958452043 +0100 +@@ -9,4 +9,4 @@ + LTLINKBINOPTS := $(shell $(SCCONFIG) --ltlinkbinopts) + + mp2: mp2.o +- $(LTLINK) $(CXX) $(CXXFLAGS) -o $@ $^ -L$(LIBDIR) -lmpqc $(LIBS) $(LTLINKBINOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ -L$(LIBDIR) -lmpqc $(LIBS) $(LTLINKBINOPTS) +--- mpqc-2.3.1.orig/src/bin/mpqc/Makefile 2005-07-28 18:57:47.000000000 +0200 ++++ mpqc-2.3.1/src/bin/mpqc/Makefile 2010-02-13 19:57:40.484216235 +0100 +@@ -82,7 +82,7 @@ + $(RANLIB) $@ + + $(TOPDIR)/lib/libmpqc.la: $(BINOBJ) +- $(LTLINK) $(CXX) -o $@ $^ $(LTLINKLIBOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(LTLINKLIBOPTS) + + install_devel:: $(TOPDIR)/lib/libmpqc.$(LIBSUF) + $(INSTALL) $(INSTALLDIROPT) $(installroot)$(libdir) +--- mpqc-2.3.1.orig/src/lib/chemistry/qc/Makefile.orig 2010-06-18 18:09:58.192621760 +0000 ++++ mpqc-2.3.1/src/lib/chemistry/qc/Makefile 2010-06-18 18:10:10.350261767 +0000 +@@ -33,7 +33,7 @@ + include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile + include $(TOPDIR)/lib/Makedirlist + +-SUBDIRS = basis oint3 intv3 wfn scf dft mbpt ++SUBDIRS = basis oint3 intv3 dft wfn scf mbpt + ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_PSI),yes) + SUBDIRS := $(SUBDIRS) psi + endif diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-blas.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-blas.patch new file mode 100644 index 000000000000..b99c82fb71da --- /dev/null +++ b/sci-chemistry/mpqc/files/mpqc-2.3.1-blas.patch @@ -0,0 +1,55 @@ + configure.in | 36 +++--------------------------------- + 1 files changed, 3 insertions(+), 33 deletions(-) + +diff --git a/configure.in b/configure.in +index ee82977..caae1f9 100644 +--- a/configure.in ++++ b/configure.in +@@ -1487,44 +1487,14 @@ AC_LANG_CPLUSPLUS + LIBSSAV="$LIBS" + LIBS="$LIBSSAV $FLIBS" + +-LIBBLAS="" +-F77_DGEMM=`$PERL $srcdir/bin/mkf77sym.pl.in -method $F77_SYMBOLS DAXPY` +-AC_CHECK_FUNC($F77_DGEMM,HAVE_BLAS=yes,[ +- AC_CHECK_LIB(essl,$F77_DGEMM,[HAVE_BLAS=yes;LIBBLAS="-lessl"], +- AC_CHECK_LIB(blas,$F77_DGEMM,[HAVE_BLAS=yes;LIBBLAS="-lblas"]) +- )] +-) +-if test X$HAVE_BLAS != Xyes; then +- LIBSSAV2="$LIBS" +- LIBS="-latlas $LIBS" +- AC_CHECK_LIB(f77blas,$F77_DGEMM,[HAVE_BLAS=yes;LIBBLAS="-lf77blas -latlas"], +- LIBS="$LIBSSAV2") +-fi +-AC_SUBST(HAVE_BLAS) +-if test X$HAVE_BLAS != Xyes; then +- echo "WARNING: Could not link to the BLAS library. It can be obtained at" +- echo "http://www.netlib.org/blas. Use --with-libdirs and/or --with-libs" +- echo "to specify the name of the library." +- AC_MSG_ERROR([BLAS is required to complete the build]) +-fi ++PKG_CHECK_MODULES([BLAS], [blas], [LIBBLAS="${BLAS_LIBS}"]) + + LIBS="$LIBSSAV $LIBBLAS $FLIBS" + +-LIBLAPACK="" +-F77_DGESVD=`$PERL $srcdir/bin/mkf77sym.pl.in -method $F77_SYMBOLS DGESVD` +-AC_CHECK_FUNC($F77_DGESVD,HAVE_LAPACK=yes,[ +- AC_CHECK_LIB(lapack,$F77_DGESVD,[HAVE_LAPACK=yes;LIBLAPACK="-llapack"] +- )] +-) +-AC_SUBST(HAVE_LAPACK) +-if test X$HAVE_LAPACK != Xyes; then +- echo "Could not link to the LAPACK library. It can be obtained at" +- echo "http://www.netlib.org/lapack. Use --with-libdirs and/or --with-libs" +- echo "to specify the name of the library." +- AC_MSG_ERROR([LAPACK is required to complete the build]) +-fi ++PKG_CHECK_MODULES([LAPACK], [lapack], [LIBLAPACK="${LAPACK_LIBS}"]) + + FLIBS="$LIBLAPACK $LIBBLAS $FLIBS" ++ + AC_LANG_RESTORE + + dnl ----------- check for Scalable BLAS library -------------- diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-respect-ldflags.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-respect-ldflags.patch new file mode 100644 index 000000000000..c38c9579ddde --- /dev/null +++ b/sci-chemistry/mpqc/files/mpqc-2.3.1-respect-ldflags.patch @@ -0,0 +1,25 @@ +--- mpqc-2.3.1.orig/configure.in 2006-03-22 19:04:54.000000000 +0100 ++++ mpqc-2.3.1/configure.in 2010-02-13 17:46:19.545557872 +0100 +@@ -10,6 +10,8 @@ + AC_CONFIG_HEADER(src/lib/scconfig.h) + AC_CONFIG_AUX_DIR(bin) + ++m4_include([lib/autoconf/cca.m4]) ++m4_include([lib/autoconf/acinclude.m4]) + AC_CANONICAL_SYSTEM + + AC_DEFINE_UNQUOTED(HOST_ARCH, "$host") +@@ -473,12 +473,10 @@ + echo Using FORTRAN runtime libraries: $withval + ) + +-LDFLAGS= +-LIBDIRS= + AC_ARG_WITH(libdirs, + [ --with-libdirs Specifies library directories (-Ldir1 -Ldir2).], + LIBDIRS=$withval +-LDFLAGS=$withval ++LDFLAGS="$LDFLAGS $withval" + echo Using extra library directories: $withval + ) + diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-test-failure-hack.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-test-failure-hack.patch new file mode 100644 index 000000000000..91fcc30d0d90 --- /dev/null +++ b/sci-chemistry/mpqc/files/mpqc-2.3.1-test-failure-hack.patch @@ -0,0 +1,11 @@ +--- mpqc-2.3.1.orig/src/bin/mpqc/validate/Makefile 2006-03-22 19:03:51.000000000 +0100 ++++ mpqc-2.3.1/src/bin/mpqc/validate/Makefile 2010-02-13 20:26:12.496370219 +0100 +@@ -52,7 +52,7 @@ + # Also need to see if --mpqc was specified. If not, then add + # --mpqc ../../mpqc. + ifeq ($(filter --mpqc%, $(ALL_MPQCRUN_ARGS)),) +-ALL_MPQCRUN_ARGS:=--mpqc ../../mpqc $(ALL_MPQCRUN_ARGS) ++ALL_MPQCRUN_ARGS:=--mpqc "LD_LIBRARY_PATH=\"../../../../../lib/.libs/\" ../../mpqc" $(ALL_MPQCRUN_ARGS) + endif + + ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_MBPTR12),yes) diff --git a/sci-chemistry/mpqc/metadata.xml b/sci-chemistry/mpqc/metadata.xml new file mode 100644 index 000000000000..6526df6225a9 --- /dev/null +++ b/sci-chemistry/mpqc/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">mpqc</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r1.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r1.ebuild new file mode 100644 index 000000000000..3eb6e335be7f --- /dev/null +++ b/sci-chemistry/mpqc/mpqc-2.3.1-r1.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="The Massively Parallel Quantum Chemistry Program" +HOMEPAGE="http://www.mpqc.org/" +SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc ppc64 x86" +IUSE="doc threads tk" + +RDEPEND=" + virtual/blas + virtual/lapack + tk? ( dev-lang/tk )" +DEPEND="${RDEPEND} + dev-lang/perl + sys-devel/flex + sys-apps/sed + virtual/pkgconfig + doc? ( + app-doc/doxygen + media-gfx/graphviz )" + +src_unpack() { + unpack ${A} + cd "${S}" + + # do not install tkmolrender if not requested + if ! use tk; then + sed \ + -e "s:.*/bin/molrender/tkmolrender.*::" \ + -e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \ + -e "s:/bin/rm -f tkmolrender::" \ + -i "./src/bin/molrender/Makefile" \ + || die "failed to disable tkmolrender" + fi +} + +src_compile() { + # Only shared will work on ppc64 - bug #62124 + # But we always want shared libraries + econf \ + $(use_enable threads) \ + --enable-shared \ + ${myconf} + + sed \ + -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS}:" \ + -e "s:^FFLAGS =.*$:FFLAGS=${FFLAGS:- -O2}:" \ + -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS}:" \ + lib/LocalMakefile + emake || die "emake failed" +} + +src_test() { + cd "${S}"/src/bin/mpqc/validate + + # we'll only run the small test set, since the + # medium and large ones take >10h and >24h on my + # 1.8Ghz P4M + emake -j1 check0 || die "failed in test routines" +} + +src_install() { + emake -j1 installroot="${D}" install install_devel install_inc \ + || die "install failed" + + dodoc CHANGES CITATION README || die "failed to install docs" + + # make extended docs + if use doc; then + cd "${S}"/doc + emake -j1 all || die "failed to generate documentation" + doman man/man1/* man/man3/* || \ + die "failed to install man pages" + dohtml -r html/ + fi +} + +pkg_postinst() { + echo + einfo "MPQC can be picky with regard to compilation flags." + einfo "If during mpqc runs you have trouble converging or " + einfo "experience oscillations during SCF interations, " + einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS." + einfo "Particularly, replacing -march=pentium4 by -march=pentium3" + einfo "might help if you encounter problems with correlation " + einfo "consistent basis sets." + echo +} diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r2.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r2.ebuild new file mode 100644 index 000000000000..0ce954f73374 --- /dev/null +++ b/sci-chemistry/mpqc/mpqc-2.3.1-r2.ebuild @@ -0,0 +1,103 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=2 + +inherit autotools eutils toolchain-funcs + +DESCRIPTION="The Massively Parallel Quantum Chemistry Program" +HOMEPAGE="http://www.mpqc.org/" +SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 x86" +IUSE="doc mpi threads tk" + +RDEPEND=" + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[cxx] ) + tk? ( dev-lang/tk )" +DEPEND="${RDEPEND} + dev-lang/perl + sys-devel/flex + sys-apps/sed + virtual/pkgconfig + doc? ( + app-doc/doxygen + media-gfx/graphviz )" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-as-needed.patch \ + "${FILESDIR}"/${P}-respect-ldflags.patch \ + "${FILESDIR}"/${P}-test-failure-hack.patch + # do not install tkmolrender if not requested + if ! use tk; then + sed \ + -e "s:.*/bin/molrender/tkmolrender.*::" \ + -e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \ + -e "s:/bin/rm -f tkmolrender::" \ + -i "./src/bin/molrender/Makefile" \ + || die "failed to disable tkmolrender" + fi + eautoreconf +} + +src_configure() { + tc-export CC CXX + if use mpi; then + export CC=mpicc + export CXX=mpicxx + fi + econf \ + $(use_enable threads) \ + $(use_enable mpi parallel) \ + --enable-shared \ + ${myconf} + + sed \ + -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS}:" \ + -e "s:^FFLAGS =.*$:FFLAGS=${FFLAGS:- -O2}:" \ + -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS}:" \ + lib/LocalMakefile +} + +src_test() { + cd "${S}"/src/bin/mpqc/validate + + # we'll only run the small test set, since the + # medium and large ones take >10h and >24h on my + # 1.8Ghz P4M + emake -j1 check0 || die "failed in test routines" +} + +src_install() { + emake installroot="${D}" install install_devel install_inc \ + || die "install failed" + + dodoc CHANGES CITATION README || die "failed to install docs" + + # make extended docs + if use doc; then + cd "${S}"/doc + emake -j1 all || die "failed to generate documentation" + doman man/man1/* man/man3/* || \ + die "failed to install man pages" + dohtml -r html/ + fi +} + +pkg_postinst() { + echo + einfo "MPQC can be picky with regard to compilation flags." + einfo "If during mpqc runs you have trouble converging or " + einfo "experience oscillations during SCF interations, " + einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS." + einfo "Particularly, replacing -march=pentium4 by -march=pentium3" + einfo "might help if you encounter problems with correlation " + einfo "consistent basis sets." + echo +} diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r3.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r3.ebuild new file mode 100644 index 000000000000..d457ffebfc72 --- /dev/null +++ b/sci-chemistry/mpqc/mpqc-2.3.1-r3.ebuild @@ -0,0 +1,107 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils toolchain-funcs + +DESCRIPTION="The Massively Parallel Quantum Chemistry Program" +HOMEPAGE="http://www.mpqc.org/" +SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc ppc64 x86" +IUSE="doc mpi threads static-libs tk" + +RDEPEND=" + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[cxx] ) + tk? ( dev-lang/tk )" +DEPEND="${RDEPEND} + dev-lang/perl + sys-devel/flex + sys-apps/sed + virtual/pkgconfig + doc? ( + app-doc/doxygen + media-gfx/graphviz )" + +PATCHES=( + "${FILESDIR}"/${P}-as-needed.patch + "${FILESDIR}"/${P}-respect-ldflags.patch + "${FILESDIR}"/${P}-test-failure-hack.patch + "${FILESDIR}"/${P}-blas.patch + ) + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +DOCS=(CHANGES CITATION README) + +src_prepare() { + # do not install tkmolrender if not requested + if ! use tk; then + sed \ + -e "s:.*/bin/molrender/tkmolrender.*::" \ + -e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \ + -e "s:/bin/rm -f tkmolrender::" \ + -i "./src/bin/molrender/Makefile" \ + || die "failed to disable tkmolrender" + fi + autotools-utils_src_prepare +} + +src_configure() { + tc-export CC CXX + if use mpi; then + export CC=mpicc + export CXX=mpicxx + fi + local myeconfargs=( + $(use_enable threads) + $(use_enable mpi parallel) ) + + autotools-utils_src_configure + sed \ + -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS}:" \ + -e "s:^FFLAGS =.*$:FFLAGS=${FFLAGS:- -O2}:" \ + -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS}:" \ + -i lib/LocalMakefile || die +} + +src_test() { + cd "${AUTOTOOLS_BUILD_DIR}"/src/bin/mpqc/validate + + # we'll only run the small test set, since the + # medium and large ones take >10h and >24h on my + # 1.8Ghz P4M + emake -j1 check1 +} + +src_install() { + autotools-utils_src_install installroot="${D}" install install_devel install_inc + + # make extended docs + if use doc; then + cd "${AUTOTOOLS_BUILD_DIR}"/doc + emake -j1 all + doman man/man1/* man/man3/* + dohtml -r html + fi +} + +pkg_postinst() { + echo + einfo "MPQC can be picky with regard to compilation flags." + einfo "If during mpqc runs you have trouble converging or " + einfo "experience oscillations during SCF interations, " + einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS." + einfo "Particularly, replacing -march=pentium4 by -march=pentium3" + einfo "might help if you encounter problems with correlation " + einfo "consistent basis sets." + echo +} diff --git a/sci-chemistry/mrbump/Manifest b/sci-chemistry/mrbump/Manifest new file mode 100644 index 000000000000..db81a16d3eba --- /dev/null +++ b/sci-chemistry/mrbump/Manifest @@ -0,0 +1 @@ +DIST mrbump-0.4.4.tar.gz 9220116 RMD160 2b81e1aee9d2cf697c14712a7a7afe3f06c67a68 SHA1 eb474602bbfc3ec8e3d1282b2c6b3000c7194558 SHA256 499634815cf316ca273900252dab16b91f6421b0f85a548108258f9934dccd6a diff --git a/sci-chemistry/mrbump/files/0.4.4-superpose.patch b/sci-chemistry/mrbump/files/0.4.4-superpose.patch new file mode 100644 index 000000000000..c9941e9ece2a --- /dev/null +++ b/sci-chemistry/mrbump/files/0.4.4-superpose.patch @@ -0,0 +1,11 @@ +--- share/mrbump/include/mr/Ensemble.py 2008-07-28 16:40:47.000000000 +0200 ++++ share/mrbump/include/mr/Ensemble.py.new 2009-08-26 22:26:44.000000000 +0200 +@@ -29,7 +29,7 @@ + self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose.exe') + self.pdbsetEXE=os.path.join(os.environ['CBIN'], 'pdbset.exe') + else: +- self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose') ++ self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose-ccp4') + self.pdbsetEXE=os.path.join(os.environ['CBIN'], 'pdbset') + + self.SPxyz_template='' diff --git a/sci-chemistry/mrbump/metadata.xml b/sci-chemistry/mrbump/metadata.xml new file mode 100644 index 000000000000..4aaae064be71 --- /dev/null +++ b/sci-chemistry/mrbump/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher (jlec)</name> + </maintainer> +</pkgmetadata> + diff --git a/sci-chemistry/mrbump/mrbump-0.4.4.ebuild b/sci-chemistry/mrbump/mrbump-0.4.4.ebuild new file mode 100644 index 000000000000..66ec9309e1cd --- /dev/null +++ b/sci-chemistry/mrbump/mrbump-0.4.4.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" + +inherit eutils multilib python + +DESCRIPTION="An automated scheme for Molecular Replacement" +HOMEPAGE="http://www.ccp4.ac.uk/MrBUMP" +SRC_URI="${HOMEPAGE}/release/${P}.tar.gz" + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="X perl" + +RDEPEND=">=sci-chemistry/ccp4-apps-6.1.3[X?] + || ( sci-biology/mafft + sci-biology/clustalw:2 + sci-biology/probcons + sci-biology/t-coffee ) + sci-biology/fasta + X? ( media-gfx/graphviz ) + perl? ( dev-perl/SOAP-Lite )" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_unpack(){ + unpack ${A} + cd "${S}" + unpack ./"${PN}".tar.gz +} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-superpose.patch + python_convert_shebangs 2 setup_lib/* +} + +src_install(){ + insinto /usr/$(get_libdir)/ccp4/ccp4i + doins -r ccp4i/{MrBUMP-ccp4i.tar.gz,MrBUMP/{help,scripts,tasks,templates}} || \ + die "failed to install interface" + + insinto /usr/share/${PN} + doins -r share/${PN}/{data,include} || die "failed to install mrbump data" + + dobin share/${PN}/bin/* || die "failed to install binaries" + + dodoc README.txt || die + dohtml html/mrbump_doc.html || die +} diff --git a/sci-chemistry/msms-bin/Manifest b/sci-chemistry/msms-bin/Manifest new file mode 100644 index 000000000000..7cffef46c709 --- /dev/null +++ b/sci-chemistry/msms-bin/Manifest @@ -0,0 +1,2 @@ +DIST msms_i86Linux2_2.6.1.tar.gz 112762 RMD160 5bbf6102471026112e4f688f56f0a6b8730124c9 SHA1 6ee76d87f3ac3ae543a15d2ea9f86bf3f67d5d4c SHA256 ab4f9e60df6fe18a5ac05550bf074b287792638a818a047697ead049d8737caf +DIST msms_i86_64Linux2_2.6.1.tar.gz 593147 RMD160 a239db5e85afc445c32a165f4086d186010ab123 SHA1 39f9aa955016927138c4014ec0bb40c6a8df18a2 SHA256 5f0ca50360b5938e74c538e0399d582abc4a40ef4cf410e66f31a1f91e6e3e1f diff --git a/sci-chemistry/msms-bin/metadata.xml b/sci-chemistry/msms-bin/metadata.xml new file mode 100644 index 000000000000..51426ab8d003 --- /dev/null +++ b/sci-chemistry/msms-bin/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild b/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild new file mode 100644 index 000000000000..8b4267088281 --- /dev/null +++ b/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +DESCRIPTION="MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces" +HOMEPAGE="http://mgl.scripps.edu/people/sanner/html/msms_home.html" +SRC_URI=" + amd64? ( msms_i86_64Linux2_2.6.1.tar.gz ) + x86? ( msms_i86Linux2_2.6.1.tar.gz ) +" + +LICENSE="MSMS" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RESTRICT="fetch" + +S="${WORKDIR}" + +QA_PREBUILT="${EROOT#/}opt/bin/.*" + +pkg_nofetch() { + einfo "Please download ${A} from http://mgltools.scripps.edu/downloads#msms and place it to ${DISTDIR}" +} + +src_install() { + doman msms.1 + dodoc README msms.html ReleaseNotes + exeinto /opt/bin + if use amd64; then + newexe ${PN%-bin}.x86_64Linux2.${PV} msms + elif use x86; then + newexe ${PN%-bin}.i86Linux2.${PV} msms + fi + insinto /usr/share/${PN}/ + doins atmtypenumbers + sed \ + -e 's:nawk:awk:g' \ + -e "s:./atmtypenumbers:${EPREFIX}/usr/share/${PN}/atmtypenumbers:g" \ + -i pdb_to_xyz* || die + dobin pdb_to_xyz* +} diff --git a/sci-chemistry/mustang/Manifest b/sci-chemistry/mustang/Manifest new file mode 100644 index 000000000000..46a7a80261ed --- /dev/null +++ b/sci-chemistry/mustang/Manifest @@ -0,0 +1 @@ +DIST mustang_v3.2.1.tgz 161216 RMD160 980dd41e24a65f02e77a4b0d60364bbb8423f0d0 SHA1 0a9b55633bfa836d9851be115e2815f8d17839ca SHA256 38f8ec10f15466a42ade770eb6c3ed0ed2449bb070a53b5e8d3125f2596b1556 diff --git a/sci-chemistry/mustang/files/mustang-3-gcc43.patch b/sci-chemistry/mustang/files/mustang-3-gcc43.patch new file mode 100644 index 000000000000..ef2818b92ed8 --- /dev/null +++ b/sci-chemistry/mustang/files/mustang-3-gcc43.patch @@ -0,0 +1,55 @@ +diff -u MUSTANG_v.3.orig/src/ew_2.cpp MUSTANG_v.3/src/ew_2.cpp +--- MUSTANG_v.3.orig/src/ew_2.cpp 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/ew_2.cpp 2008-12-09 10:47:22.000000000 -0700 +@@ -36,6 +36,7 @@ + using std::ifstream; + + #include<math.h> ++#include <cstdlib> + #include "macros.h" + #include "globals.h" + #include "ew.h" +diff -u MUSTANG_v.3.orig/src/multiple_superposition.cpp MUSTANG_v.3/src/multiple_superposition.cpp +--- MUSTANG_v.3.orig/src/multiple_superposition.cpp 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/multiple_superposition.cpp 2008-12-09 10:49:00.000000000 -0700 +@@ -51,6 +51,7 @@ + #include "alloc_routines.h" + #include "de_alloc_routines.h" + #include <cmath> ++#include <cstdlib> + #define THRESH 0.0001 + + void MOVE_TO_CENTER_OF_GRAVITY( int NSTRUC , int NRES , float ***R , float **CMs ) +diff -u MUSTANG_v.3.orig/src/multiple_superposition.h MUSTANG_v.3/src/multiple_superposition.h +--- MUSTANG_v.3.orig/src/multiple_superposition.h 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/multiple_superposition.h 2008-12-09 10:48:11.000000000 -0700 +@@ -25,3 +25,4 @@ + #define MULT_SUPERPOSE + void M_SUPERPOSE( int , int , float***, float** , float*** ) ; + #endif ++#include <cstdlib> +diff -u MUSTANG_v.3.orig/src/pdb_ripper.h MUSTANG_v.3/src/pdb_ripper.h +--- MUSTANG_v.3.orig/src/pdb_ripper.h 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/pdb_ripper.h 2008-12-09 10:46:47.000000000 -0700 +@@ -29,4 +29,5 @@ + void PARSE_ENTIRE_PDB_STRUCTURE( char * , int ) ; + + #endif ++#include <cstdlib> + +diff -u MUSTANG_v.3.orig/src/progress_align.h MUSTANG_v.3/src/progress_align.h +--- MUSTANG_v.3.orig/src/progress_align.h 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/progress_align.h 2008-12-09 10:47:50.000000000 -0700 +@@ -25,3 +25,4 @@ + #define PROG_ALGN_H + void PROGRESSIVE_ALIGNMENT_USING_EXTENDED_EDGE_WEIGHTS() ; + #endif ++#include <cstdlib> +diff -u MUSTANG_v.3.orig/src/read_structures.h MUSTANG_v.3/src/read_structures.h +--- MUSTANG_v.3.orig/src/read_structures.h 2008-01-15 11:18:34.000000000 -0700 ++++ MUSTANG_v.3/src/read_structures.h 2008-12-09 10:46:22.000000000 -0700 +@@ -26,3 +26,4 @@ + void READ_STRUCTURES( char **paths ); + void READ_ENTIRE_PDBS( char **paths) ; + #endif ++#include <cstdlib> diff --git a/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch new file mode 100644 index 000000000000..9e5dea85afeb --- /dev/null +++ b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch @@ -0,0 +1,16 @@ + src/superpose_on_core_2.cpp | 2 ++ + 1 files changed, 2 insertions(+), 0 deletions(-) + +diff --git a/src/superpose_on_core_2.cpp b/src/superpose_on_core_2.cpp +index ae137de..059dfe3 100644 +--- a/src/superpose_on_core_2.cpp ++++ b/src/superpose_on_core_2.cpp +@@ -55,6 +55,8 @@ using std::ofstream ; + #include "multiple_superposition.h" + #include "3D_manip_functions.h" + ++#include <unistd.h> ++ + int **core_columns ; + int *core_columns_2 , NCORE = 0 ; + int **algn_to_seq_hash ; diff --git a/sci-chemistry/mustang/metadata.xml b/sci-chemistry/mustang/metadata.xml new file mode 100644 index 000000000000..e42d0af60f42 --- /dev/null +++ b/sci-chemistry/mustang/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/mustang/mustang-3.2.1.ebuild b/sci-chemistry/mustang/mustang-3.2.1.ebuild new file mode 100644 index 000000000000..4486569db228 --- /dev/null +++ b/sci-chemistry/mustang/mustang-3.2.1.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_PN="MUSTANG" +SRC_P="${PN}_v${PV}" +MY_P="${MY_PN}_v${PV}" + +DESCRIPTION="MUltiple STructural AligNment AlGorithm" +HOMEPAGE="http://www.csse.monash.edu.au/~karun/Site/mustang.html" +SRC_URI="http://www.csse.unimelb.edu.au/~arun/${PN}/${SRC_P}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc-4.7.patch +} + +src_compile() { + emake \ + CPP=$(tc-getCXX) \ + CPPFLAGS="${CXXFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_test() { + ./bin/${P} -f ./data/test/test_zf-CCHH || die +} + +src_install() { + newbin bin/${P} mustang + doman man/${PN}.1 + dodoc README +} + +pkg_postinst() { + elog "If you use this program for an academic paper, please cite:" + elog "Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey, and Arthur M. Lesk" + elog "Proteins: Structure, Function, and Bioinformatics. 64(3):559-574, Aug. 2006" +} diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest new file mode 100644 index 000000000000..80b19cddaea7 --- /dev/null +++ b/sci-chemistry/namd/Manifest @@ -0,0 +1,2 @@ +DIST NAMD_2.10_Source.tar.gz 9200234 SHA256 a5282c172524c2fbe6b9ba56f2de8c84f1093405c914ffbc70442dd0dd4e4289 SHA512 3712a03841fad76c502ac4e41469162ff78e6152560d0f6855d61d2b5583241a661e2a3e7446029b56a6f6f1100f25cb51b2c3df6571542397961d3bb625bc92 WHIRLPOOL b97e47c1d73d505620c26a2eca2e2e91807ebeff19e8820d9be7ea6ddd84c59cd5839846a18a2615ae993a1a6fc22b90e5080cf9d8a72aa412f6b81354e0f284 +DIST NAMD_2.9_Source.tar.gz 8814042 SHA256 9ba6a1f87d4600a62847728d7c223295be214f9a72b5bb62552f74d644108424 SHA512 0644814a2799b560d9dcf807ba0047325bc9f0a26e3831b0465d95180784f038d69595e036daac85d59cd919c92d11a0343031975d99deb1fa3052c8a649bdd6 WHIRLPOOL 5494ccb2ee2f2792fe52ad7dcfe6da9d11453f0a9b0859d30698dea56b00d92fae73465967f82bd708abee5cd4ff50b0a6ffde86451e859e2f515af203e09286 diff --git a/sci-chemistry/namd/files/namd-2.10-gentoo.patch b/sci-chemistry/namd/files/namd-2.10-gentoo.patch new file mode 100644 index 000000000000..e578c131c36d --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.10-gentoo.patch @@ -0,0 +1,124 @@ +diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw NAMD_2.10_Source/arch/Linux-x86_64.fftw +--- NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/arch/Linux-x86_64.fftw 2015-03-06 17:54:46.641162629 -0700 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux-x86_64 ++FFTDIR=/usr + FFTINCL=-I$(FFTDIR)/include +-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw ++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + +diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Linux-x86_64.tcl +--- NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/arch/Linux-x86_64.tcl 2015-03-06 17:54:46.641162629 -0700 +@@ -1,9 +1,9 @@ + + #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 +-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded ++TCLDIR=/usr + TCLINCL=-I$(TCLDIR)/include + #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl +-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread ++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread + TCLFLAGS=-DNAMD_TCL + TCL=$(TCLINCL) $(TCLFLAGS) + +diff -Naur NAMD_2.10_Source.orig/Makefile NAMD_2.10_Source/Makefile +--- NAMD_2.10_Source.orig/Makefile 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/Makefile 2015-03-06 18:01:32.645966590 -0700 +@@ -389,10 +389,10 @@ + $(DSTDIR)/stringhash.o + + # definitions for Charm routines +-CHARMC = $(CHARM)/bin/charmc +-CHARMXI = $(CHARM)/bin/charmc +-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 +-CHARMLIB = $(CHARM)/lib ++CHARMC = /usr/bin/charmc ++CHARMXI = /usr/bin/charmc ++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 ++CHARMLIB = /usr/gentoo-libdir + CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast + #CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB +@@ -418,7 +418,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun ++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -434,7 +434,7 @@ + + namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +- $(CHARMC) -verbose -ld++-option \ ++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ + '$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \ + "$(CHARM_MODULES)" -language charm++ \ + $(BUILDINFO).o \ +@@ -484,11 +484,8 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) +- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm ++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + + psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm +@@ -506,7 +503,7 @@ + $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm + + flipdcd: $(SRCDIR)/flipdcd.c +- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ + echo "#!/bin/sh\necho unavailable on this platform" > $@; \ + chmod +x $@ + +@@ -516,7 +513,7 @@ + chmod +x $@ + + fixdcd: $(SRCDIR)/fixdcd.c +- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c + + dumpdcd: $(SRCDIR)/dumpdcd.c + $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c +@@ -711,9 +708,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2 +- +-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL) ++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -724,17 +719,9 @@ + for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \ + /bin/rm -rf $$f; \ + done +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ +- fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ +- fi + chmod -R a+rX $(RELEASE_DIR_NAME) + tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) + gzip $(RELEASE_DIR_NAME).tar +- echo $(CHARM) +- ls -l $(CHARM)/lib + -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done + + winrelease: winall diff --git a/sci-chemistry/namd/files/namd-2.6-gentoo.patch b/sci-chemistry/namd/files/namd-2.6-gentoo.patch new file mode 100644 index 000000000000..9a71de8d3bd7 --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.6-gentoo.patch @@ -0,0 +1,107 @@ +diff -Naur NAMD_2.6_Source/Makefile NAMD_2.6_Source.new/Makefile +--- NAMD_2.6_Source/Makefile 2006-08-30 00:19:25.000000000 -0400 ++++ NAMD_2.6_Source.new/Makefile 2006-09-19 15:56:17.000000000 -0400 +@@ -232,10 +232,10 @@ + $(DSTDIR)/stringhash.o + + # definitions for Charm routines +-CHARMC = $(CHARM)/bin/charmc +-CHARMXI = $(CHARM)/bin/charmc +-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 +-CHARMLIB = $(CHARM)/lib ++CHARMC = /usr/bin/charmc ++CHARMXI = /usr/bin/charmc ++CHARMINC = /usr/include/charm-5.9 $(COPTD)CMK_OPTIMIZE=1 ++CHARMLIB = /usr/lib + + # Libraries we may have changed + LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) +@@ -255,7 +255,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb ++BINARIES = namd2 psfgen flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -284,11 +284,6 @@ + $(CHARMOPTS) \ + -lm -o namd2 + +-charmrun: $(CHARM)/bin/charmrun # XXX +- $(COPY) $(CHARM)/bin/charmrun $@ +- +-windowsbinaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe +- + namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) + $(CHARMC) -verbose \ +@@ -309,9 +304,6 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(DSTDIR) $(SBOBJS) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + +@@ -571,9 +563,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2 +- +-WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL) ++RELEASE_FILES = flipdcd flipbinpdb psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -582,17 +572,9 @@ + for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done + cp -r .rootdir/lib $(RELEASE_DIR_NAME) + /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ +- fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ +- fi + chmod -R a+rX $(RELEASE_DIR_NAME) + tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) + gzip $(RELEASE_DIR_NAME).tar +- echo $(CHARM) +- ls -l $(CHARM)/lib + -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done + + winrelease: winall +diff -Naur NAMD_2.6_Source/arch/Linux-i686.fftw NAMD_2.6_Source.new/arch/Linux-i686.fftw +--- NAMD_2.6_Source/arch/Linux-i686.fftw 2004-02-20 17:38:36.000000000 -0500 ++++ NAMD_2.6_Source.new/arch/Linux-i686.fftw 2006-09-19 15:52:32.000000000 -0400 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux +-FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include +-FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw ++#FFTDIR=/Projects/namd2/fftw/linux ++FFTINCL=-I/usr/include ++FFTLIB=-L/usr/lib -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + +diff -Naur NAMD_2.6_Source/arch/Linux-i686.tcl NAMD_2.6_Source.new/arch/Linux-i686.tcl +--- NAMD_2.6_Source/arch/Linux-i686.tcl 2004-10-27 17:40:55.000000000 -0400 ++++ NAMD_2.6_Source.new/arch/Linux-i686.tcl 2006-09-19 15:56:45.000000000 -0400 +@@ -1,8 +1,8 @@ + +-TCLDIR=/Projects/namd2/tcl/linux ++#TCLDIR=/Projects/namd2/tcl/linux + #TCLDIR=$(HOME)/tcl/cray-xt3 +-TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include +-TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl ++TCLINCL=-I/usr/include ++TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl + TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST + TCL=$(TCLINCL) $(TCLFLAGS) + diff --git a/sci-chemistry/namd/files/namd-2.7-gentoo.patch b/sci-chemistry/namd/files/namd-2.7-gentoo.patch new file mode 100644 index 000000000000..28a580e3113c --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7-gentoo.patch @@ -0,0 +1,117 @@ +diff -aurN NAMD_2.7b1_Source.orig/Make.charm NAMD_2.7b1_Source/Make.charm +--- NAMD_2.7b1_Source.orig/Make.charm 2009-06-07 15:15:11.000000000 -0500 ++++ NAMD_2.7b1_Source/Make.charm 2009-06-07 15:15:11.000000000 -0500 +@@ -2,5 +2,5 @@ + # The config script will override this setting if there is a directory + # called charm-6.1 or charm in the NAMD base directory. + +-CHARMBASE = /Projects/namd2/charm-6.1 ++CHARMBASE = /usr/include/charm-6.1.2 + +diff -aurN NAMD_2.7b1_Source.orig/Makefile NAMD_2.7b1_Source/Makefile +--- NAMD_2.7b1_Source.orig/Makefile 2009-06-07 15:15:11.000000000 -0500 ++++ NAMD_2.7b1_Source/Makefile 2009-06-07 15:15:11.000000000 -0500 +@@ -297,10 +297,10 @@ + $(DSTDIR)/stringhash.o + + # definitions for Charm routines +-CHARMC = $(CHARM)/bin/charmc +-CHARMXI = $(CHARM)/bin/charmc +-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 +-CHARMLIB = $(CHARM)/lib ++CHARMC = /usr/bin/charmc ++CHARMXI = /usr/bin/charmc ++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 ++CHARMLIB = /usr/gentoo-libdir + + # Libraries we may have changed + LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) +@@ -320,7 +320,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb ++BINARIES = namd2 psfgen flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -351,14 +351,6 @@ + $(CHARMOPTS) \ + -lm -o namd2 + +-charmrun: $(CHARM)/bin/charmrun # XXX +- $(COPY) $(CHARM)/bin/charmrun $@ +- +-WINDOWSBINARIES = namd2.exe psfgen.exe +-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe +- +-windowsbinaries: $(WINDOWSBINARIES) +- + namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL) + $(MAKEBUILDINFO) + $(CHARMC) -verbose \ +@@ -381,9 +373,6 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + +@@ -700,9 +689,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2 +- +-WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL) ++RELEASE_FILES = flipdcd flipbinpdb psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -711,17 +698,9 @@ + for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done + cp -r .rootdir/lib $(RELEASE_DIR_NAME) + /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ +- fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ +- fi + chmod -R a+rX $(RELEASE_DIR_NAME) + tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) + gzip $(RELEASE_DIR_NAME).tar +- echo $(CHARM) +- ls -l $(CHARM)/lib + -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done + + winrelease: winall +diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw NAMD_2.7b1_Source/arch/Linux-x86_64.fftw +--- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw 2009-06-07 15:15:11.000000000 -0500 ++++ NAMD_2.7b1_Source/arch/Linux-x86_64.fftw 2009-06-07 15:15:11.000000000 -0500 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux-x86_64 ++FFTDIR=/usr + FFTINCL=-I$(FFTDIR)/include +-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw ++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + +diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl NAMD_2.7b1_Source/arch/Linux-x86_64.tcl +--- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl 2009-06-07 15:15:11.000000000 -0500 ++++ NAMD_2.7b1_Source/arch/Linux-x86_64.tcl 2009-06-07 18:25:07.000000000 -0500 +@@ -1,7 +1,7 @@ + +-TCLDIR=/Projects/namd2/tcl/linux-x86_64 ++TCLDIR=/usr + TCLINCL=-I$(TCLDIR)/include +-TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl ++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl -ldl + TCLFLAGS=-DNAMD_TCL + TCL=$(TCLINCL) $(TCLFLAGS) + diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch new file mode 100644 index 000000000000..e5ee3bd6c818 --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch @@ -0,0 +1,24 @@ +diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c +index 94b71ba..01a2529 100644 +--- a/src/flipbinpdb.c ++++ b/src/flipbinpdb.c +@@ -9,6 +9,7 @@ + #include <sys/mman.h> + #include <fcntl.h> + #include <stdio.h> ++#include <stdlib.h> + + #ifndef MAP_FILE + #define MAP_FILE 0 +diff --git a/src/flipdcd.c b/src/flipdcd.c +index 8ec85b7..1c23433 100644 +--- a/src/flipdcd.c ++++ b/src/flipdcd.c +@@ -13,6 +13,7 @@ + #include <sys/mman.h> + #include <fcntl.h> + #include <stdio.h> ++#include <stdlib.h> + + #ifndef MAP_FILE + #define MAP_FILE 0 diff --git a/sci-chemistry/namd/files/namd-2.7-ldflags.patch b/sci-chemistry/namd/files/namd-2.7-ldflags.patch new file mode 100644 index 000000000000..686eba83a2de --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7-ldflags.patch @@ -0,0 +1,41 @@ +diff --git a/Makefile b/Makefile +index fd20f12..0821bed 100644 +--- a/Makefile ++++ b/Makefile +@@ -339,7 +339,7 @@ all: $(BINARIES) $(LIBCUDARTSO) + + namd2: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +- $(CHARMC) -verbose -ld++-option \ ++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ + "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \ + -module NeighborLB -module commlib -language charm++ \ + $(BUILDINFO).o \ +@@ -394,23 +394,23 @@ charmrun.exe: + $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe + + psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) +- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm ++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + + psfgen.exe: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + + flipdcd: $(SRCDIR)/flipdcd.c +- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ + echo "#!/bin/sh\necho unavailable on this platform" > $@; \ + chmod +x $@ + + flipbinpdb: $(SRCDIR)/flipbinpdb.c +- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \ + echo "#!/bin/sh\necho unavailable on this platform" > $@; \ + chmod +x $@ + + fixdcd: $(SRCDIR)/fixdcd.c +- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c + + dumpdcd: $(SRCDIR)/dumpdcd.c + $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c diff --git a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch new file mode 100644 index 000000000000..898d6b5d0980 --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch @@ -0,0 +1,126 @@ +diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw NAMD_2.7b2_Source//arch/Linux-x86_64.fftw +--- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw 2010-04-23 14:40:54.566510874 -0500 ++++ NAMD_2.7b2_Source//arch/Linux-x86_64.fftw 2010-04-23 14:41:08.106528893 -0500 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux-x86_64 ++FFTDIR=/usr + FFTINCL=-I$(FFTDIR)/include +-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw ++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + +diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl NAMD_2.7b2_Source//arch/Linux-x86_64.tcl +--- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl 2010-04-23 14:40:54.566510874 -0500 ++++ NAMD_2.7b2_Source//arch/Linux-x86_64.tcl 2010-04-23 14:41:08.106528893 -0500 +@@ -1,7 +1,7 @@ + +-TCLDIR=/Projects/namd2/tcl/linux-x86_64 ++TCLDIR=/usr + TCLINCL=-I$(TCLDIR)/include +-TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl ++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl + TCLFLAGS=-DNAMD_TCL + TCL=$(TCLINCL) $(TCLFLAGS) + +diff -ur NAMD_2.7b2_Source.orig//Make.charm NAMD_2.7b2_Source//Make.charm +--- NAMD_2.7b2_Source.orig//Make.charm 2010-04-23 14:40:54.556517020 -0500 ++++ NAMD_2.7b2_Source//Make.charm 2010-04-23 14:42:16.026530011 -0500 +@@ -2,5 +2,5 @@ + # The config script will override this setting if there is a directory + # called charm-6.1 or charm in the NAMD base directory. + +-CHARMBASE = /Projects/namd2/charm-6.1.3 ++CHARMBASE = /usr/include/charm-6.1.3 + +Only in NAMD_2.7b2_Source/: Make.charm.~1~ +Only in NAMD_2.7b2_Source/: Make.charm.porig +diff -ur NAMD_2.7b2_Source.orig//Makefile NAMD_2.7b2_Source//Makefile +--- NAMD_2.7b2_Source.orig//Makefile 2010-04-23 14:40:54.556517020 -0500 ++++ NAMD_2.7b2_Source//Makefile 2010-04-23 14:42:59.446523306 -0500 +@@ -300,10 +300,10 @@ + $(DSTDIR)/stringhash.o + + # definitions for Charm routines +-CHARMC = $(CHARM)/bin/charmc +-CHARMXI = $(CHARM)/bin/charmc +-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 +-CHARMLIB = $(CHARM)/lib ++CHARMC = /usr/bin/charmc ++CHARMXI = /usr/bin/charmc ++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 ++CHARMLIB = /usr/gentoo-libdir + + # Libraries we may have changed + LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) +@@ -323,7 +323,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb ++BINARIES = namd2 psfgen flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -354,9 +354,6 @@ + $(CHARMOPTS) \ + -lm -o namd2 + +-charmrun: $(CHARM)/bin/charmrun # XXX +- $(COPY) $(CHARM)/bin/charmrun $@ +- + $(LIBCUDARTSO): + if [ -r $(CUDADIR)/lib64/$(LIBCUDARTSO) ]; then \ + $(COPY) $(CUDADIR)/lib64/$(LIBCUDARTSO) $@; \ +@@ -364,10 +361,6 @@ + $(COPY) $(CUDADIR)/lib/$(LIBCUDARTSO) $@; \ + fi + +-WINDOWSBINARIES = namd2.exe psfgen.exe +-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe +-windowsbinaries: $(WINDOWSBINARIES) +- + namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL) + $(MAKEBUILDINFO) + $(CHARMC) -verbose \ +@@ -390,9 +383,6 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + +@@ -716,9 +706,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2 +- +-WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL) ++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -727,17 +715,9 @@ + for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done + cp -r .rootdir/lib $(RELEASE_DIR_NAME) + /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ +- fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ +- fi + chmod -R a+rX $(RELEASE_DIR_NAME) + tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) + gzip $(RELEASE_DIR_NAME).tar +- echo $(CHARM) +- ls -l $(CHARM)/lib + -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done + + winrelease: winall +Only in NAMD_2.7b2_Source/: Makefile.porig diff --git a/sci-chemistry/namd/files/namd-2.9-gentoo.patch b/sci-chemistry/namd/files/namd-2.9-gentoo.patch new file mode 100644 index 000000000000..583cc52645df --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.9-gentoo.patch @@ -0,0 +1,151 @@ +diff -Naur NAMD_2.9_Source.original/Make.charm NAMD_2.9_Source/Make.charm +--- NAMD_2.9_Source.original/Make.charm 2012-02-29 19:12:11.000000000 -0700 ++++ NAMD_2.9_Source/Make.charm 2013-09-13 21:23:26.000000000 -0600 +@@ -2,5 +2,5 @@ + # The config script will override this setting if there is a directory + # called charm-6.4.0 or charm in the NAMD base directory. + +-CHARMBASE = /Projects/namd2/charm-6.4.0 ++CHARMBASE = /usr/include/charm-6.4.0 + +diff -Naur NAMD_2.9_Source.original/Makefile NAMD_2.9_Source/Makefile +--- NAMD_2.9_Source.original/Makefile 2012-04-27 09:53:24.000000000 -0600 ++++ NAMD_2.9_Source/Makefile 2013-09-13 21:30:15.000000000 -0600 +@@ -344,10 +344,10 @@ + $(DSTDIR)/stringhash.o + + # definitions for Charm routines +-CHARMC = $(CHARM)/bin/charmc +-CHARMXI = $(CHARM)/bin/charmc +-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 +-CHARMLIB = $(CHARM)/lib ++CHARMC = /usr/bin/charmc ++CHARMXI = /usr/bin/charmc ++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 ++CHARMLIB = /usr/gentoo-libdir + CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #MSA = -DCHARM_HAS_MSA +@@ -370,7 +370,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen sortreplicas charmrun flipdcd flipbinpdb ++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -386,7 +386,7 @@ + + namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +- $(CHARMC) -verbose -ld++-option \ ++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ + "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \ + "$(CHARM_MODULES)" -language charm++ \ + $(BUILDINFO).o \ +@@ -402,16 +402,9 @@ + $(EXTRALINKLIBS) \ + -lm -o namd2 + +-charmrun: $(CHARM)/bin/charmrun # XXX +- $(COPY) $(CHARM)/bin/charmrun $@ +- + $(LIBCUDARTSO): + $(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@; + +-WINDOWSBINARIES = namd2.exe psfgen.exe sortreplicas.exe +-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe +-windowsbinaries: $(WINDOWSBINARIES) +- + namd2.exe: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) $(TCLDLL) + $(MAKEBUILDINFO) + $(CHARMC) -verbose \ +@@ -434,11 +427,8 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) +- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm ++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + + psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm +@@ -456,7 +446,7 @@ + $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm + + flipdcd: $(SRCDIR)/flipdcd.c +- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ + echo "#!/bin/sh\necho unavailable on this platform" > $@; \ + chmod +x $@ + +@@ -466,7 +456,7 @@ + chmod +x $@ + + fixdcd: $(SRCDIR)/fixdcd.c +- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c + + dumpdcd: $(SRCDIR)/dumpdcd.c + $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c +@@ -665,9 +655,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2 +- +-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL) ++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -678,17 +666,9 @@ + for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \ + /bin/rm -rf $$f; \ + done +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ +- fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ +- fi + chmod -R a+rX $(RELEASE_DIR_NAME) + tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) + gzip $(RELEASE_DIR_NAME).tar +- echo $(CHARM) +- ls -l $(CHARM)/lib + -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done + + winrelease: winall +diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.fftw NAMD_2.9_Source/arch/Linux-x86_64.fftw +--- NAMD_2.9_Source.original/arch/Linux-x86_64.fftw 2009-02-21 21:16:04.000000000 -0700 ++++ NAMD_2.9_Source/arch/Linux-x86_64.fftw 2013-09-13 20:55:02.000000000 -0600 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux-x86_64 ++FFTDIR=/usr + FFTINCL=-I$(FFTDIR)/include +-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw ++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + +diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.tcl NAMD_2.9_Source/arch/Linux-x86_64.tcl +--- NAMD_2.9_Source.original/arch/Linux-x86_64.tcl 2011-06-17 14:38:43.000000000 -0600 ++++ NAMD_2.9_Source/arch/Linux-x86_64.tcl 2013-09-13 20:56:30.000000000 -0600 +@@ -1,9 +1,9 @@ + + #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 +-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded ++TCLDIR=/usr + TCLINCL=-I$(TCLDIR)/include + #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl +-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread ++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread + TCLFLAGS=-DNAMD_TCL + TCL=$(TCLINCL) $(TCLFLAGS) + diff --git a/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch new file mode 100644 index 000000000000..40e8e68b5ba3 --- /dev/null +++ b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch @@ -0,0 +1,61 @@ +# patch to fix compile error on gcc-3.x + +diff -Naur NAMD_2.6b1_Source/src/BackEnd.C NAMD_2.6b1_Source_patched/src/BackEnd.C +--- NAMD_2.6b1_Source/src/BackEnd.C 2003-12-31 06:37:15.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/src/BackEnd.C 2005-08-22 18:59:59.000000000 +0000 +@@ -162,7 +162,7 @@ + } + + // start QD and scheduler +-void BackEnd::barrier(void) { ++void BackEnd::namd_barrier(void) { + awaken(); + suspend(); + } +diff -Naur NAMD_2.6b1_Source/src/BackEnd.h NAMD_2.6b1_Source_patched/src/BackEnd.h +--- NAMD_2.6b1_Source/src/BackEnd.h 2000-01-29 00:20:05.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/src/BackEnd.h 2005-08-22 18:59:47.000000000 +0000 +@@ -17,7 +17,7 @@ + + static void suspend(void); // Let message code run... + static void awaken(void); // ...then return +- static void barrier(void); // Let message code run, then return ++ static void namd_barrier(void); // Let message code run, then return + static void ExitSchedOn(int pe); // Tell a remote processor to stop + // his scheduler + +diff -Naur NAMD_2.6b1_Source/src/ScriptTcl.C NAMD_2.6b1_Source_patched/src/ScriptTcl.C +--- NAMD_2.6b1_Source/src/ScriptTcl.C 2005-06-23 18:47:00.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/src/ScriptTcl.C 2005-08-22 19:00:21.000000000 +0000 +@@ -56,7 +56,7 @@ + } + + void ScriptTcl::barrier() { +- BackEnd::barrier(); ++ BackEnd::namd_barrier(); + } + + void ScriptTcl::initcheck() { +diff -Naur NAMD_2.6b1_Source/src/main.C NAMD_2.6b1_Source_patched/src/main.C +--- NAMD_2.6b1_Source/src/main.C 2005-05-27 22:56:49.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/src/main.C 2005-08-22 19:17:34.000000000 +0000 +@@ -67,7 +67,9 @@ + + #ifndef NOHOSTNAME + iout << iINFO << +- "Sending usage information to NAMD developers via UDP. Sent data is:\n" ++ "Markus says: I don't want to send usage information \n" ++ << endi; ++ iout << iINFO << "to NAMD developers :) Data not sent is:\n" + << endi; + + char sendbuf[TBSOFT_TRACK_MAXLEN]; +@@ -88,7 +90,7 @@ + sprintf(sendbuf, "1 %s %s %s %s %s %s %s", + program, versionnum, platform, numcpus, miscinfo, host, user); + iout << iINFO << sendbuf << "\n" << endi; +- send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf)); ++ //send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf)); + + #endif + return 0; diff --git a/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch b/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch new file mode 100644 index 000000000000..731ea2337e91 --- /dev/null +++ b/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch @@ -0,0 +1,15 @@ +# adjust paths for proper linking to fftw libs + +--- NAMD_2.6b1_Source/arch/Linux-i686.fftw 2004-02-20 22:38:36.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/arch/Linux-i686.fftw 2005-08-22 18:50:38.000000000 +0000 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux +-FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include +-FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw ++#FFTDIR=/Projects/namd2/fftw/linux ++FFTINCL=-I/usr/include ++FFTLIB=-L/usr/lib -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + diff --git a/sci-chemistry/namd/files/namd-makefile-gentoo.patch b/sci-chemistry/namd/files/namd-makefile-gentoo.patch new file mode 100644 index 000000000000..4ee5822ccb8f --- /dev/null +++ b/sci-chemistry/namd/files/namd-makefile-gentoo.patch @@ -0,0 +1,88 @@ +# provide paths for charm++ provided includes/libraries/binaries + +--- NAMD_2.6b1_Source-patched/Makefile 2005-07-22 18:50:58.000000000 +0000 ++++ NAMD_2.6b1_Source/Makefile 2005-09-30 02:28:35.000000000 +0000 +@@ -227,10 +227,10 @@ + $(DSTDIR)/stringhash.o + + # definitions for Charm routines +-CHARMC = $(CHARM)/bin/charmc +-CHARMXI = $(CHARM)/bin/charmc +-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 +-CHARMLIB = $(CHARM)/lib ++CHARMC = /usr/bin/charmc ++CHARMXI = /usr/bin/charmc ++CHARMINC = /usr/include/charm-5.9 $(COPTD)CMK_OPTIMIZE=1 ++CHARMLIB = /usr/lib + + # Libraries we may have changed + LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) +@@ -250,7 +250,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb ++BINARIES = namd2 psfgen flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -279,10 +279,7 @@ + $(CHARMOPTS) \ + -lm -o namd2 + +-charmrun: $(CHARM)/bin/charmrun # XXX +- $(COPY) $(CHARM)/bin/charmrun $@ +- +-win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe ++win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe + + namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +@@ -304,9 +301,6 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(DSTDIR) $(SBOBJS) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + +@@ -565,9 +559,9 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = namd2 psfgen charmrun flipdcd flipbinpdb ++RELEASE_FILES = namd2 psfgen flipdcd flipbinpdb + +-WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL) ++WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe $(TCLDLL) + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -575,18 +569,18 @@ + cp $(RELEASE_FILES) $(RELEASE_DIR_NAME) + for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done + cp -r .rootdir/lib $(RELEASE_DIR_NAME) +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ ++ if [ -r /usr/bin/charmd ]; then \ ++ $(COPY) /usr/bin/charmd $(RELEASE_DIR_NAME); \ + fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ ++ if [ -r /usr/bin/charmd_faceless ]; then \ ++ $(COPY) /usr/bin/charmd_faceless $(RELEASE_DIR_NAME); \ + fi + chmod -R a+rX $(RELEASE_DIR_NAME) + tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) + gzip $(RELEASE_DIR_NAME).tar +- echo $(CHARM) +- ls -l $(CHARM)/lib +- echo $(CHARM) ++ echo /usr ++ ls -l /usr/lib ++ echo /usr + file $(RELEASE_FILES) + + winrelease: winall diff --git a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch new file mode 100644 index 000000000000..0e6f0dd337e5 --- /dev/null +++ b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch @@ -0,0 +1,16 @@ +# adjust paths for proper linking to tcl libs + +--- NAMD_2.6b1_Source/arch/Linux-i686.tcl 2004-10-27 21:40:55.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/arch/Linux-i686.tcl 2005-09-14 20:50:14.000000000 +0000 +@@ -1,8 +1,8 @@ + +-TCLDIR=/Projects/namd2/tcl/linux ++#TCLDIR=/Projects/namd2/tcl/linux + #TCLDIR=$(HOME)/tcl/cray-xt3 +-TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include +-TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl ++TCLINCL=-I/usr/include ++TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl + TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST + TCL=$(TCLINCL) $(TCLFLAGS) + diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml new file mode 100644 index 000000000000..c73650100bed --- /dev/null +++ b/sci-chemistry/namd/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>nicolasbock@gentoo.org</email> + <name>Nicolas Bock</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/namd/namd-2.10.ebuild b/sci-chemistry/namd/namd-2.10.ebuild new file mode 100644 index 000000000000..05e3fd7275dd --- /dev/null +++ b/sci-chemistry/namd/namd-2.10.ebuild @@ -0,0 +1,105 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils multilib toolchain-funcs flag-o-matic + +DESCRIPTION="A powerful and highly parallelized molecular dynamics code" +LICENSE="namd" +HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/" + +MY_PN="NAMD" + +SRC_URI="${MY_PN}_${PV}_Source.tar.gz" + +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +RESTRICT="fetch" + +RDEPEND=" + >=sys-cluster/charm-6.5.1-r2 + sci-libs/fftw:3.0 + dev-lang/tcl:0=" + +DEPEND="${RDEPEND} + app-shells/tcsh" + +NAMD_ARCH="Linux-x86_64-g++" + +NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD" + +S="${WORKDIR}/${MY_PN}_${PV}_Source" + +pkg_nofetch() { + echo + einfo "Please download ${MY_PN}_${PV}_Source.tar.gz from" + einfo "${NAMD_DOWNLOAD}" + einfo "after agreeing to the license and then move it to" + einfo "${DISTDIR}" + einfo "Be sure to select the ${PV} version!" + echo +} + +src_prepare() { + CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3) + + # apply a few small fixes to make NAMD compile and + # link to the proper libraries + epatch "${FILESDIR}"/namd-2.10-gentoo.patch + epatch "${FILESDIR}"/namd-2.7-iml-dec.patch + sed \ + -e "/CHARMBASE =/s:= .*:= /usr/bin/charm-${CHARM_VERSION}:" \ + -i Make.charm || die + + # Remove charm distribution. We don't need it. + rm -f charm-*.tar + + # proper compiler and cflags + sed \ + -e "s/g++.*/$(tc-getCXX)/" \ + -e "s/gcc.*/$(tc-getCC)/" \ + -e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \ + -e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \ + -i arch/${NAMD_ARCH}.arch || die + + sed \ + -e "s/gentoo-libdir/$(get_libdir)/g" \ + -e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \ + -i Makefile || die "Failed gentooizing Makefile." + sed -e "s@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die + sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die +} + +src_configure() { + # configure + ./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die +} + +src_compile() { + # build namd + cd "${S}/${NAMD_ARCH}" + emake +} + +src_install() { + dodoc announce.txt license.txt notes.txt + cd "${S}/${NAMD_ARCH}" + + # the binaries + dobin ${PN}2 psfgen flipbinpdb flipdcd +} + +pkg_postinst() { + echo + einfo "For detailed instructions on how to run and configure" + einfo "NAMD please consults the extensive documentation at" + einfo "http://www.ks.uiuc.edu/Research/namd/" + einfo "and the NAMD tutorials available at" + einfo "http://www.ks.uiuc.edu/Training/Tutorials/" + einfo "Have fun :)" + echo +} diff --git a/sci-chemistry/namd/namd-2.9-r1.ebuild b/sci-chemistry/namd/namd-2.9-r1.ebuild new file mode 100644 index 000000000000..feeba40a7c45 --- /dev/null +++ b/sci-chemistry/namd/namd-2.9-r1.ebuild @@ -0,0 +1,105 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils multilib toolchain-funcs flag-o-matic + +DESCRIPTION="A powerful and highly parallelized molecular dynamics code" +LICENSE="namd" +HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/" + +MY_PN="NAMD" + +SRC_URI="${MY_PN}_${PV}_Source.tar.gz" + +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +RESTRICT="fetch" + +RDEPEND=" + >=sys-cluster/charm-6.5.1-r2 + sci-libs/fftw:3.0 + dev-lang/tcl:0=" + +DEPEND="${RDEPEND} + app-shells/tcsh" + +NAMD_ARCH="Linux-x86_64-g++" + +NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD" + +S="${WORKDIR}/${MY_PN}_${PV}_Source" + +pkg_nofetch() { + echo + einfo "Please download ${MY_PN}_${PV}_Source.tar.gz from" + einfo "${NAMD_DOWNLOAD}" + einfo "after agreeing to the license and then move it to" + einfo "${DISTDIR}" + einfo "Be sure to select the ${PV} version!" + echo +} + +src_prepare() { + CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3) + + # apply a few small fixes to make NAMD compile and + # link to the proper libraries + epatch "${FILESDIR}"/namd-2.9-gentoo.patch + epatch "${FILESDIR}"/namd-2.7-iml-dec.patch + sed \ + -e "s:charm-.\+:charm-${CHARM_VERSION}:" \ + -i Make.charm || die + + # Remove charm distribution. We don't need it. + rm -f charm-6.4.0.tar || die + + # proper compiler and cflags + sed \ + -e "s/g++.*/$(tc-getCXX)/" \ + -e "s/gcc.*/$(tc-getCC)/" \ + -e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \ + -e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \ + -i arch/${NAMD_ARCH}.arch || die + + sed \ + -e "s/gentoo-libdir/$(get_libdir)/g" \ + -e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \ + -i Makefile || die "Failed gentooizing Makefile." + sed -e "s@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die + sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die +} + +src_configure() { + # configure + ./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die +} + +src_compile() { + # build namd + cd "${S}/${NAMD_ARCH}" + emake +} + +src_install() { + dodoc announce.txt license.txt notes.txt + cd "${S}/${NAMD_ARCH}" + + # the binaries + dobin ${PN}2 psfgen flipbinpdb flipdcd +} + +pkg_postinst() { + echo + einfo "For detailed instructions on how to run and configure" + einfo "NAMD please consults the extensive documentation at" + einfo "http://www.ks.uiuc.edu/Research/namd/" + einfo "and the NAMD tutorials available at" + einfo "http://www.ks.uiuc.edu/Training/Tutorials/" + einfo "Have fun :)" + echo +} diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest new file mode 100644 index 000000000000..4eb824ac2a3b --- /dev/null +++ b/sci-chemistry/nmrglue/Manifest @@ -0,0 +1,2 @@ +DIST nmrglue-0.4-corrected.tar.gz 128298 SHA256 85c45750aef431f2c1326a9f4856eeac4da8aedbc94c6255de6e08e3ea35f316 SHA512 c2376ba8e8f993e6e4b536d67d4a780087ac8f811b2d5a846ff8b4785b02c0a4e86956c4205f90a17c5c0a2dc620d75fb7886fbad9cca314b548e3368137eda0 WHIRLPOOL eb8a2a5064b5fa5b60d16a70cf51667daa55f1584ed9d0ca3092af4672ed2c5cef56d135e82b35c107856d338fb0893248a1719b673a4e96c1edb2fb75243d08 +DIST nmrglue-0.5.tar.gz 142604 SHA256 a05c880bd0d5f0b388156409e18a5618742f829f2532d19970d05b11bfcc6103 SHA512 2a4b94eb6bae966000bfdee4dd16f4e312568915fb5f19f59f84c6deff690703f54f76366d3f9299f7ec187192ff64f2bf62836617a424d4c5c895c67d819af2 WHIRLPOOL 78f9d094a2ab1ebc01f452717fdc1cdeccc27951195c9dd6e97069a575722acf25442009b4ccede03ad728b0767fced4a2220a8072ccc1d604a9f62e9c45af4a diff --git a/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch b/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch new file mode 100644 index 000000000000..103f5b154d0b --- /dev/null +++ b/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch @@ -0,0 +1,33 @@ +From ba1eee9e71623110511545c058afe2a92e139aa5 Mon Sep 17 00:00:00 2001 +From: Jonathan Helmus <jjhelmus@gmail.com> +Date: Tue, 3 Mar 2015 19:47:05 -0600 +Subject: [PATCH] pipe_proc.py tp function correctly sets FDSIZE. + +Fixes issue #27 +--- + nmrglue/process/pipe_proc.py | 7 +++++-- + 1 file changed, 5 insertions(+), 2 deletions(-) + +diff --git a/nmrglue/process/pipe_proc.py b/nmrglue/process/pipe_proc.py +index 79b6303..8c1271c 100644 +--- a/nmrglue/process/pipe_proc.py ++++ b/nmrglue/process/pipe_proc.py +@@ -1527,13 +1527,16 @@ def tp(dic, data, hyper=False, nohyper=False, auto=False, nohdr=False): + data = np.array(p.tp_hyper(data), dtype="complex64") + else: + data = p.tp(data) +- if dic[fn2 + "QUADFLAG"] != 1 and nohyper is not True: ++ if dic[fn2 + "QUADFLAG"] != 1 and nohyper is False: + # unpack complex as needed + data = np.array(p.c2ri(data), dtype="complex64") + + # update the dimentionality and order + dic["FDSLICECOUNT"] = data.shape[0] +- if data.dtype == 'float32': ++ if (data.dtype == 'float32') and (nohyper is True): ++ # when nohyper is True and the new last dimension was complex ++ # prior to transposing then FDSIZE is set as if the dimension was ++ # converted to complex data, that is half the actual size. + dic["FDSIZE"] = data.shape[1] / 2 + else: + dic["FDSIZE"] = data.shape[1] diff --git a/sci-chemistry/nmrglue/metadata.xml b/sci-chemistry/nmrglue/metadata.xml new file mode 100644 index 000000000000..d1c1fa8f0564 --- /dev/null +++ b/sci-chemistry/nmrglue/metadata.xml @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +Nmrglue has the ability to read, write and convert between a number of NMR file +formats including Agilent/Varian, Bruker, NMRPipe, Sparky, SIMPSON, Rowland NMR +Toolkit files. The files, which are represented in Python as dictionaries of +spectral parameters and NumPy ndarray objects, can be easily examined, modified +and processed as desired. + +Nmrglue provides a number of functions for processing NMR data such as +apodization, spectral shifting, Fourier and other transformations, baseline +smoothing and flattening, and linear prediction modeling and extrapolation. +In addition new processing schemes can be implemented easily using the nmrglue +provided functions and the multitude of numerical routines provided by the NumPy +and SciPy packages. + +When used in conjunction with the matplotlib (or other) python plotting library +nmrglue can be used to create publication quality figures of NMR spectrum or +examine data interactively. +</longdescription> + <upstream> + <remote-id type="github">jjhelmus/nmrglue</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/nmrglue/nmrglue-0.4.ebuild b/sci-chemistry/nmrglue/nmrglue-0.4.ebuild new file mode 100644 index 000000000000..d39fd44820ce --- /dev/null +++ b/sci-chemistry/nmrglue/nmrglue-0.4.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="A module for working with NMR data in Python" +HOMEPAGE="http://nmrglue.com/" +SRC_URI="https://nmrglue.googlecode.com/files/${P}-corrected.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-python/ipython[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}]" +DEPEND="" diff --git a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild new file mode 100644 index 000000000000..08dd91a5ab21 --- /dev/null +++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{3,4} ) + +inherit distutils-r1 + +DESCRIPTION="A module for working with NMR data in Python" +HOMEPAGE="http://nmrglue.com/" +SRC_URI="https://github.com/jjhelmus/nmrglue/releases/download/v${PV}/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + dev-python/ipython[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}]" +DEPEND=" + test? ( + ${RDEPEND} + dev-python/nose[${PYTHON_USEDEP}] + ) +" + +PATCHES=( "${FILESDIR}"/${P}-nohyper.patch ) + +python_test() { + nosetests --verbosity=3 || die +} diff --git a/sci-chemistry/numbat/Manifest b/sci-chemistry/numbat/Manifest new file mode 100644 index 000000000000..6c26ed4a268f --- /dev/null +++ b/sci-chemistry/numbat/Manifest @@ -0,0 +1 @@ +DIST Numbat-0.999.tar.gz 1791471 SHA256 aef72903f262c5a25e542429f3cc7aca4d2dbc920c08b59847d5cb325855e9ab SHA512 0887f77905bbb476b0d12a7015d5d5745023740acc974ea9cd452de7d38a75a92e6090015127588b38ba62353d38c2be20f57be5df3011b51050c4934dfd206c WHIRLPOOL 8282bf5481a93d17a833f809c28d927d681d6d5016552a07b9267bdb78e99fc568370321567d7d6a87a84f31eea8fae9494c1ae8c0109157fca779c7c06805d9 diff --git a/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch b/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch new file mode 100644 index 000000000000..942f5871e50b --- /dev/null +++ b/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch @@ -0,0 +1,42 @@ + src/error_analysis.c | 20 ++++++++++---------- + 1 file changed, 10 insertions(+), 10 deletions(-) + +diff --git a/src/error_analysis.c b/src/error_analysis.c +index eb86a6f..c0edf5f 100644 +--- a/src/error_analysis.c ++++ b/src/error_analysis.c +@@ -848,11 +848,11 @@ void write_sanson_mac(FILE * F, char * name_plot, char * name_world, int number_ + } + + fprintf(F, "reset\n"); +- fprintf(F, "set noxtics\n"); +- fprintf(F, "set noytics\n"); ++ fprintf(F, "unset xtics\n"); ++ fprintf(F, "unset ytics\n"); + fprintf(F, "set angles degrees\n"); +- fprintf(F, "set nogrid\n"); +- fprintf(F, "set noborder\n"); ++ fprintf(F, "unset grid\n"); ++ fprintf(F, "unset border\n"); + //fprintf(F, "width=40\n"); + //fprintf(F, "height=width*(3./4.)\n"); + //fprintf(F, "set xrange [-width : width]\n"); +@@ -867,12 +867,12 @@ void write_sanson_mac(FILE * F, char * name_plot, char * name_world, int number_ + fprintf(F, "YC(lat,lon)=(lon-long0)*cos(lat)\n"); + fprintf(F, "plot '%s' using (YC($2,$1)):(XC($2,$1)) t '' with lines lw 0.1 lt -1", name_world); + for(i = 0; i < number_of_tensor; i++){ +- fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot, +- 6*i+2, 6*i+1, 6*i+2, 6*i+1, 3*i+1); +- fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot, +- 6*i+4, 6*i+3, 6*i+4, 6*i+3, 3*i+2); +- fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot, +- 6*i+6, 6*i+5, 6*i+6, 6*i+5, 3*i+3); ++ fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot, ++ 6*i+2, 6*i+1, 6*i+2, 6*i+1); ++ fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot, ++ 6*i+4, 6*i+3, 6*i+4, 6*i+3); ++ fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot, ++ 6*i+6, 6*i+5, 6*i+6, 6*i+5); + } + fprintf(F, "\n"); + //fprintf(F, "pause 2\n"); diff --git a/sci-chemistry/numbat/metadata.xml b/sci-chemistry/numbat/metadata.xml new file mode 100644 index 000000000000..054dc8435cf6 --- /dev/null +++ b/sci-chemistry/numbat/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +Numbat is a user friendly software that fits dX-tensor to a set of PCS +measurements and a structure from a PDB file. It has also been designed to +assist in the semi automatic process of PCS assignment. A detailed description +of the software can be found in this publication: + +Christophe Schmitz, Mitchell J. Stanton-Cook, Xun-Cheng Su, Gottfried Otting, +and Thomas Huber (2008). Numbat: an interactive software tool for fitting +Δχ-tensors to molecular coordinates using pseudocontact shifts. Journal of +Biomolecular NMR. 41:179-189. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/numbat/numbat-0.999-r1.ebuild b/sci-chemistry/numbat/numbat-0.999-r1.ebuild new file mode 100644 index 000000000000..c34f931aa5b1 --- /dev/null +++ b/sci-chemistry/numbat/numbat-0.999-r1.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +MY_PN="Numbat" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="new user-friendly method built for automatic dX-tensor determination" +HOMEPAGE="http://www.nmr.chem.uu.nl/~christophe/numbat.html" +SRC_URI="http://comp-bio.anu.edu.au/private/downloads/Numbat/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +CDEPEND=" + gnome-base/libglade:2.0 + sci-libs/gsl + x11-libs/gtk+:2" +DEPEND="${CDEPEND} + virtual/pkgconfig" +RDEPEND="${CDEPEND} + sci-chemistry/molmol + sci-chemistry/pymol + sci-visualization/gnuplot" + +S="${WORKDIR}"/${MY_P} + +PATCHES=( +# "${FILESDIR}"/${P}-glade.patch + "${FILESDIR}"/${P}-gnuplot.patch ) + +src_prepare() { + sed \ + -e '/COPYING/d' \ + -e "s:doc/numbat:share/doc/${PF}:g" \ + -i Makefile.am src/common.h || die + rm missing + emake distclean + autotools-utils_src_prepare +} + +src_install() { + docompress -x /usr/share/doc/${PF} + autotools-utils_src_install +} diff --git a/sci-chemistry/oasis/Manifest b/sci-chemistry/oasis/Manifest new file mode 100644 index 000000000000..e87a831c1fe3 --- /dev/null +++ b/sci-chemistry/oasis/Manifest @@ -0,0 +1 @@ +DIST oasis4.0_Linux.zip 6714528 SHA256 56da70ce0c2750aaddf64ad2cd7852fc341d2022209484beb356b4e73dec61ba SHA512 b43b8315e8e3bc8531e11021605100f231635e2363256a19ed0f51015913221eb9e37b3891b9b1239bf83c9ada8f65a1bdc79ec5745201436f8c3b5019bd4bf7 WHIRLPOOL 24d337391997d036bd657ab22aecc77d36f7fa0af573d17433869a29640a8a10368c75ebee114071c577cc0cce34d838271147599d99e2c389088b8c6185f41b diff --git a/sci-chemistry/oasis/files/4.0-makefile.patch b/sci-chemistry/oasis/files/4.0-makefile.patch new file mode 100644 index 000000000000..f27a350a1fd2 --- /dev/null +++ b/sci-chemistry/oasis/files/4.0-makefile.patch @@ -0,0 +1,15 @@ +diff --git a/src/Makefile b/src/Makefile +index 1e9128f..eb9edaf 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -20,8 +20,8 @@ IRIX: + @ ${F77} -O2 -mips3 -nocpp -OPT:Olimit=1500 -w -rpath ${CCP4_LIB} -o oasis4-0 oasis4-0.f -L${CCP4_LIB}/src -lccp4f -lccp4c -lmmdb -lC -lm -L/usr/lib32 -lblas + @ ${F77} -O2 -mips3 -nocpp -OPT:Olimit=1500 -w -rpath ${CCP4_LIB} -o fnp2fp fnp2fp.f -L${CCP4_LIB}/src -lccp4f -lccp4c -lmmdb -lC -lm -L/usr/lib32 -lblas + Linux: +- @ ${F77} -O -w -fno-second-underscore -fno-globals -fno-automatic -o oasis4-0 oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lg2c -lm -L${CCP4_LIB} +- @ ${F77} -O -w -fno-second-underscore -fno-globals -fno-automatic -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lg2c -lm -L${CCP4_LIB} ++ ${F77} $(CFLAGS) $(LDFLAGS) -o oasis oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lm -L${CCP4_LIB} ++ ${F77} $(CFLAGS) $(LDFLAGS) -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lm -L${CCP4_LIB} + Darwin: + @ ${F77} -O2 -fno-second-underscore -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lgcc_s.10.5 -lSystem -lm + @ ${F77} -O2 -fno-second-underscore -o oasis4-0 oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lgcc_s.10.5 -lSystem -lm diff --git a/sci-chemistry/oasis/metadata.xml b/sci-chemistry/oasis/metadata.xml new file mode 100644 index 000000000000..8412c2f3d312 --- /dev/null +++ b/sci-chemistry/oasis/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <use> + <flag name="minimal">Restricts functionality on free software</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/oasis/oasis-4.0-r3.ebuild b/sci-chemistry/oasis/oasis-4.0-r3.ebuild new file mode 100644 index 000000000000..8c259f6be9a3 --- /dev/null +++ b/sci-chemistry/oasis/oasis-4.0-r3.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils fortran-2 multilib toolchain-funcs + +MY_P="${PN}${PV}_Linux" + +DESCRIPTION="A direct-method program for SAD/SIR phasing" +HOMEPAGE="http://cryst.iphy.ac.cn/Project/protein/protein-I.html" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${MY_P}.zip" + +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +LICENSE="ccp4 oasis" +IUSE="examples +minimal" + +RDEPEND=" + sci-chemistry/ccp4-apps + sci-chemistry/pymol + sci-libs/mmdb:0 + sci-visualization/gnuplot + !minimal? ( + sci-chemistry/solve-resolve-bin + sci-chemistry/arp-warp-bin + )" +DEPEND="${RDEPEND} + sci-libs/ccp4-libs" + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + rm bin/{fnp2fp,gnuplot,oasis4-0,seq} || die + epatch "${FILESDIR}"/${PV}-makefile.patch +} + +src_compile() { + emake \ + -C src \ + F77="$(tc-getFC)" \ + CFLAGS="${FFLAGS}" \ + CCP4_LIB="${EPREFIX}/usr/$(get_libdir)" \ + Linux +} + +src_install() { + exeinto /usr/libexec/ccp4/bin/ + doexe src/{${PN},fnp2fp} + + exeinto /usr/$(get_libdir)/${PN} + doexe bin/*.*sh + + insinto /usr/share/doc/${PF}/html + doins bin/html/* + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/html + chmod 755 "${ED}"/usr/share/doc/${PF}/html/*.{*sh,awk} || die + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi + + cat >> "${T}"/25oasis <<- EOF + oasisbin="${EPREFIX}/usr/$(get_libdir)/${PN}" + EOF + + doenvd "${T}"/25oasis +} diff --git a/sci-chemistry/openbabel-perl/Manifest b/sci-chemistry/openbabel-perl/Manifest new file mode 100644 index 000000000000..082e5b029843 --- /dev/null +++ b/sci-chemistry/openbabel-perl/Manifest @@ -0,0 +1 @@ +DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 WHIRLPOOL 74eff18b73d24c8f702e5573a58ba6afba8402e9ce8782de95dc0568575a7d2d632dbc8e8a98b3cd25efdfa7379494f7dcd449342c81ddf73f42a387bce77aaa diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.0-makefile.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.0-makefile.patch new file mode 100644 index 000000000000..597c9a79c103 --- /dev/null +++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.0-makefile.patch @@ -0,0 +1,28 @@ + scripts/CMakeLists.txt | 2 +- + scripts/perl/Makefile.PL | 1 + + 2 files changed, 2 insertions(+), 1 deletions(-) + +diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt +index bf2527b..3c45111 100644 +--- a/scripts/CMakeLists.txt ++++ b/scripts/CMakeLists.txt +@@ -223,7 +223,7 @@ if (DO_PERL_BINDINGS) + COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/Makefile.PL ${openbabel_BINARY_DIR}/scripts/perl + COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm ${openbabel_BINARY_DIR}/scripts/perl + COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp ${openbabel_BINARY_DIR}/scripts/perl +- COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc SRC_DIR=${openbabel_SOURCE_DIR} OBJ_DIR=${openbabel_BINARY_DIR} ${PERL_EXECUTABLE} ${openbabel_BINARY_DIR}/scripts/perl/Makefile.PL ${PERL_PREFIX_TEXT} ++ COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc SRC_DIR=${openbabel_SOURCE_DIR} OBJ_DIR=${openbabel_BINARY_DIR} ${PERL_EXECUTABLE} ${openbabel_BINARY_DIR}/scripts/perl/Makefile.PL INSTALLDIRS=vendor ${PERL_PREFIX_TEXT} + COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc make + DEPENDS ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp + WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl +diff --git a/scripts/perl/Makefile.PL b/scripts/perl/Makefile.PL +index a3a2116..44ad27d 100644 +--- a/scripts/perl/Makefile.PL ++++ b/scripts/perl/Makefile.PL +@@ -32,5 +32,6 @@ WriteMakefile( + 'CC' => $CC, + 'LD' => '$(CC)', + 'INC' => '-I../../include -I'.$cmakesrcdir.'/include', ++ 'DESTDIR' => @ENV{"D"}, + 'OBJECT' => 'openbabel-perl.o' + ); diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.0-swig.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.0-swig.patch new file mode 100644 index 000000000000..6beacf74880c --- /dev/null +++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.0-swig.patch @@ -0,0 +1,25 @@ + scripts/CMakeLists.txt | 6 +----- + 1 files changed, 1 insertions(+), 5 deletions(-) + +diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt +index bf2527b..16feeb4 100644 +--- a/scripts/CMakeLists.txt ++++ b/scripts/CMakeLists.txt +@@ -8,16 +8,12 @@ if (RUN_SWIG) + # SWIG_EXECUTABLE - the path to the swig executable + # SWIG_VERSION - the version number of the swig executable + +- find_package(SWIG) ++ find_package(SWIG 2.0.0) + if (NOT SWIG_FOUND) + message(STATUS "SWIG NOT found") + return() + endif (NOT SWIG_FOUND) + message(STATUS "SWIG version is ${SWIG_VERSION}") +- if (NOT ${SWIG_VERSION} STREQUAL "2.0.0" AND NOT ${SWIG_VERSION} STREQUAL "2.0.1") +- message(STATUS "SWIG version 2.0.0 exactly is required") +- return() +- endif (NOT ${SWIG_VERSION} STREQUAL "2.0.0" AND NOT ${SWIG_VERSION} STREQUAL "2.0.1") + endif (RUN_SWIG) + + ################### diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.1-makefile.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.1-makefile.patch new file mode 100644 index 000000000000..88248b4432f1 --- /dev/null +++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.1-makefile.patch @@ -0,0 +1,9 @@ +--- scripts/perl/Makefile.PL ++++ scripts/perl/Makefile.PL +@@ -37,5 +37,6 @@ 'LDFROM' => $ldfrom, + 'CC' => $CC, + 'LD' => '$(CC)', + 'INC' => '-I../../include -I'.$cmakesrcdir.'/include', ++ 'DESTDIR' => @ENV{"D"}, + 'OBJECT' => 'openbabel-perl.o' + ); diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch new file mode 100644 index 000000000000..92e126a77d86 --- /dev/null +++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch @@ -0,0 +1,108 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 449f4b4..1c9ad00 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -252,7 +252,8 @@ if(NOT MSVC) + } + " SCANDIR_NEEDS_CONST) + +- set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}") ++ set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}" ++ CACHE PATH "Set to system install for bindings only build") + add_definitions(-DOB_MODULE_PATH="\\"${OB_MODULE_PATH}\\"") + + # Add some visibility support when using GCC +@@ -380,7 +381,8 @@ if(UNIX AND BUILD_SHARED) + if(APPLE) + set(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}) + else() +- set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}") ++ set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}" ++ CACHE PATH "Set sane rpath") + set(CMAKE_SKIP_BUILD_RPATH FALSE) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) +@@ -477,6 +479,13 @@ endif() + # Should the language bindings be regenereted? + option(RUN_SWIG "Generate language bindings with SWIG" OFF) + ++# Build bindings only ++option(BINDINGS_ONLY "Build bindings only" OFF) ++ ++# Point to library if building bindings only ++set(BABEL_SYSTEM_LIBRARY ${BABEL_LIBRARY} ++ CACHE PATH "Point to openbabel library if building bindings only") ++ + # Should all bindings be built? + option(ALL_BINDINGS "Build all languages bindings" OFF) + +diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt +index 16e9000..8f92e91 100644 +--- a/scripts/CMakeLists.txt ++++ b/scripts/CMakeLists.txt +@@ -92,16 +92,30 @@ if (DO_PYTHON_BINDINGS) + endif(RUN_SWIG) + + add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel-python.cpp) +- target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY}) ++ if(BINDINGS_ONLY) ++ target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_SYSTEM_LIBRARY}) ++ else() ++ target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY}) ++ endif() ++ + if(NOT WIN32) + set_target_properties(bindings_python PROPERTIES + OUTPUT_NAME _openbabel + PREFIX "" + SUFFIX .so ) +- add_dependencies(bindings_python openbabel) +- install(TARGETS bindings_python LIBRARY DESTINATION ${LIB_INSTALL_DIR}) +- install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py DESTINATION ${LIB_INSTALL_DIR}) +- install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py DESTINATION ${LIB_INSTALL_DIR}) ++ if(NOT BINDINGS_ONLY) ++ add_dependencies(bindings_python openbabel) ++ endif() ++ ++ install(TARGETS bindings_python ++ LIBRARY DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) ++ install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py ++ DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) ++ install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py ++ DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) + else(NOT WIN32) + set_target_properties(bindings_python PROPERTIES + OUTPUT_NAME _openbabel +@@ -231,13 +245,25 @@ if (DO_PERL_BINDINGS) + endif (RUN_SWIG) + + add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp) +- target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY} ${PERL_EXTRA_LINK_FLAGS}) ++ if(BINDINGS_ONLY) ++ target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_SYSTEM_LIBRARY} ${PERL_EXTRA_LINK_FLAGS}) ++ else() ++ target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY} ${PERL_EXTRA_LINK_FLAGS}) ++ endif() ++ + set_target_properties(bindings_perl PROPERTIES + PREFIX "" + OUTPUT_NAME OpenBabel) +- add_dependencies(bindings_perl openbabel) +- install(TARGETS bindings_perl LIBRARY DESTINATION ${LIB_INSTALL_DIR}) +- install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm DESTINATION ${LIB_INSTALL_DIR}) ++ if(NOT BINDINGS_ONLY) ++ add_dependencies(bindings_perl openbabel) ++ endif() ++ ++ install(TARGETS bindings_perl ++ LIBRARY DESTINATION ${LIB_INSTALL_DIR}/auto/Chemistry/OpenBabel/ ++ COMPONENT bindings_perl) ++ install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm ++ DESTINATION ${LIB_INSTALL_DIR}/Chemistry/ ++ COMPONENT bindings_perl) + + endif (DO_PERL_BINDINGS) + diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch new file mode 100644 index 000000000000..b72a622a3afb --- /dev/null +++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch @@ -0,0 +1,41 @@ +diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt +index e7298ce..16e9000 100644 +--- a/scripts/CMakeLists.txt ++++ b/scripts/CMakeLists.txt +@@ -231,36 +239,6 @@ if (DO_PERL_BINDINGS) + install(TARGETS bindings_perl LIBRARY DESTINATION ${LIB_INSTALL_DIR}) + install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm DESTINATION ${LIB_INSTALL_DIR}) + +- set(PERL_INSTALLDIRS_TEXT "") +- if (OBPERL_INSTALLDIRS) +- set(PERL_INSTALLDIRS_TEXT "INSTALLDIRS=${OBPERL_INSTALLDIRS}") +- endif (OBPERL_INSTALLDIRS) +- +- if (NOT MSVC) +- add_custom_target(pre_bindings_perl ALL +- # Create the scripts/perl directory; we cannot do this inside +- # bindings_perl as the WORKING_DIRECTORY needs to already exist! +- COMMAND ${CMAKE_COMMAND} -E make_directory ${openbabel_BINARY_DIR}/scripts/perl +- ) +- add_custom_target(bindings_perl ALL +- COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/Makefile.PL ${openbabel_BINARY_DIR}/scripts/perl +- COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm ${openbabel_BINARY_DIR}/scripts/perl +- COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp ${openbabel_BINARY_DIR}/scripts/perl +- COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc SRC_DIR=${openbabel_SOURCE_DIR} OBJ_DIR=${openbabel_BINARY_DIR} ${PERL_EXECUTABLE} ${openbabel_BINARY_DIR}/scripts/perl/Makefile.PL ${PERL_PREFIX_TEXT} ${PERL_INSTALLDIRS_TEXT} +- COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc make +- DEPENDS openbabel ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp +- WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl +- ) +- add_dependencies(bindings_perl pre_bindings_perl openbabel) +- install(CODE "execute_process(COMMAND make install DESTDIR=\$ENV{DESTDIR} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)") +- +- else (NOT MSVC) +- add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp) +- target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY}) +- set_target_properties(bindings_perl PROPERTIES +- OUTPUT_NAME openbabel_perl ) +- endif(NOT MSVC) +- + endif (DO_PERL_BINDINGS) + + ################### diff --git a/sci-chemistry/openbabel-perl/metadata.xml b/sci-chemistry/openbabel-perl/metadata.xml new file mode 100644 index 000000000000..068b6b2c4442 --- /dev/null +++ b/sci-chemistry/openbabel-perl/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> +OpenBabel is a chemical toolbox designed to speak the many languages of +chemical data. It's an open, collaborative project allowing anyone to +search, convert, analyze, or store data from molecular modeling, chemistry, +solid-state materials, biochemistry, or related areas. +This package enables to access OpenBabel library from Perl programs. +</longdescription> + <upstream> + <remote-id type="sourceforge">openbabel</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild b/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild new file mode 100644 index 000000000000..71a41ba76d7d --- /dev/null +++ b/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils eutils perl-module + +DESCRIPTION="Perl bindings for OpenBabel" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" + +KEYWORDS="amd64 ~arm ppc x86 ~amd64-linux ~x86-linux" +SLOT="0" +LICENSE="GPL-2" +IUSE="" + +RDEPEND=" + dev-lang/perl:= + ~sci-chemistry/openbabel-${PV}" +DEPEND="${RDEPEND} + >=dev-util/cmake-2.4.8 + >=dev-lang/swig-2" + +S="${WORKDIR}/openbabel-${PV}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-trunk_cmake.patch \ + "${FILESDIR}"/${P}-bindings_only.patch + perl_set_version +} + +src_configure() { + local mycmakeargs="${mycmakeargs} + -DCMAKE_INSTALL_RPATH= + -DBINDINGS_ONLY=ON + -DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so" + -DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}" + -DLIB_INSTALL_DIR="${D}/${VENDOR_ARCH}" + -DPERL_BINDINGS=ON + -DRUN_SWIG=ON" + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile bindings_perl +} + +src_test() { + mkdir "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry" + cp \ + "${CMAKE_USE_DIR}/scripts/perl/OpenBabel.pm" \ + "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry/" + for i in "${CMAKE_USE_DIR}"/scripts/perl/t/*; do + einfo "Running test: ${i}" + perl -I"${CMAKE_BUILD_DIR}/$(get_libdir)" "${i}" || die + done +} + +src_install() { + cd "${CMAKE_BUILD_DIR}" + cmake -DCOMPONENT=bindings_perl -P cmake_install.cmake +} diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest new file mode 100644 index 000000000000..082e5b029843 --- /dev/null +++ b/sci-chemistry/openbabel-python/Manifest @@ -0,0 +1 @@ +DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 WHIRLPOOL 74eff18b73d24c8f702e5573a58ba6afba8402e9ce8782de95dc0568575a7d2d632dbc8e8a98b3cd25efdfa7379494f7dcd449342c81ddf73f42a387bce77aaa diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch new file mode 100644 index 000000000000..2e776b4029ec --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch @@ -0,0 +1,209 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 449f4b4..1c9ad00 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -252,7 +252,8 @@ if(NOT MSVC) + } + " SCANDIR_NEEDS_CONST) + +- set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}") ++ set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}" ++ CACHE PATH "Set to system install for bindings only build") + add_definitions(-DOB_MODULE_PATH="\\"${OB_MODULE_PATH}\\"") + + # Add some visibility support when using GCC +@@ -380,7 +381,8 @@ if(UNIX AND BUILD_SHARED) + if(APPLE) + set(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}) + else() +- set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}") ++ set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}" ++ CACHE PATH "Set sane rpath") + set(CMAKE_SKIP_BUILD_RPATH FALSE) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) +@@ -477,6 +479,13 @@ endif() + # Should the language bindings be regenereted? + option(RUN_SWIG "Generate language bindings with SWIG" OFF) + ++# Build bindings only ++option(BINDINGS_ONLY "Build bindings only" OFF) ++ ++# Point to library if building bindings only ++set(BABEL_SYSTEM_LIBRARY ${BABEL_LIBRARY} ++ CACHE PATH "Point to openbabel library if building bindings only") ++ + # Should all bindings be built? + option(ALL_BINDINGS "Build all languages bindings" OFF) + +diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt +index 16e9000..ecd2295 100644 +--- a/scripts/CMakeLists.txt ++++ b/scripts/CMakeLists.txt +@@ -92,16 +92,30 @@ if (DO_PYTHON_BINDINGS) + endif(RUN_SWIG) + + add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel-python.cpp) +- target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY}) ++ if(BINDINGS_ONLY) ++ target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_SYSTEM_LIBRARY}) ++ else() ++ target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY}) ++ endif() ++ + if(NOT WIN32) + set_target_properties(bindings_python PROPERTIES + OUTPUT_NAME _openbabel + PREFIX "" + SUFFIX .so ) +- add_dependencies(bindings_python openbabel) +- install(TARGETS bindings_python LIBRARY DESTINATION ${LIB_INSTALL_DIR}) +- install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py DESTINATION ${LIB_INSTALL_DIR}) +- install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py DESTINATION ${LIB_INSTALL_DIR}) ++ if(NOT BINDINGS_ONLY) ++ add_dependencies(bindings_python openbabel) ++ endif() ++ ++ install(TARGETS bindings_python ++ LIBRARY DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) ++ install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py ++ DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) ++ install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py ++ DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) + else(NOT WIN32) + set_target_properties(bindings_python PROPERTIES + OUTPUT_NAME _openbabel +diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt +index 7841782..6f3495f 100644 +--- a/test/CMakeLists.txt ++++ b/test/CMakeLists.txt +@@ -2,7 +2,12 @@ + add_definitions(-DTESTDATADIR="\\"${CMAKE_SOURCE_DIR}/test/files/\\"") + + # define FORMATDIR for location of format plugin binaries +-add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib/\\"") ++if(BINDINGS_ONLY) ++ set(FORMATDIR "${OB_MODULE_PATH}/") ++else() ++ set(FORMATDIR "${openbabel_BINARY_DIR}/lib${LIB_SUFFIX}/") ++endif() ++add_definitions(-DFORMATDIR="\\"${FORMATDIR}/\\"") + + ########################################################### + # new tests using obtest.h +@@ -89,7 +94,7 @@ foreach(test ${tests}) + add_test(${test}_Test ${TEST_PATH}/test_${test}) + set_tests_properties(${test}_Test PROPERTIES + FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed" +- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib") ++ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}") + endforeach(test ${tests}) + + ############################################################ +@@ -152,7 +157,7 @@ if(WITH_INCHI) + ${TEST_PATH}/test_inchiwrite ${inchidata}/${test} ${inchidata}/${test}.txt) + set_tests_properties(inchi${test}_Test PROPERTIES + FAIL_REGULAR_EXPRESSION "Not ok" +- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib" ++ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + endforeach(test ${inchitests}) + endif(WITH_INCHI) +@@ -166,7 +171,7 @@ foreach(test ${old_tests}) + add_test(${test}_Test ${TEST_PATH}/test_${test}) + set_tests_properties(${test}_Test PROPERTIES + FAIL_REGULAR_EXPRESSION "not ok" +- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib" ++ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + endforeach(test ${old_tests}) + +@@ -181,8 +186,8 @@ if(NOT BUILD_SHARED AND NOT BUILD_MIXED) + endif() + install(TARGETS roundtrip + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + + ########################### +@@ -199,10 +204,10 @@ if(NOT MINGW AND NOT CYGWIN) + babel sym smartssym fastsearch unique kekule) + foreach(pytest ${pytests}) + SET_SOURCE_FILES_PROPERTIES(test${pytest}.py PROPERTIES +- PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib" +- BABEL_LIBDIR "${CMAKE_BINARY_DIR}/lib" ++ PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" ++ BABEL_LIBDIR "${FORMATDIR}" + BABEL_DATADIR "${CMAKE_SOURCE_DIR}/data" +- LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib" ++ LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + ADD_PYTHON_TEST(pytest_${pytest} test${pytest}.py) + set_tests_properties(pytest_${pytest} PROPERTIES +@@ -221,10 +226,10 @@ if (PYTHON_BINDINGS) + bindings _pybel example) + foreach(pybindtest ${pybindtests}) + SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES +- PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib" +- BABEL_LIBDIR "${CMAKE_BINARY_DIR}/lib" ++ PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" ++ BABEL_LIBDIR "${FORMATDIR}" + BABEL_DATADIR "${CMAKE_SOURCE_DIR}/data" +- LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib" ++ LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + if(MSVC) + SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES +diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt +index 1f547bf..fb98441 100644 +--- a/tools/CMakeLists.txt ++++ b/tools/CMakeLists.txt +@@ -38,8 +38,8 @@ if(BUILD_SHARED) + target_link_libraries(${tool} ${BABEL_LIBRARY}) + install(TARGETS ${tool} + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + endforeach(tool) + +@@ -53,8 +53,8 @@ if(BUILD_SHARED) + target_link_libraries(obspectrophore ${BABEL_LIBRARY}) + install(TARGETS obspectrophore + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + + # obgrep -- requires getopt +@@ -66,8 +66,8 @@ if(BUILD_SHARED) + target_link_libraries(obgrep ${BABEL_LIBRARY}) + install(TARGETS obgrep + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + endif(NOT MINIMAL_BUILD) + +@@ -146,7 +146,7 @@ else(BUILD_SHARED) + + install(TARGETS babel + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib) ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX}) + + endif(BUILD_SHARED) diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch new file mode 100644 index 000000000000..d30efd55bd92 --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch @@ -0,0 +1,97 @@ + scripts/openbabel-python.i | 34 +++++++++++++++++----------------- + 1 file changed, 17 insertions(+), 17 deletions(-) + +diff --git a/scripts/openbabel-python.i b/scripts/openbabel-python.i +index 7cb8f24..d893129 100644 +--- a/scripts/openbabel-python.i ++++ b/scripts/openbabel-python.i +@@ -227,7 +227,7 @@ CAST_GENERICDATA_TO(SquarePlanarStereo) + %include <openbabel/math/transform3d.h> + %include <openbabel/math/spacegroup.h> + +-# CloneData should be used instead of the following method ++// CloneData should be used instead of the following method + %ignore OpenBabel::OBBase::SetData; + %include <openbabel/base.h> + +@@ -289,7 +289,7 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue + %ignore OpenBabel::OBDescriptor::LessThan; + %include <openbabel/descriptor.h> + +-# Ignore shadowed methods ++// Ignore shadowed methods + %ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const double *const, double *); + %ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const double, double *); + %include <openbabel/forcefield.h> +@@ -310,7 +310,7 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue + + %warnfilter(503) OpenBabel::OBBitVec; // Not wrapping any of the overloaded operators + %include <openbabel/bitvec.h> +-# Ignore shadowed method ++// Ignore shadowed method + %ignore OpenBabel::OBRotor::GetRotAtoms() const; + %include <openbabel/rotor.h> + %ignore OpenBabel::Swab; +@@ -321,13 +321,13 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue + %include <openbabel/math/align.h> + #endif + +-# The following %ignores avoid warning messages due to shadowed classes. +-# This does not imply a loss of functionality as (in this case) +-# the shadowed class is identical (from the point of view of SWIG) to +-# the shadowing class. +-# This is because C++ references (&) are transformed by SWIG back into +-# pointers, so that OBAtomIter(OBMol &) would be treated the same as +-# OBAtomIter(OBMol *). ++// The following %ignores avoid warning messages due to shadowed classes. ++// This does not imply a loss of functionality as (in this case) ++// the shadowed class is identical (from the point of view of SWIG) to ++// the shadowing class. ++// This is because C++ references (&) are transformed by SWIG back into ++// pointers, so that OBAtomIter(OBMol &) would be treated the same as ++// OBAtomIter(OBMol *). + + %ignore OBAtomAtomIter(OBAtom &); + %ignore OBAtomBondIter(OBAtom &); +@@ -346,9 +346,9 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue + %ignore OBResidueIter(OBMol &); + %ignore OBResidueAtomIter(OBResidue &); + +-# These classes are renamed so that they can be replaced by Python +-# classes of the same name which provide Pythonic iterators +-# (see %pythoncode section below) ++// These classes are renamed so that they can be replaced by Python ++// classes of the same name which provide Pythonic iterators ++// (see %pythoncode section below) + + %rename(_OBAtomAtomIter) OpenBabel::OBAtomAtomIter; + %rename(_OBAtomBondIter) OpenBabel::OBAtomBondIter; +@@ -367,8 +367,8 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue + + %include <openbabel/obiter.h> + +-# The following class, OBiter, is subclassed to provide Python iterators +-# equivalent to the C++ iterators in obiter.h and the plugin iterators ++// The following class, OBiter, is subclassed to provide Python iterators ++// equivalent to the C++ iterators in obiter.h and the plugin iterators + + %pythoncode %{ + class OBIter(object): +@@ -459,7 +459,7 @@ def double_array(mylist): + return c + %} + +-# Copy some of the global variables in cvar into the openbabel namespace ++// Copy some of the global variables in cvar into the openbabel namespace + + %pythoncode %{ + obErrorLog = cvar.obErrorLog +@@ -470,7 +470,7 @@ atomtyper = cvar.atomtyper + aromtyper = cvar.aromtyper + %} + +-# Functions to set the log file to std::cout and std::cerr ++// Functions to set the log file to std::cout and std::cerr + + %ignore OBForceField::SetLogFile(std::ostream *pos); + %extend OpenBabel::OBForceField { diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch new file mode 100644 index 000000000000..7a0114975fff --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch @@ -0,0 +1,28 @@ +From b34edb6de512e5735d87cb0893804a4abd14f9b7 Mon Sep 17 00:00:00 2001 +From: baoilleach <baoilleach@71e0b675-c112-0410-beda-96664073b5c2> +Date: Mon, 1 Oct 2012 20:40:36 +0000 +Subject: [PATCH] scripts/python/testpybel.py: Minor fix to enable failing + test to pass. Failures due to the new MOL Chiral Flag data + that I stored a while ago. + +git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk@5022 71e0b675-c112-0410-beda-96664073b5c2 +--- + scripts/python/examples/testpybel.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/scripts/python/examples/testpybel.py b/scripts/python/examples/testpybel.py +index aa5fcd4..7951851 100644 +--- a/scripts/python/examples/testpybel.py ++++ b/scripts/python/examples/testpybel.py +@@ -336,7 +336,7 @@ class TestPybel(TestToolkit): + tpsaname = "TPSA" + Nbits = 3 + Nfpbits = 32 +- datakeys = ['NSC', 'Comment', 'OpenBabel Symmetry Classes'] ++ datakeys = ['NSC', 'Comment', 'OpenBabel Symmetry Classes', 'MOL Chiral Flag'] + + def testFP_FP3(self): + "Checking the results from FP3" +-- +1.7.12.3 + diff --git a/sci-chemistry/openbabel-python/metadata.xml b/sci-chemistry/openbabel-python/metadata.xml new file mode 100644 index 000000000000..2fec701db8fc --- /dev/null +++ b/sci-chemistry/openbabel-python/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> +OpenBabel is a chemical toolbox designed to speak the many languages of +chemical data. It's an open, collaborative project allowing anyone to +search, convert, analyze, or store data from molecular modeling, chemistry, +solid-state materials, biochemistry, or related areas. This package enables +to access OpenBabel library from Python programs. +</longdescription> + <upstream> + <remote-id type="sourceforge">openbabel</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild new file mode 100644 index 000000000000..593e536eb844 --- /dev/null +++ b/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild @@ -0,0 +1,90 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{3,4} ) + +inherit cmake-utils eutils multilib python-r1 + +DESCRIPTION="Python bindings for OpenBabel (including Pybel)" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" + +KEYWORDS="amd64 ~arm ppc x86 ~amd64-linux ~x86-linux" +SLOT="0" +LICENSE="GPL-2" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + !sci-chemistry/babel + ~sci-chemistry/openbabel-${PV} + sys-libs/zlib" +DEPEND="${RDEPEND} + >=dev-lang/swig-2" + +S="${WORKDIR}"/openbabel-${PV} + +PATCHES=( + "${FILESDIR}"/${P}-testpybel.patch + "${FILESDIR}"/${P}-bindings_only.patch + "${FILESDIR}"/${P}-swig-3.0.3.patch + ) + +src_prepare() { + cmake-utils_src_prepare + sed \ + -e "s:\"\.\.\":\"${EPREFIX}/usr\":g" \ + -i test/testbabel.py || die + swig -python -c++ -small -O -templatereduce -naturalvar \ + -I"${EPREFIX}/usr/include/openbabel-2.0" \ + -o scripts/python/openbabel-python.cpp \ + -DHAVE_EIGEN \ + -outdir scripts/python \ + scripts/openbabel-python.i \ + || die "Regeneration of openbabel-python.cpp failed" +} + +src_configure() { + my_impl_src_configure() { + local mycmakeargs="${mycmakeargs} + -DCMAKE_INSTALL_RPATH= + -DBINDINGS_ONLY=ON + -DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so" + -DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}" + -DLIB_INSTALL_DIR="${ED}/usr/$(get_libdir)/${EPYTHON}/site-packages" + -DPYTHON_BINDINGS=ON + -DPYTHON_EXECUTABLE=${PYTHON} + -DPYTHON_INCLUDE_DIR="${EPREFIX}/usr/include/${EPYTHON}" + -DPYTHON_INCLUDE_PATH="${EPREFIX}/usr/include/${EPYTHON}" + -DPYTHON_LIBRARY="${EPREFIX}/usr/$(get_libdir)/lib${EPYTHON}.so" + -DENABLE_TESTS=ON" + + cmake-utils_src_configure + } + + python_foreach_impl my_impl_src_configure +} + +src_compile() { + python_foreach_impl cmake-utils_src_make bindings_python +} + +src_test() { + python_foreach_impl cmake-utils_src_test -R py +} + +src_install() { + my_impl_src_install() { + cd "${BUILD_DIR}" || die + + cmake -DCOMPONENT=bindings_python -P cmake_install.cmake + + python_optimize + } + + python_foreach_impl my_impl_src_install +} diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest new file mode 100644 index 000000000000..082e5b029843 --- /dev/null +++ b/sci-chemistry/openbabel/Manifest @@ -0,0 +1 @@ +DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 WHIRLPOOL 74eff18b73d24c8f702e5573a58ba6afba8402e9ce8782de95dc0568575a7d2d632dbc8e8a98b3cd25efdfa7379494f7dcd449342c81ddf73f42a387bce77aaa diff --git a/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch b/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch new file mode 100644 index 000000000000..1354f52685c6 --- /dev/null +++ b/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch @@ -0,0 +1,27 @@ +diff -ru old/openbabel-2.3.0/test/CMakeLists.txt new/openbabel-2.3.0/test/CMakeLists.txt +--- old/openbabel-2.3.0/test/CMakeLists.txt 2010-10-26 17:39:01.000000000 +0300 ++++ new/openbabel-2.3.0/test/CMakeLists.txt 2010-11-14 18:13:32.000000000 +0200 +@@ -2,7 +2,7 @@ + add_definitions(-DTESTDATADIR="\\"${CMAKE_SOURCE_DIR}/test/files/\\"") + + # define FORMATDIR for location of format plugin binaries +-add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib/\\"") ++add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib${LIB_SUFFIX}/\\"") + + ########################################################### + # new tests using obtest.h +@@ -32,12 +35,12 @@ set(tests + uniqueid + ) + +-if (EIGEN2_FOUND) ++if(EIGEN2_FOUND OR EIGEN3_FOUND) + set(tests + align + ${tests} + ) +-endif (EIGEN2_FOUND) ++endif() + + set(TEST_PATH ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}) + diff --git a/sci-chemistry/openbabel/metadata.xml b/sci-chemistry/openbabel/metadata.xml new file mode 100644 index 000000000000..3353dfa452a4 --- /dev/null +++ b/sci-chemistry/openbabel/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> + Open Babel is a chemical toolbox designed to speak the many languages of + chemical data. It's an open, collaborative project allowing anyone to + search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas. + </longdescription> + <upstream> + <remote-id type="sourceforge">openbabel</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/openbabel/openbabel-2.3.2.ebuild b/sci-chemistry/openbabel/openbabel-2.3.2.ebuild new file mode 100644 index 000000000000..c0a06edd6006 --- /dev/null +++ b/sci-chemistry/openbabel/openbabel-2.3.2.ebuild @@ -0,0 +1,82 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +WX_GTK_VER="2.8" + +inherit cmake-utils eutils wxwidgets + +DESCRIPTION="Interconverts file formats used in molecular modeling" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="amd64 ~arm ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc openmp test wxwidgets" + +RDEPEND=" + !sci-chemistry/babel + dev-cpp/eigen:3 + dev-libs/libxml2:2 + sci-libs/inchi + sys-libs/zlib + wxwidgets? ( x11-libs/wxGTK:2.8[X] )" +DEPEND="${RDEPEND} + >=dev-util/cmake-2.4.8 + doc? ( app-doc/doxygen )" + +DOCS="AUTHORS ChangeLog NEWS README THANKS doc/*.inc doc/README* doc/*.mol2" + +PATCHES=( "${FILESDIR}"/${P}-test_lib_path.patch ) + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + FORTRAN_NEED_OPENMP=1 + fi +} + +src_configure() { + local mycmakeargs="" + mycmakeargs="${mycmakeargs} + -DOPENBABEL_USE_SYSTEM_INCHI=ON + $(cmake-utils_use_enable openmp OPENMP) + $(cmake-utils_use wxwidgets BUILD_GUI)" + + cmake-utils_src_configure +} + +src_install() { + dohtml doc/{*.html,*.png} + if use doc ; then + insinto /usr/share/doc/${PF}/API/html + doins doc/API/html/* + fi + + cmake-utils_src_install +} + +src_test() { + local mycmakeargs="" + mycmakeargs="${mycmakeargs} + -DOPENBABEL_USE_SYSTEM_INCHI=ON + -DPYTHON_EXECUTABLE=false + $(cmake-utils_use_enable openmp OPENMP) + $(cmake-utils_use wxwidgets BUILD_GUI) + $(cmake-utils_use_enable test TESTS)" + + cmake-utils_src_configure + cmake-utils_src_compile + cmake-utils_src_test -E py +} + +pkg_postinst() { + optfeature "perl support" sci-chemistry/openbabel-perl + optfeature "python support" sci-chemistry/openbabel-python +} diff --git a/sci-chemistry/ortep3/Manifest b/sci-chemistry/ortep3/Manifest new file mode 100644 index 000000000000..97e21c481c22 --- /dev/null +++ b/sci-chemistry/ortep3/Manifest @@ -0,0 +1 @@ +DIST ortep.f 177237 SHA256 622cdd2801d3959c08f71514de865cc18511fd8522b0b229467d0387047fc374 diff --git a/sci-chemistry/ortep3/metadata.xml b/sci-chemistry/ortep3/metadata.xml new file mode 100644 index 000000000000..e42d0af60f42 --- /dev/null +++ b/sci-chemistry/ortep3/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/ortep3/ortep3-1.0.3-r1.ebuild b/sci-chemistry/ortep3/ortep3-1.0.3-r1.ebuild new file mode 100644 index 000000000000..3850c40e6854 --- /dev/null +++ b/sci-chemistry/ortep3/ortep3-1.0.3-r1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit fortran-2 toolchain-funcs + +DESCRIPTION="Thermal ellipsoid plot program for crystal structure illustrations" +HOMEPAGE="http://www.ornl.gov/sci/ortep/" +SRC_URI="ftp://ftp.ornl.gov/pub/ortep/src/ortep.f" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + sci-libs/pgplot + x11-libs/libX11" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +src_unpack() { + cp "${DISTDIR}"/${A} "${S}" || die +} + +src_compile() { + COMMAND="$(tc-getFC) ${FFLAGS:- -O2} ${LDFLAGS} -o ${PN} ortep.f -lpgplot -lX11" + echo ${COMMAND} + ${COMMAND} || die "Compilation failed" +} + +src_install() { + dobin ${PN} +} diff --git a/sci-chemistry/p3d/Manifest b/sci-chemistry/p3d/Manifest new file mode 100644 index 000000000000..9b2f9b5b9c4d --- /dev/null +++ b/sci-chemistry/p3d/Manifest @@ -0,0 +1 @@ +DIST p3d-0.4.3.tar.gz 7213577 RMD160 2a251097bf7f83b27e519b20e4110fe330b2b6a3 SHA1 ced099dcaa28517c6095c1153f3a19bb6c78494c SHA256 b968eb37c0d27ad1f4f46f8a942fb2b62fbcdb50b31a1e66875e2cdc036a9932 diff --git a/sci-chemistry/p3d/metadata.xml b/sci-chemistry/p3d/metadata.xml new file mode 100644 index 000000000000..bd602bd0e68a --- /dev/null +++ b/sci-chemistry/p3d/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +p3d was developed in order to offer a Python module that is powerful and fast, +yet intuitive to use. The simplicity of p3d is due to the usage of object +oriented programming (i.e. atoms are treated as vectors), the implementation +of a query parser that translates queries readable by humans into a combination +of algebra set operations the fact that no additional Python packages are +necessary. The speed is due to the usage of a binary space partitioning (BSP) +tree which allows very fast queries in 3D (Henry et al. 1980). The additional +synergy is obtained by the flexible combination of both speed and complexity in +the queries to the structural data. The combination of these factors makes p3d +the optimal module to rapidly develop new and powerful bioinformatic tools that +follow the Python philosophy of making the source code readable. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/p3d/p3d-0.4.3.ebuild b/sci-chemistry/p3d/p3d-0.4.3.ebuild new file mode 100644 index 000000000000..294acb075860 --- /dev/null +++ b/sci-chemistry/p3d/p3d-0.4.3.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="2" +SUPPORT_PYTHON_ABIS="1" + +inherit distutils versionator + +MY_P="${PN}-$(replace_version_separator 3 -)" +GITHUB_ID="gb8b9a75" + +DESCRIPTION="Python module for structural bioinformatics" +HOMEPAGE="http://p3d.fufezan.net/" +SRC_URI="https://nodeload.github.com/fu/${PN}/tarball/${PV} -> ${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-3" +IUSE="examples" + +src_prepare() { + mv fu* ${P} + distutils_src_prepare +} + +src_install() { + distutils_src_install + if use examples; then + insinto /usr/share/${PN} + doins -r pdbs exampleScripts || die + fi +} diff --git a/sci-chemistry/p3d/p3d-9999.ebuild b/sci-chemistry/p3d/p3d-9999.ebuild new file mode 100644 index 000000000000..e0f8087a0cc2 --- /dev/null +++ b/sci-chemistry/p3d/p3d-9999.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="2" +SUPPORT_PYTHON_ABIS="1" + +inherit git-2 distutils versionator + +DESCRIPTION="Python module for structural bioinformatics" +HOMEPAGE="http://p3d.fufezan.net/" +SRC_URI="" +EGIT_REPO_URI="git://github.com/fu/p3d.git" + +SLOT="0" +KEYWORDS="" +LICENSE="GPL-3" +IUSE="examples" + +S="${WORKDIR}"/${PN} + +src_install() { + distutils_src_install + if use examples; then + insinto /usr/share/${PN} + doins -r pdbs exampleScripts || die + fi +} diff --git a/sci-chemistry/parassign/Manifest b/sci-chemistry/parassign/Manifest new file mode 100644 index 000000000000..d4edb48300ce --- /dev/null +++ b/sci-chemistry/parassign/Manifest @@ -0,0 +1 @@ +DIST PARAssign_Linux_x64_86.tgz 76693208 SHA256 56a322a8825c13cd3e7d90998471c47fb6062e79e2d20108b4fb6ed24664c89d SHA512 63018b0f1e3ce7821cebb90cd59ef5fdfa44b7ce6776956184b55a6247009f5e9df435332772dfa0db7294308c4d930ff0104daf45a46df709fb132dac10bd79 WHIRLPOOL 87ae85974f2a84c3814d261390e011f7ef2a012881df15f0f8ba4a7b5e88992e7932f12566847eaa38958394f7a243a4f0d536375e4640377d6f183e793bccc5 diff --git a/sci-chemistry/parassign/metadata.xml b/sci-chemistry/parassign/metadata.xml new file mode 100644 index 000000000000..144ad6d646ca --- /dev/null +++ b/sci-chemistry/parassign/metadata.xml @@ -0,0 +1,27 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +The use of paramagnetic NMR data for the refinement of structures of proteins +and protein complexes is widespread. However, the power of paramagnetism for +protein assignment has not yet been fully exploited. PARAssign is software that +uses pseudocontact shift data derived from several paramagnetic centers attached +to the protein to obtain amide and methyl assignments. The ability of PARAssign +to perform assignment when the positions of the paramagnetic centers are known +and unknown is demonstrated. PARAssign has been tested using synthetic data for +methyl assignment of a 47 kDa protein, and using both synthetic and experimental +data for amide assignment of a 14 kDa protein. The complex fitting space +involved in such an assignment procedure necessitates that good starting +conditions are found, both regarding placement and strength of paramagnetic +centers. These starting conditions are obtained through automated tensor +placement and user-defined tensor parameters. The results presented herein +demonstrate that PARAssign is able to successfully perform resonance assignment +in large systems with a high degree of reliability. This software provides a +method for obtaining the assignments of large systems, which may previously have +been unassignable, by using 2D NMR spectral data and a known protein structure. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/parassign/parassign-20130522.ebuild b/sci-chemistry/parassign/parassign-20130522.ebuild new file mode 100644 index 000000000000..8ecbd0060d10 --- /dev/null +++ b/sci-chemistry/parassign/parassign-20130522.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 python-r1 + +DESCRIPTION="Assign protein nuclei solely on the basis of pseudocontact shifts (PCS)" +HOMEPAGE="http://protchem.lic.leidenuniv.nl/software/parassign/registration" +SRC_URI="PARAssign_Linux_x64_86.tgz" +RESTRICT="fetch" + +SLOT="0" +LICENSE="Apache-2.0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS}" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/scientificpython[${PYTHON_USEDEP}] + sci-biology/biopython[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}]" + +S="${WORKDIR}"/PARAssign_Linux_x64_86/ + +src_prepare() { + sed \ + -e '1i#!/usr/bin/python2' \ + -i code/*py || die + + if use x86; then + sed \ + -e "s:munkres64:munkres:g" \ + -i modules/setup.py || die + elif use amd64; then + sed \ + -e "s:munkres:munkres64:g" \ + -i code/*py || die + fi + cd modules || die + rm *o *c || die + distutils-r1_src_prepare +} + +src_compile() { + cd modules || die + distutils-r1_src_compile +} + +src_install() { + python_parallel_foreach_impl python_doscript code/* || die + + dodoc PARAssign_Tutorial.pdf README + + cd modules || die + distutils-r1_src_install +} diff --git a/sci-chemistry/pdb-extract/Manifest b/sci-chemistry/pdb-extract/Manifest new file mode 100644 index 000000000000..328a586d96cd --- /dev/null +++ b/sci-chemistry/pdb-extract/Manifest @@ -0,0 +1,2 @@ +DIST pdb-extract-v3.004-prod-src.tar.gz 942450 RMD160 3d5d46e668a52109678fdf59afbe664dac1643f9 SHA1 7b5d7ce200d33e68fa352cd3658e382bc37e9768 SHA256 58bef2aba4869cdd16a79ddc588da5596a2ccd1f5c925f300b63b6d8299bb953 +DIST pdb-extract-v3.11-prod-src.tar.gz 1016140 RMD160 8845b8ec69b398c22fc398df34d056ed11c1f085 SHA1 4fb471068c220cbae9cbf0a8116fcb288c28b36b SHA256 cc56ab58e4b4f0914dcd61834cae673ade5b12688861ea5f0197a33f5939d131 diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch new file mode 100644 index 000000000000..3a6f5498ffba --- /dev/null +++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch @@ -0,0 +1,46 @@ +--- Makefile 2008-12-05 14:36:44.000000000 +0100 ++++ Makefile.new 2008-12-05 14:37:21.000000000 +0100 +@@ -19,13 +19,7 @@ + CHECKOUT_SCRIPT_MODULE = util + CHECKOUT_SCRIPT = checkout.sh + +-LIBDIRS = cifobj-common-v4.1 \ +- tables-v8.0 \ +- regex-v2.2 \ +- cif-file-v1.0 \ +- misclib-v2.2 \ +- cifparse-obj-v7.0 \ +- $(EXTRACT) ++LIBDIRS = $(EXTRACT) + + all: compile + +--- pdb-extract-v3.0/Makefile 2008-12-05 14:42:58.000000000 +0100 ++++ pdb-extract-v3.0/Makefile.new 2008-12-05 14:42:15.510315392 +0100 +@@ -6,6 +6,7 @@ + + M_INCL_DIR = ../include + M_LIB_DIR = ../lib ++M_LIB_DIR_GENTOO = @GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR + M_BIN_DIR = ../bin + + PROJ_DIR = . +@@ -37,12 +38,12 @@ + include ../etc/Makefile.platform + + # Dependent libraries for the pdbml-parser +-CIF_FILE_LIB = $(M_LIB_DIR)/cif-file.a +-CIFPARSE_LIB = $(M_LIB_DIR)/cifparse-obj.a +-CIF_TABLE_LIB = $(M_LIB_DIR)/cif-table-obj.a +-CIFOBJ_COMMON_LIB = $(M_LIB_DIR)/cifobj-common.a +-REGEX_LIB = $(M_LIB_DIR)/regex.a +-MISCLIB_LIB = $(M_LIB_DIR)/misclib.a ++CIF_FILE_LIB = $(M_LIB_DIR_GENTOO)/cif-file.a ++CIFPARSE_LIB = $(M_LIB_DIR_GENTOO)/cifparse-obj.a ++CIF_TABLE_LIB = $(M_LIB_DIR_GENTOO)/tables.a ++CIFOBJ_COMMON_LIB = $(M_LIB_DIR_GENTOO)/common.a ++REGEX_LIB = $(M_LIB_DIR_GENTOO)/regex.a ++MISCLIB_LIB = $(M_LIB_DIR_GENTOO)/misclib.a + + ALL_DEP_LIBS = $(CIF_FILE_LIB) $(CIFPARSE_LIB) \ + $(CIF_TABLE_LIB) $(CIFOBJ_COMMON_LIB) $(REGEX_LIB) $(MISCLIB_LIB) diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch new file mode 100644 index 000000000000..cdf48e4784c6 --- /dev/null +++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch @@ -0,0 +1,199 @@ +diff -Naur pdb-extract-v3.004-prod-src/Makefile pdb-extract-v3.004-prod-src.new/Makefile +--- pdb-extract-v3.004-prod-src/Makefile 2007-09-11 11:19:46.000000000 -0400 ++++ pdb-extract-v3.004-prod-src.new/Makefile 2009-12-03 21:34:10.000000000 -0500 +@@ -52,7 +52,7 @@ + echo "------------------------------------------------------------"; \ + echo "**** Making $$libdir ****"; \ + echo "------------------------------------------------------------"; \ +- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \ ++ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \ + done + + beta: +diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3 +--- pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 2007-09-11 11:19:46.000000000 -0400 ++++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3 2009-12-03 21:34:10.000000000 -0500 +@@ -91,7 +91,7 @@ + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -159,7 +159,7 @@ + STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) + + # Fortran linker + F77_LINKER=f77 +diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4 +--- pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 2007-09-11 11:19:46.000000000 -0400 ++++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4 2009-12-03 21:34:10.000000000 -0500 +@@ -92,7 +92,7 @@ + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -160,7 +160,7 @@ + STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) + + # Fortran linker + F77_LINKER=f77 +diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3 +--- pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 2007-09-11 11:19:46.000000000 -0400 ++++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3 2009-12-03 21:34:10.000000000 -0500 +@@ -6,6 +6,8 @@ + ## + ########################################################################## + ++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR ++ + #-----Lexer and Parser section-------------------------------------------# + + # Lexer executable +@@ -89,7 +91,7 @@ + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -107,8 +109,8 @@ + C_WARNINGS=$(WARNINGS) + + # C compiler flags +-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) +-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ ++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ + $(INCLUDES) + + ## C++ compiler +@@ -128,9 +130,9 @@ + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ ++C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ + $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party + # source code that is not maintained by PDB +@@ -144,7 +146,7 @@ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -154,11 +156,11 @@ + #-----Linkers section----------------------------------------------------# + + # Static linking option. If not defined, dynamic linking is used. +-STATIC_LINKING=-static ++STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) +-LDFLAGS_NO_STATIC=$(ABI) -w ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) ++LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w + + # Fortran linker + F77_LINKER=f77 +diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4 +--- pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 2007-09-11 11:19:46.000000000 -0400 ++++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4 2009-12-03 21:34:10.000000000 -0500 +@@ -6,6 +6,8 @@ + ## + ########################################################################## + ++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR ++ + #-----Lexer and Parser section-------------------------------------------# + + # Lexer executable +@@ -34,7 +36,7 @@ + + # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all + # warnings as errors. +-WARNINGS_AS_ERRORS=-Werror ++WARNINGS_AS_ERRORS= + + # ALL_WARNINGS defines flags to instruct all compilers to report all + # warnings. +@@ -90,7 +92,7 @@ + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -108,8 +110,8 @@ + C_WARNINGS=$(WARNINGS) + + # C compiler flags +-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) +-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ ++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ + $(INCLUDES) + + ## C++ compiler +@@ -129,9 +131,9 @@ + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ ++C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ + $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party + # source code that is not maintained by PDB +@@ -145,7 +147,7 @@ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -155,11 +157,11 @@ + #-----Linkers section----------------------------------------------------# + + # Static linking option. If not defined, dynamic linking is used. +-STATIC_LINKING=-static ++STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) +-LDFLAGS_NO_STATIC=$(ABI) -w ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) ++LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w + + # Fortran linker + F77_LINKER=f77 diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch new file mode 100644 index 000000000000..6506713742b6 --- /dev/null +++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch @@ -0,0 +1,11 @@ +--- pdb-extract-v3.0/src/extract.C 2007-09-11 17:19:48.000000000 +0200 ++++ pdb-extract-v3.0/src/extract.C.new 2008-12-05 17:49:59.000000000 +0100 +@@ -1689,7 +1689,7 @@ + open_file_error(inpfile, "get_mmcif"); + } + +- (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT"); ++ (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT_ROOT"); + if(temp != NULL) { + strcpy(pdb_extract, ""); + strcpy(pdb_extract_sf, ""); diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch new file mode 100644 index 000000000000..6907399c27df --- /dev/null +++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch @@ -0,0 +1,20 @@ +--- cifobj-common-v4.1/src/GenString.C 2008-11-13 10:44:01.000000000 +0100 ++++ cifobj-common-v4.1/src/GenString.C.new 2008-11-13 10:43:54.000000000 +0100 +@@ -144,6 +144,7 @@ + #include <string> + #include <algorithm> + #include <sstream> ++#include <string.h> + + #include "GenString.h" + +--- tables-v8.0/src/ISTable.C 2007-09-11 17:19:47.000000000 +0200 ++++ tables-v8.0/src/ISTable.C.new 2008-11-13 10:48:18.000000000 +0100 +@@ -150,6 +150,7 @@ + #include <sstream> + #include <iostream> + #include <iomanip> ++#include <limits.h> + + #include "Exceptions.h" + #include "GenString.h" diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch new file mode 100644 index 000000000000..7383811b5bfd --- /dev/null +++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch @@ -0,0 +1,207 @@ + Makefile | 2 +- + etc/make.platform.darwin3 | 4 ++-- + etc/make.platform.darwin4 | 4 ++-- + etc/make.platform.gnu3 | 20 +++++++++++--------- + etc/make.platform.gnu4 | 20 +++++++++++--------- + 5 files changed, 27 insertions(+), 23 deletions(-) + +diff --git a/Makefile b/Makefile +index 627d256..72c7e59 100644 +--- a/Makefile ++++ b/Makefile +@@ -52,7 +52,7 @@ compile: + echo "------------------------------------------------------------"; \ + echo "**** Making $$libdir ****"; \ + echo "------------------------------------------------------------"; \ +- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \ ++ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \ + done + + beta: +diff --git a/etc/make.platform.darwin3 b/etc/make.platform.darwin3 +index c5f7b06..4c1c97c 100644 +--- a/etc/make.platform.darwin3 ++++ b/etc/make.platform.darwin3 +@@ -91,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -159,7 +159,7 @@ F77LIBS= + STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) + + # Fortran linker + F77_LINKER=f77 +diff --git a/etc/make.platform.darwin4 b/etc/make.platform.darwin4 +index 4619b34..f481fdb 100644 +--- a/etc/make.platform.darwin4 ++++ b/etc/make.platform.darwin4 +@@ -92,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -160,7 +160,7 @@ F77LIBS= + STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) + + # Fortran linker + F77_LINKER=f77 +diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3 +index 7fd442e..9bec4dc 100644 +--- a/etc/make.platform.gnu3 ++++ b/etc/make.platform.gnu3 +@@ -6,6 +6,8 @@ + ## + ########################################################################## + ++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR ++ + #-----Lexer and Parser section-------------------------------------------# + + # Lexer executable +@@ -89,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -107,8 +109,8 @@ NON_ANSI_C_FLAG= + C_WARNINGS=$(WARNINGS) + + # C compiler flags +-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) +-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ ++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ + $(INCLUDES) + + ## C++ compiler +@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ ++C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ + $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party + # source code that is not maintained by PDB +@@ -144,7 +146,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -154,11 +156,11 @@ F77LIBS= + #-----Linkers section----------------------------------------------------# + + # Static linking option. If not defined, dynamic linking is used. +-STATIC_LINKING=-static ++STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) +-LDFLAGS_NO_STATIC=$(ABI) -w ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) ++LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w + + # Fortran linker + F77_LINKER=f77 +diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4 +index 78a0007..bc85308 100644 +--- a/etc/make.platform.gnu4 ++++ b/etc/make.platform.gnu4 +@@ -6,6 +6,8 @@ + ## + ########################################################################## + ++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR ++ + #-----Lexer and Parser section-------------------------------------------# + + # Lexer executable +@@ -34,7 +36,7 @@ ABI= + + # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all + # warnings as errors. +-WARNINGS_AS_ERRORS=-Werror ++WARNINGS_AS_ERRORS= + + # ALL_WARNINGS defines flags to instruct all compilers to report all + # warnings. +@@ -90,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -108,8 +110,8 @@ NON_ANSI_C_FLAG= + C_WARNINGS=$(WARNINGS) + + # C compiler flags +-CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) +-CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) ++CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) + + ## C++ compiler + ## This part defines C++ compiler information +@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS=$(CCC_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ ++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ + $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES) + + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party +@@ -145,7 +147,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -158,8 +160,8 @@ F77LIBS= + STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) +-LDFLAGS_NO_STATIC=$(ABI) -w ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) ++LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w + + # Fortran linker + F77_LINKER=f77 diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch new file mode 100644 index 000000000000..5284bd745d53 --- /dev/null +++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch @@ -0,0 +1,64 @@ + common-v4.5/src/mapped_ptr_vector.C | 14 +++++++------- + 1 files changed, 7 insertions(+), 7 deletions(-) + +diff --git a/common-v4.5/src/mapped_ptr_vector.C b/common-v4.5/src/mapped_ptr_vector.C +index d7c61f3..e20a236 100644 +--- a/common-v4.5/src/mapped_ptr_vector.C ++++ b/common-v4.5/src/mapped_ptr_vector.C +@@ -263,12 +263,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(T* inP, + _vector.push_back(inP); + + typename tIndex::value_type valuePair(inP->GetName(), +- make_pair(_vector.size() - 1, fileIndex)); ++ std::make_pair(_vector.size() - 1, fileIndex)); + + _index.insert(valuePair); + + _currentName = inP->GetName(); +- _currentIndices = make_pair(_vector.size() - 1, fileIndex); ++ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex); + + } + +@@ -281,12 +281,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(const string& name, + _vector.push_back(NULL); + + typename tIndex::value_type valuePair(name, +- make_pair(_vector.size() - 1, fileIndex)); ++ std::make_pair(_vector.size() - 1, fileIndex)); + + _index.insert(valuePair); + + _currentName = name; +- _currentIndices = make_pair(_vector.size() - 1, fileIndex); ++ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex); + } + + +@@ -454,7 +454,7 @@ void mapped_ptr_vector<T, StringCompareT>::erase(const string& name) + if (is_equal(_currentName, name, keyComp)) + { + _currentName.clear(); +- _currentIndices = make_pair(_vector.size(), (unsigned int)0); ++ _currentIndices = std::make_pair(_vector.size(), (unsigned int)0); + } + + } +@@ -539,7 +539,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic + if (_vector.empty()) + { + // Empty container. Return invalid index. +- return(make_pair(_vector.size(), (unsigned int)0)); ++ return(std::make_pair(_vector.size(), (unsigned int)0)); + } + + typename tIndex::key_compare keyComp = _index.key_comp(); +@@ -563,7 +563,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic + else + { + // Not found. Return invalid index. +- return(make_pair(_vector.size(), (unsigned int)0)); ++ return(std::make_pair(_vector.size(), (unsigned int)0)); + } + } + diff --git a/sci-chemistry/pdb-extract/metadata.xml b/sci-chemistry/pdb-extract/metadata.xml new file mode 100644 index 000000000000..e42d0af60f42 --- /dev/null +++ b/sci-chemistry/pdb-extract/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild new file mode 100644 index 000000000000..836d76f5c007 --- /dev/null +++ b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +inherit eutils toolchain-funcs multilib prefix + +MY_P="${PN}-v${PV}-prod-src" + +DESCRIPTION="Tools for extracting mmCIF data from structure determination applications" +HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html" +SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz" + +LICENSE="PDB" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="!<app-text/html-xml-utils-5.3" +DEPEND="${RDEPEND} + >=sci-libs/cifparse-obj-7.025" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-cflags-install.patch \ + "${FILESDIR}"/${P}-gcc-4.3.patch \ + "${FILESDIR}"/${P}-Makefile.patch \ + "${FILESDIR}"/${P}-env.patch + + sed -i "s:GENTOOLIBDIR:$(get_libdir):g" \ + pdb-extract-v3.0/Makefile \ + || die "Failed to fix libdir" + + # Get rid of unneeded directories, to make sure we use system files + ebegin "Deleting redundant directories" + rm -rf cif-file-v1.0 cifobj-common-v4.1 cifparse-obj-v7.0 \ + misclib-v2.2 regex-v2.2 tables-v8.0 + eend + + sed -i \ + -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \ + -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ + -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \ + -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ + "${S}"/etc/make.* \ + || die "Failed to fix makefiles" + + eprefixify pdb-extract-v3.0/Makefile etc/* +} + +src_install() { + exeinto /usr/libexec/ccp4/bin + doexe bin/pdb_extract{,_sf} bin/extract \ + || die "failed to install binaries" + insinto /usr/include/rcsb + doins include/* || die "failed to install include files" + dodoc README* || die "failed to install docs" + insinto /usr/share/rcsb/ + doins -r pdb-extract-data || die "failed to install data files" + + cat >> "${T}"/envd <<- EOF + PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/" + PDB_EXTRACT_ROOT="${EPREFIX}/usr/" + EOF + + newenvd "${T}"/envd 20pdb-extract \ + || die "failed to install env files" +} diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild new file mode 100644 index 000000000000..04351c8a125a --- /dev/null +++ b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs multilib prefix + +MY_P="${PN}-v${PV}-prod-src" + +DESCRIPTION="Tools for extracting mmCIF data from structure determination applications" +HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html" +SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz" + +LICENSE="PDB" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="!<app-text/html-xml-utils-5.3" +DEPEND="${RDEPEND} + >=sci-libs/cifparse-obj-7.025" + +S="${WORKDIR}/${MY_P}" + +MAKEOPTS+=" -j1" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-cflags-install.patch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${PN}-3.004-env.patch + + sed -i \ + -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \ + -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ + -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \ + -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ + "${S}"/etc/make.* \ + || die "Failed to fix makefiles" + + eprefixify pdb-extract-v3.0/Makefile etc/* +} + +src_install() { + exeinto /usr/libexec/ccp4/bin + doexe bin/pdb_extract{,_sf} bin/extract + insinto /usr/include/rcsb + doins include/* + dodoc README* + insinto /usr/share/rcsb/ + doins -r pdb-extract-data + + cat >> "${T}"/envd <<- EOF + PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/" + PDB_EXTRACT_ROOT="${EPREFIX}/usr/" + EOF + + newenvd "${T}"/envd 20pdb-extract +} diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest new file mode 100644 index 000000000000..bf2e4bfa7dce --- /dev/null +++ b/sci-chemistry/pdb-tools/Manifest @@ -0,0 +1 @@ +DIST pdbTools_0.2.1.tar.gz 103835 SHA256 317a5246e806a2b3d0425d080d679646fc77388e3e855412527603f945fa37ae SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 WHIRLPOOL 36d8cf71ba9f9b28e3ad59828539f4e94bbb8bc4514f050ddcbec63857b154ecdc7c32c2945c0d15f4d718c4fe5ab3adcb2e62a4368bfd819b80e9641a9dfd88 diff --git a/sci-chemistry/pdb-tools/metadata.xml b/sci-chemistry/pdb-tools/metadata.xml new file mode 100644 index 000000000000..13e9a3c93979 --- /dev/null +++ b/sci-chemistry/pdb-tools/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <upstream> + <remote-id type="google-code">pdb-tools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild new file mode 100644 index 000000000000..ad4ab1dec397 --- /dev/null +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 pypy ) + +inherit fortran-2 python-single-r1 toolchain-funcs + +MY_PN="pdbTools" + +DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files" +HOMEPAGE="http://code.google.com/p/pdb-tools/" +SRC_URI="http://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS}" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_PN}_${PV} + +pkg_setup() { + python-single-r1_pkg_setup + fortran-2_pkg_setup +} + +src_prepare() { + sed \ + -e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \ + -i pdb_sasa.py || die + sed \ + -e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \ + -i pdb_satk.py || die + sed \ + -e 's:> %:>%:g' \ + -i pdb_seq.py || die +} + +src_compile() { + mkdir bin + cd satk + for i in *.f; do + einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}" + $(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die + $(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die + sed \ + -e "s:${i/.f}.out:${i/.f}:g" \ + -i ../pdb_satk.py || die + done +} + +src_install() { + local script + insinto /usr/share/${PN} + doins -r pdb_data/peptides + rm -rf pdb_data/peptides || die + + python_domodule helper pdb_data + + python_moduleinto ${PN/-/_} + python_domodule *.py + + for i in pdb_*.py; do + cat > ${i/.py} <<- EOF + #!${EPREFIX}/bin/bash + ${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@ + EOF + dobin ${i/.py} + done + + dobin bin/* + dodoc README +} diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild new file mode 100644 index 000000000000..e56798f3c95b --- /dev/null +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit fortran-2 python-single-r1 toolchain-funcs + +MY_PN="pdbTools" + +DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files" +HOMEPAGE="http://code.google.com/p/pdb-tools/" +SRC_URI="http://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS}" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_PN}_${PV} + +pkg_setup() { + python-single-r1_pkg_setup + fortran-2_pkg_setup +} + +src_prepare() { + sed \ + -e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \ + -i pdb_sasa.py || die + sed \ + -e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \ + -i pdb_satk.py || die + sed \ + -e 's:> %:>%:g' \ + -i pdb_seq.py || die + + sed \ + -e "/import/s:helper:${PN/-/_}.helper:g" \ + -i *.py || die +} + +src_compile() { + mkdir bin + cd satk + for i in *.f; do + einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}" + $(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die + $(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die + sed \ + -e "s:${i/.f}.out:${i/.f}:g" \ + -i ../pdb_satk.py || die + done +} + +src_install() { + local script + insinto /usr/share/${PN} + doins -r pdb_data/peptides + rm -rf pdb_data/peptides || die + + python_domodule pdb_data + + python_moduleinto ${PN/-/_} + python_domodule helper *.py + + for i in pdb_*.py; do + cat > ${i/.py} <<- EOF + #!${EPREFIX}/bin/bash + ${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@ + EOF + dobin ${i/.py} + done + + dobin bin/* + dodoc README +} diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest new file mode 100644 index 000000000000..a34457524075 --- /dev/null +++ b/sci-chemistry/pdb2pqr/Manifest @@ -0,0 +1 @@ +DIST pdb2pqr-src-1.9.0.tar.gz 9051969 SHA256 d9d91bf27a023732be33d1d780ef283ae28d3b0e256c53e86c37ac001dd7ef53 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f WHIRLPOOL 4a4b883200dad3e7467392e508c2372ad6876e78005da14e5747f3b7b12d0e3d5695e3cc590812b835ae67703819b201620809dff05af0a7c363c23d22046bae diff --git a/sci-chemistry/pdb2pqr/files/pdb2pka b/sci-chemistry/pdb2pqr/files/pdb2pka new file mode 100644 index 000000000000..2406b0c4773f --- /dev/null +++ b/sci-chemistry/pdb2pqr/files/pdb2pka @@ -0,0 +1,13 @@ +#!/usr/bin/env python + +import subprocess +import site +import sys +import os + +sitepackages = site.getsitepackages()[0] + +_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pka", "pka.py")] +_cmd.extend(sys.argv[1:]) + +subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr) diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr b/sci-chemistry/pdb2pqr/files/pdb2pqr new file mode 100644 index 000000000000..8c0635aea94e --- /dev/null +++ b/sci-chemistry/pdb2pqr/files/pdb2pqr @@ -0,0 +1,13 @@ +#!/usr/bin/env python + +import subprocess +import site +import sys +import os + +sitepackages = site.getsitepackages()[0] + +_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pqr.py")] +_cmd.extend(sys.argv[1:]) + +subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr) diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch new file mode 100644 index 000000000000..fac32b233e6b --- /dev/null +++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch @@ -0,0 +1,45 @@ + pdb2pka/SConscript | 9 ++++++++- + pdb2pka/substruct/SConscript | 6 ++++++ + 2 files changed, 14 insertions(+), 1 deletion(-) + +diff --git a/pdb2pka/SConscript b/pdb2pka/SConscript +index 583cdc5..6c30011 100644 +--- a/pdb2pka/SConscript ++++ b/pdb2pka/SConscript +@@ -1,4 +1,11 @@ + Import('env')
++import os
++
++env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
++env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
++env['CXX'] = os.environ['CXX']
++env['LINK'] = os.environ['CXX']
++
+
+ if env['REBUILD_SWIG']:
+ pyc = env.LoadableModule('_pMC_mult', ['pMC_mult.cpp', 'pMC_mult.i'])
+@@ -9,4 +16,4 @@ Default(pyc) +
+ algorithms_module = SConscript('substruct/SConscript')
+
+-Return('pyc algorithms_module') +\ No newline at end of file ++Return('pyc algorithms_module')
+diff --git a/pdb2pka/substruct/SConscript b/pdb2pka/substruct/SConscript +index 7dbcdb0..56fb577 100644 +--- a/pdb2pka/substruct/SConscript ++++ b/pdb2pka/substruct/SConscript +@@ -1,7 +1,13 @@ + import distutils
+ import numpy
++import os
+ Import('env')
+
++env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
++env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
++env['CXX'] = os.environ['CXX']
++env['LINK'] = os.environ['CXX']
++
+ env.Append(CPPPATH=[distutils.sysconfig.get_python_inc(), numpy.get_include()])
+
+ algorithms_pyc = env.LoadableModule('Algorithms', ['Algorithms.cpp'])
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch new file mode 100644 index 000000000000..2695b013c66a --- /dev/null +++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch @@ -0,0 +1,15 @@ + SConscript-install.py | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/SConscript-install.py b/SConscript-install.py +index e2f9f09..1fdf1a8 100644 +--- a/SConscript-install.py ++++ b/SConscript-install.py +@@ -41,6 +41,7 @@ def installFile(file_name, build_target='install'): + if GetOption("clean"):
+ env.Default(result)
+ Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), result))
++ Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))
+ else:
+ Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))
+
diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml new file mode 100644 index 000000000000..81003ba2152a --- /dev/null +++ b/sci-chemistry/pdb2pqr/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <use> + <flag name="opal">Add web interface via opal</flag> + <flag name="pdb2pka">Install experimental pdb2pka interface</flag> + </use> + <upstream> + <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild new file mode 100644 index 000000000000..7359b9094128 --- /dev/null +++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild @@ -0,0 +1,130 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs + +DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations" +HOMEPAGE="http://www.poissonboltzmann.org/" +SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz" + +SLOT="0" +LICENSE="BSD" +IUSE="doc examples opal +pdb2pka" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + dev-python/numpy[${PYTHON_USEDEP}] + sci-chemistry/openbabel-python[${PYTHON_USEDEP}] + opal? ( dev-python/zsi[${PYTHON_USEDEP}] ) + pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )" +DEPEND="${RDEPEND} + dev-lang/swig:0" + +PATCHES=( + "${FILESDIR}"/${P}-flags.patch + "${FILESDIR}"/${P}-install-py.patch +) + +pkg_setup() { + if [[ -z ${MAXATOMS} ]]; then + einfo "If you like to have support for more then 10000 atoms," + einfo "export MAXATOMS=\"your value\"" + export MAXATOMS=10000 + else + einfo "Allow usage of ${MAXATOMS} during calculations" + fi + fortran-2_pkg_setup +} + +src_prepare() { + find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die + + export CXXFLAGS="${CXXFLAGS}" + export LDFLAGS="${LDFLAGS}" + + epatch ${PATCHES[@]} + tc-export CXX + rm -rf scons || die + + python_copy_sources +} + +src_configure() { + python_configure() { + cd "${BUILD_DIR}" || die + + cat > build_config.py <<- EOF + PREFIX="${D}/$(python_get_sitedir)/${PN}" + #URL="http://<COMPUTER NAME>/pdb2pqr/" + APBS="${EPREFIX}/usr/bin/apbs" + #OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8" + #APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3" + MAX_ATOMS=${MAXATOMS} + BUILD_PDB2PKA=$(usex pdb2pka True False) + REBUILD_SWIG=True + EOF + } + + python_foreach_impl python_configure +} + +src_compile() { + python_compile() { + cd "${BUILD_DIR}" || die + escons + } + python_foreach_impl python_compile +} + +src_test() { + python_test() { + local myesconsargs=( -j1 ) + cd "${BUILD_DIR}" || die + escons test + escons advtest + escons complete-test + } + python_foreach_impl python_test +} + +src_install() { + dodir /usr/share/doc/${PF}/html + python_install() { + local lib + + cd "${BUILD_DIR}" || die + + escons install + + find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die + + python_doscript "${FILESDIR}"/{${PN},pdb2pka} + + for lib in apbslib.py{,c,o}; do + dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib} + done + dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so + python_optimize + } + python_foreach_impl python_install + + if use doc; then + pushd doc > /dev/null + docinto html + dodoc -r *.html images pydoc + popd > /dev/null + fi + + use examples && \ + insinto /usr/share/${PN}/ && \ + doins -r examples + + dodoc *md NEWS +} diff --git a/sci-chemistry/pdbcat/Manifest b/sci-chemistry/pdbcat/Manifest new file mode 100644 index 000000000000..80690fe7ac00 --- /dev/null +++ b/sci-chemistry/pdbcat/Manifest @@ -0,0 +1 @@ +DIST pdbcat-1.3.tar.gz 12750 SHA256 a9c554c00b34e5131ca1be61aad9332ab26eca5a905b716c47f657521368babc SHA512 369ac0c4c1d8396eaa0450feb9852d2d75ebd9862a2e403ccd42a2801e924f99c28c5d71c0b66feb4588076a8948b503823d2c75420128dd04d020253f821f4c WHIRLPOOL ba6599d06814929bf23c83bb6df7084592fcc23603a8e3116e2661df3c9d97b335c627d09249be6c862466b2d83a0100d94b366df171e1c45ec6221a22b2ca78 diff --git a/sci-chemistry/pdbcat/files/CMakeLists.txt b/sci-chemistry/pdbcat/files/CMakeLists.txt new file mode 100644 index 000000000000..7a6f348f5929 --- /dev/null +++ b/sci-chemistry/pdbcat/files/CMakeLists.txt @@ -0,0 +1,11 @@ +cmake_minimum_required (VERSION 2.6) +project (pdbcat) +add_executable(pdbcat + Common.C + Common.h + pdbcat.C + PDBData.C + PDBData.h) + +install (TARGETS pdbcat DESTINATION bin) + diff --git a/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch b/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch new file mode 100644 index 000000000000..b45c36bd8a8d --- /dev/null +++ b/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch @@ -0,0 +1,17 @@ + pdbcat.C | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/pdbcat.C b/pdbcat.C +index 0786d9b..387edf9 100644 +--- a/pdbcat.C ++++ b/pdbcat.C +@@ -17,7 +17,8 @@ + #include <stdlib.h> // for exit + #include <stdio.h> // for feof() and other file manip stuff + #include <string.h> // for strcasecmp +-#include <iostream.h> ++#include <iostream> ++using namespace std; + #include "Common.h" + #include "PDBData.h" + diff --git a/sci-chemistry/pdbcat/metadata.xml b/sci-chemistry/pdbcat/metadata.xml new file mode 100644 index 000000000000..54c920d084c3 --- /dev/null +++ b/sci-chemistry/pdbcat/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +The Brookhaven Protein Data Bank stores atomic coordinate information +for protein structures in a column based format. This is designed to +be read easily read by FORTRAN programs. Indeed, if you get the +format description (from anonymous ftp to ftp.pdb.bnl.gov, the file +/pub/format.desc.ps) they show the single input line needed to read +each record type. +However, I am a C/C++ programmer in the Unix environment. It is a +easier for me to deal with field based input than column based ones. +If the fields are white space delimited I can easily use awk and perl +to manipulate the coordinate information. So I needed some way to +convert the ATOM and HETATM records of PDB files from the standard +column based format to a field based one and back again. It needed +to denote missing fields if they exist. +That converter is `pdbcat'. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/pdbcat/pdbcat-1.3.ebuild b/sci-chemistry/pdbcat/pdbcat-1.3.ebuild new file mode 100644 index 000000000000..f0d0b263a446 --- /dev/null +++ b/sci-chemistry/pdbcat/pdbcat-1.3.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils + +DESCRIPTION="Manipulate and process PDB files using commonly available tools such as Perl, awk, etc" +HOMEPAGE="http://www.ks.uiuc.edu/Development/MDTools/pdbcat/" +SRC_URI="http://www.ks.uiuc.edu/Development/MDTools/${PN}/files/${P}.tar.gz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +PATCHES=( "${FILESDIR}"/${P}-gcc.patch ) +DOCS=( README ) + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + cmake-utils_src_prepare +} diff --git a/sci-chemistry/pdbcns/Manifest b/sci-chemistry/pdbcns/Manifest new file mode 100644 index 000000000000..f6f839594082 --- /dev/null +++ b/sci-chemistry/pdbcns/Manifest @@ -0,0 +1 @@ +DIST pdbcns.2.0.010504.perl.tgz 6806 RMD160 9398bb4e766b45365827663e8cf72eee63ec42a7 SHA1 61f9a8655b2d6d2df6709d8b5bc853de0498fe4f SHA256 a2c66e44e036b6a1ff2eff90b59c4adf20edb70d3f704bd7bc7f356040d8f98a diff --git a/sci-chemistry/pdbcns/metadata.xml b/sci-chemistry/pdbcns/metadata.xml new file mode 100644 index 000000000000..1837bbc07a6e --- /dev/null +++ b/sci-chemistry/pdbcns/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild b/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild new file mode 100644 index 000000000000..94b8c6138845 --- /dev/null +++ b/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +DESCRIPTION="Convert atom names for common amino acids and nucleic acid bases from PDB format to CNS or back" +HOMEPAGE="http://www.mybiosoftware.com/3d-molecular-model/314/" +#SRC_URI="http://kinemage.biochem.duke.edu/php/downlode.php?filename=/downloads/software/scripts/${PN}.${PV}.perl.tgz" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${PN}.${PV}.perl.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl" + +S="${WORKDIR}"/${PN} + +src_install() { + newbin ${PN}*.pl ${PN} + dohtml *html +} diff --git a/sci-chemistry/pdbmat/Manifest b/sci-chemistry/pdbmat/Manifest new file mode 100644 index 000000000000..2a19bccb5f04 --- /dev/null +++ b/sci-chemistry/pdbmat/Manifest @@ -0,0 +1 @@ +DIST pdbmat-3.89.tar.gz 124727 SHA256 98f75acd3da3f172213de0688825abad8b3a59c516b5b4ac411a494f6d355f72 SHA512 2c7f8f32344fe1abc662878c2556c10bd6671e683787231827399866f485389c3a63253b00d5a5bdbe8d0b8b779891e846962c9372d927b94c45f0fac59a4fb6 WHIRLPOOL 62f0b8cb2a99797d49c427a085ad24b41e045ba96433cb8c1769c614402cf729737b2335fcb356ad42de1e24079eadccd2c3db6eaa8ff062eb1249a13723b7f0 diff --git a/sci-chemistry/pdbmat/files/CMakeLists.txt b/sci-chemistry/pdbmat/files/CMakeLists.txt new file mode 100644 index 000000000000..2f1937d84b3f --- /dev/null +++ b/sci-chemistry/pdbmat/files/CMakeLists.txt @@ -0,0 +1,14 @@ +cmake_minimum_required (VERSION 2.6) +project (PDBMAT Fortran) + +option (EXAMPLES "Instal additional example files" OFF) + +add_executable(diagstd diagstd.f) +add_executable(pdbmat pdbmat.f) + +install (TARGETS diagstd pdbmat DESTINATION bin) +install (FILES diagstd.README pdbmat.README DESTINATION share/doc/pdbmat) + +if ( EXAMPLES ) + install (DIRECTORY ../Try_ENM2011 DESTINATION share/pdbmat/examples) +endif (EXAMPLES) diff --git a/sci-chemistry/pdbmat/metadata.xml b/sci-chemistry/pdbmat/metadata.xml new file mode 100644 index 000000000000..d542eb59e001 --- /dev/null +++ b/sci-chemistry/pdbmat/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +A fortran program in which Tirion's model (also called the Elastic Network +Model) is implemented. Within the frame of this model, atoms (particles) +less than cutoff (angstroms) away from each others are linked by springs of +same strength. Alternatively, a list of interacting atoms can be given to the +program. +Requirements: a file with the coordinates of the system, in PDB (Protein Data +Bank) or "x y z mass" format. + +Output: the hessian (the mass-weighted second derivatives of energy matrix), +in the "i j non-zero-ij-matrix-element" format. + +Diagstd, a fortran program with a standard diagonalization routine, can next +be used in order to obtain the corresponding normal modes of the system. If +the system is large, the RTB approximation can prove usefull (see below). +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/pdbmat/pdbmat-3.89.ebuild b/sci-chemistry/pdbmat/pdbmat-3.89.ebuild new file mode 100644 index 000000000000..89445471ef73 --- /dev/null +++ b/sci-chemistry/pdbmat/pdbmat-3.89.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils fortran-2 + +DESCRIPTION="Calculate Tirion's model from pdb structures" +HOMEPAGE="http://ecole.modelisation.free.fr/modes.html" +SRC_URI="http://ecole.modelisation.free.fr/enm2011.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="CeCILL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +S="${WORKDIR}"/Source_ENM2011 + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die +} + +src_configure() { + mycmakeargs=( + $(cmake-utils_use examples EXAMPLES) + ) + cmake-utils_src_configure +} diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest new file mode 100644 index 000000000000..33872db5dc96 --- /dev/null +++ b/sci-chemistry/phaser/Manifest @@ -0,0 +1 @@ +DIST ccp4-6.1.13-phaser-cctbx-src.tar.gz 22021353 SHA256 e6c4365cb34da5ce2dd5f1e74b8927258064016194446163418c8a3139a4b804 diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch new file mode 100644 index 000000000000..5311cb332785 --- /dev/null +++ b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch @@ -0,0 +1,13 @@ +diff --git a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py +index 3b1bd3a..8939a74 100755 +--- a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py ++++ b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py +@@ -802,8 +802,6 @@ class environment: + else: + action = self.write_bin_sh_dispatcher + ext = "" +- try: os.chmod(source_file, 0755) +- except OSError: pass + target_file_ext = target_file + ext + remove_or_rename(target_file_ext) + try: action(source_file, target_file_ext) diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml new file mode 100644 index 000000000000..6b4826474daa --- /dev/null +++ b/sci-chemistry/phaser/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <description>ccp4 maintainer</description> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild new file mode 100644 index 000000000000..86fa57f52603 --- /dev/null +++ b/sci-chemistry/phaser/phaser-2.1.4.ebuild @@ -0,0 +1,115 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils flag-o-matic python-single-r1 toolchain-funcs + +CCP4VER="6.1.13" + +DESCRIPTION="A program for phasing macromolecular crystal structures" +HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser" +SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-${PN}-cctbx-src.tar.gz" + +LICENSE="|| ( phaser phaser-com ccp4 )" +SLOT="0" +#KEYWORDS="~amd64 ~x86" +KEYWORDS="" +IUSE="openmp" + +RDEPEND="" +DEPEND="${RDEPEND} + app-shells/tcsh" + +S="${WORKDIR}"/ccp4-${CCP4VER} + +src_prepare() { + epatch \ + "${FILESDIR}"/phaser-2.1.4-chmod.patch \ + "${FILESDIR}"/phaser-2.1.4-ldflags.patch + + use openmp && append-flags -fopenmp + + for i in ${CXXFLAGS}; do + OPTS="${OPTS} \"${i}\"," + done + + OPTS=${OPTS%,} + + sed -i \ + -e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \ + "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die + + for i in ${LDFLAGS}; do + OPTSLD="${OPTSLD} \"${i}\"," + done + + sed -i \ + -e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \ + -e "s:\[\"-static:\[${OPTSLD} \"-static:g" \ + "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die + +} + +src_configure() { + local compiler + local mtype + local mversion + local nproc + + # Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc, + # unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC, + # darwin_c++, darwin_gcc. The build systems seems to prepend + # unix_ all by itself. Can this be derived from $(tc-getCC)? + compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') + + # Breaks cross compilation. + mtype=$(src/${PN}/bin/machine_type) + mversion=$(src/${PN}/bin/machine_version) + + einfo "Creating build directory" + mkdir build + cd build + ln -sf "${S}/lib/cctbx/cctbx_sources/scons" scons + ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx + + einfo "Configuring phaser components" + $(PYTHON) "libtbx/configure.py" \ + --build=release \ + --compiler=${compiler} \ + --repository="${S}"/src/${PN}/source \ + --repository="${S}"/lib/cctbx/cctbx_sources \ + --static_libraries \ + ccp4io="${S}" \ + mmtbx \ + phaser || die "configure.py failed" +} + +src_compile() { + nproc=`echo "-j1 ${MAKEOPTS}" \ + | sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"` + + cd build + einfo "Setting up build environment" + source setpaths.sh + + einfo "Compiling phaser components" + libtbx.scons -j ${nproc} || die "libtbx.scons failed" +} + +src_install() { + dobin build/exe/phaser || die + + cat >> "${T}"/53${PN} <<- EOF + PHASER="${EPREFIX}/usr/bin" + PHASER_ENVIRONMENT="1" + PHASER_MTYPE="${mtype}" + PHASER_MVERSION="${mversion}" + PHASER_VERSION="${PV}" + EOF + + doenvd "${T}"/53${PN} || die +} diff --git a/sci-chemistry/platon/Manifest b/sci-chemistry/platon/Manifest new file mode 100644 index 000000000000..df5e86cadaa7 --- /dev/null +++ b/sci-chemistry/platon/Manifest @@ -0,0 +1 @@ +DIST platon-20110126.tar.gz 10893404 SHA256 23651224b5f3653c82673f7d6c2339cfee1e8f59ad32fa51d7c9770f5cb014d6 diff --git a/sci-chemistry/platon/files/20110126-buffer-overflow.patch b/sci-chemistry/platon/files/20110126-buffer-overflow.patch new file mode 100644 index 000000000000..548bd2b20ca4 --- /dev/null +++ b/sci-chemistry/platon/files/20110126-buffer-overflow.patch @@ -0,0 +1,15 @@ +--- xdrvr.c 2010-06-27 15:21:49.026967128 +0200 ++++ xdrvr_new.c 2010-06-27 15:22:57.132069867 +0200 +@@ -864,11 +864,9 @@ + int zdate_(string) + char *string; + { +- static char tmp[25]; + time_t now; + now = time(NULL); +- strcpy(tmp,ctime(&now)); +- strncpy(string,tmp,25); ++ strncpy(string,ctime(&now),25); + return(1); + } + int slaap_(int *i)
\ No newline at end of file diff --git a/sci-chemistry/platon/metadata.xml b/sci-chemistry/platon/metadata.xml new file mode 100644 index 000000000000..e42d0af60f42 --- /dev/null +++ b/sci-chemistry/platon/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/platon/platon-20110126.ebuild b/sci-chemistry/platon/platon-20110126.ebuild new file mode 100644 index 000000000000..2c376a367c25 --- /dev/null +++ b/sci-chemistry/platon/platon-20110126.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 flag-o-matic multilib toolchain-funcs + +DESCRIPTION="Versatile, SHELX-97 compatible, multipurpose crystallographic tool" +HOMEPAGE="http://www.cryst.chem.uu.nl/platon/" +SRC_URI="http://www.cryst.chem.uu.nl/xraysoft/unix/${PN}.tar.gz -> ${P}.tar.gz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +# Can't do libf2c dependent on whether <gcc-4 is selected for the build, +# so we must always require it +RDEPEND="x11-libs/libX11" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}/${PN}" + +pkg_nofetch() { + elog "If there is a digest mismatch, please file a bug" + elog "at https://bugs.gentoo.org/ -- a version bump" + elog "is probably required." +} + +src_unpack() { + unpack ${A} + cd "${S}" + gunzip platon.f.gz xdrvr.c.gz || die +} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-buffer-overflow.patch +} + +src_compile() { + # easy to ICE, at least on gcc 4.3 + strip-flags + + COMMAND="$(tc-getCC) -c ${CFLAGS} xdrvr.c" + echo ${COMMAND} + ${COMMAND} || die "Compilation of xdrvr.c failed" + COMMAND="$(tc-getFC) -c ${FFLAGS:- -O2} -fno-second-underscore platon.f" + echo ${COMMAND} + ${COMMAND} || die "Compilation of platon.f failed" + COMMAND="$(tc-getFC) -o platon ${LDFLAGS} platon.o xdrvr.o -lX11 ${F2C}" + echo ${COMMAND} + ${COMMAND} || die "Linking failed" +} + +src_install() { + dobin platon + + for bin in pluton s cifchk helena stidy; do + dosym platon /usr/bin/${bin} + done + + insinto /usr/$(get_libdir)/platon + doins check.def + + echo "CHECKDEF=\"${EPREFIX}/usr/$(get_libdir)/platon/check.def\"" > "${T}"/env.d + newenvd "${T}"/env.d 50platon + + dodoc README.* + + if use examples; then + insinto /usr/share/${PN} + doins -r TEST + fi +} diff --git a/sci-chemistry/pointless/Manifest b/sci-chemistry/pointless/Manifest new file mode 100644 index 000000000000..63884312ae57 --- /dev/null +++ b/sci-chemistry/pointless/Manifest @@ -0,0 +1,2 @@ +DIST pointless-1.6.14.tar.gz 423657 SHA256 68f0c1f65239b1451310fe885c2b9d51fc558de7b43af1e584750e05dc5635d8 SHA512 9dd524a7c842edc01206450c52ca1a01e8e3ee6f9ff71742789943ee10e006b5452b0be3aa509dd16bb85f1b9c3d7954616a78ec2fef2daea7c0ab42cdaa42b9 WHIRLPOOL 5085afbd88713384039ef2c2b4b2f7fddd8f078dca9df54062b0415e970791868c61df98f4044b4e061077a73b4e129b6e5db34852d64cace48108db9c6ae50f +DIST pointless-1.6.2.tar.gz 412244 SHA256 5e09ca592ea565e8ace142fc0edff39d0ab723f4ac6e2cadd6ba571d667c80f6 diff --git a/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch b/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch new file mode 100644 index 000000000000..ca67dbd3f336 --- /dev/null +++ b/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch @@ -0,0 +1,12 @@ +diff --git a/string_util.hh b/string_util.hh +index 66af6f3..047512b 100644 +--- a/string_util.hh ++++ b/string_util.hh +@@ -3,6 +3,7 @@ + + #include <string> + #include <vector> ++#include <stdio.h> + #include "range.hh" + + //====================================================================== diff --git a/sci-chemistry/pointless/metadata.xml b/sci-chemistry/pointless/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/pointless/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild b/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild new file mode 100644 index 000000000000..d983cb290242 --- /dev/null +++ b/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils fortran-2 multilib python-single-r1 toolchain-funcs + +DESCRIPTION="Scores crystallographic Laue and space groups" +HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html" +SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND=" + sci-chemistry/ccp4-apps + >=sci-libs/ccp4-libs-6.1.3-r10 + sci-libs/clipper + sci-libs/fftw:2.1 + sci-libs/mmdb + >=sci-libs/cctbx-2010.03.29.2334-r3[${PYTHON_USEDEP}]" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +src_prepare() { + epatch "${FILESDIR}"/1.5.1-gcc4.4.patch +} + +src_compile() { + emake \ + -f Makefile.make \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" \ + LFLAGS="${LDFLAGS}" \ + CLIB="${EPREFIX}/usr/$(get_libdir)" \ + CCTBX_VERSION=2010 \ + ICCP4=-I"${EPREFIX}/usr/include/ccp4" \ + ITBX="-I${EPREFIX}/usr/include" \ + ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \ + LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \ + SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" +} + +src_install() { + dobin pointless othercell +} diff --git a/sci-chemistry/pointless/pointless-1.6.14.ebuild b/sci-chemistry/pointless/pointless-1.6.14.ebuild new file mode 100644 index 000000000000..158bde017aea --- /dev/null +++ b/sci-chemistry/pointless/pointless-1.6.14.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" + +inherit eutils fortran-2 multilib python toolchain-funcs + +DESCRIPTION="Scores crystallographic Laue and space groups" +HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html" +SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + sci-chemistry/ccp4-apps + >=sci-libs/ccp4-libs-6.1.3-r10 + sci-libs/clipper + sci-libs/fftw:2.1 + sci-libs/mmdb + >=sci-libs/cctbx-2010.03.29.2334-r3" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +pkg_setup() { + fortran-2_pkg_setup + python_set_active_version 2 +} + +src_prepare() { + epatch "${FILESDIR}"/1.5.1-gcc4.4.patch +} + +src_compile() { + emake \ + -f Makefile.make \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" \ + LFLAGS="${LDFLAGS}" \ + CLIB="${EPREFIX}/usr/$(get_libdir)" \ + CCTBX_VERSION=2010 \ + ICCP4=-I"${EPREFIX}/usr/include/ccp4" \ + ITBX="-I${EPREFIX}/usr/include" \ + ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \ + LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \ + SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" \ + || die +} + +src_install() { + dobin pointless othercell || die +} diff --git a/sci-chemistry/pointless/pointless-1.6.2.ebuild b/sci-chemistry/pointless/pointless-1.6.2.ebuild new file mode 100644 index 000000000000..2b9f0ad4faa0 --- /dev/null +++ b/sci-chemistry/pointless/pointless-1.6.2.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +PYTHON_DEPEND="2" + +inherit eutils fortran-2 multilib python toolchain-funcs + +DESCRIPTION="Scores crystallographic Laue and space groups" +HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html" +SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + sci-chemistry/ccp4-apps + >=sci-libs/ccp4-libs-6.1.3-r10 + sci-libs/clipper + sci-libs/fftw:2.1 + sci-libs/mmdb + >=sci-libs/cctbx-2010.03.29.2334-r3" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +pkg_setup() { + fortran-2_pkg_setup + python_pkg_setup + python_set_active_version 2 +} + +src_prepare() { + epatch "${FILESDIR}"/1.5.1-gcc4.4.patch +} + +src_compile() { + emake \ + -f Makefile.make \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" \ + LFLAGS="${LDFLAGS}" \ + CLIB="${EPREFIX}/usr/$(get_libdir)" \ + CCTBX_VERSION=2010 \ + ICCP4=-I"${EPREFIX}/usr/include/ccp4" \ + ITBX="-I${EPREFIX}/usr/include" \ + ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \ + LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \ + SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" +} + +src_install() { + dobin pointless othercell +} diff --git a/sci-chemistry/povscript+/Manifest b/sci-chemistry/povscript+/Manifest new file mode 100644 index 000000000000..86635b8f451c --- /dev/null +++ b/sci-chemistry/povscript+/Manifest @@ -0,0 +1,2 @@ +DIST molscript-2.1.2pov2.19.tar.gz 845101 SHA256 4d35ed30898508df85c1db6e18385b56f8aed1f79db65195be6fdb23d3c49b68 SHA512 11796552a889ae309ebac31047440732921cd300d89ad284beb3655e2797fe1a68adf9a5a7e54e6668ea240c5b0897c22f65d839870ee43591854976000ab05f WHIRLPOOL cf19cf28304f49a1de6a1d787de18c939b4dcd5ae2d813ac48e8d5f2a572de4cee6bafdd8613e47ca7a5b5b3891108308c808687162deb23d39dcd07a69dcd35 +DIST molscript-2.1.2pov2.20.tar.gz 822930 SHA256 a3a9ae8792fbfba1df6e279c913db3ee4a89612c94b6088be874ed69372ab7a6 SHA512 f7cae4d9b583a05962742ee36ec717f0ecac6bb88086bcfa484b51b0d2e16a15920bc7c09d9d777453d7ef7b81be444924d15a889e4725bfca7bf517d4e52db2 WHIRLPOOL 8c12ea5ebc234f2277e04e502a314cb0065cb717e1cff067d9ad8d306395972f2b6d7589f3a7e58dfa019dc3eb0cf11582ee9b92f1bb3b17c8f9cfc5c4b57a2a diff --git a/sci-chemistry/povscript+/files/povscript+-2.1.2.2.19-libpng15.patch b/sci-chemistry/povscript+/files/povscript+-2.1.2.2.19-libpng15.patch new file mode 100644 index 000000000000..054967d6555c --- /dev/null +++ b/sci-chemistry/povscript+/files/povscript+-2.1.2.2.19-libpng15.patch @@ -0,0 +1,19 @@ +--- src/png_img.c ++++ src/png_img.c +@@ -18,6 +18,7 @@ + + #include MS_GL_H + ++#include <zlib.h> + #include <png.h> + + #include "clib/str_utils.h" +@@ -69,7 +70,7 @@ + info_ptr = png_create_info_struct (png_ptr); + if (info_ptr == NULL) + yyerror ("png_img: could not create PNG info structure"); +- if (setjmp (png_ptr->jmpbuf)) yyerror ("png_img: could not setjmp"); ++ if (setjmp (png_jmpbuf(png_ptr))) yyerror ("png_img: could not setjmp"); + + png_init_io (png_ptr, outfile); + png_set_compression_level (png_ptr, compression_level); diff --git a/sci-chemistry/povscript+/metadata.xml b/sci-chemistry/povscript+/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/povscript+/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild b/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild new file mode 100644 index 000000000000..a36a07a34519 --- /dev/null +++ b/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils versionator + +V1=$(get_version_component_range 1 ${PV}) +V2=$(get_version_component_range 2 ${PV}) +V3=$(get_version_component_range 3 ${PV}) +V4=$(get_version_component_range 4 ${PV}) +V5=$(get_version_component_range 5 ${PV}) + +MY_P=molscript-${V1}.${V2}.${V3}pov${V4}.${V5} + +DESCRIPTION="Modified molscript that uses POV-Ray, does thermal ellipsoids, and more" +HOMEPAGE="https://sites.google.com/site/timfenn/povscript" +SRC_URI="https://sites.google.com/site/timfenn/povscript/${MY_P}.tar.gz" + +LICENSE="glut molscript" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="" + +RDEPEND=" + dev-libs/glib:2 + media-libs/freeglut + media-libs/giflib + >=media-libs/libpng-1.4 + sci-libs/gts + sys-libs/zlib + virtual/glu + virtual/jpeg + virtual/opengl + x11-libs/libX11" +DEPEND="${RDEPEND}" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + epatch "${FILESDIR}"/${P}-libpng15.patch +} + +src_install() { + emake DESTDIR="${D}" install + cd "${D}"/usr/bin + mv molscript povscript+ + mv molauto povauto+ +} + +pkg_postinst() { + elog "You must install media-gfx/povray to use the POV backend," + elog "which is one of the main features of this over molscript." +} diff --git a/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild b/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild new file mode 100644 index 000000000000..fb12cea4396a --- /dev/null +++ b/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils versionator + +V1=$(get_version_component_range 1 ${PV}) +V2=$(get_version_component_range 2 ${PV}) +V3=$(get_version_component_range 3 ${PV}) +V4=$(get_version_component_range 4 ${PV}) +V5=$(get_version_component_range 5 ${PV}) + +MY_P=molscript-${V1}.${V2}.${V3}pov${V4}.${V5} + +DESCRIPTION="Modified molscript that uses POV-Ray, does thermal ellipsoids, and more" +HOMEPAGE="https://sites.google.com/site/timfenn/povscript" +SRC_URI="https://sites.google.com/site/timfenn/povscript/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="glut molscript" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="" + +RDEPEND=" + dev-libs/glib:2 + media-libs/freeglut + media-libs/giflib + >=media-libs/libpng-1.4 + sci-libs/gts + sys-libs/zlib + virtual/glu + virtual/jpeg + virtual/opengl + x11-libs/libX11" +DEPEND="${RDEPEND}" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + epatch "${FILESDIR}"/${PN}-2.1.2.2.19-libpng15.patch +} + +src_install() { + default + + cd "${ED}"/usr/bin || die + mv molscript povscript+ || die + mv molauto povauto+ || die +} + +pkg_postinst() { + elog "You must install media-gfx/povray to use the POV backend," + elog "which is one of the main features of this over molscript." +} diff --git a/sci-chemistry/prekin/Manifest b/sci-chemistry/prekin/Manifest new file mode 100644 index 000000000000..58c94aa2baad --- /dev/null +++ b/sci-chemistry/prekin/Manifest @@ -0,0 +1 @@ +DIST prekin.6.51.081122.src.tgz 350756 SHA256 74a771cd8be000df13ac908f23a2e945e8bd3590884c6bc6ccff75804cc0fb7a diff --git a/sci-chemistry/prekin/files/6.51.081122-Makefile.patch b/sci-chemistry/prekin/files/6.51.081122-Makefile.patch new file mode 100644 index 000000000000..5fd9d00d9b06 --- /dev/null +++ b/sci-chemistry/prekin/files/6.51.081122-Makefile.patch @@ -0,0 +1,41 @@ +diff --git a/Makefile.linux b/Makefile.linux +index 65a021a..3daacd8 100755 +--- a/Makefile.linux ++++ b/Makefile.linux +@@ -1,15 +1,15 @@ + # +-CFLAGS = -I/usr/X11R6/include ++CFLAGS += -I/usr/X11R6/include + + ifeq ($(MAKECMDGOALS),debug) + CFLAGS = -g -I/usr/X11R6/include + endif + +-LIBS = -L/usr/lib -L/usr/X11R6/lib -lXmu -lXm -lXt -lSM -lICE -lXext -lX11 ++LIBS = -L/usr/GENTOOLIBDIR -L/usr/X11R6/lib -lXmu -lXm -lXt -lSM -lICE -lXext -lX11 + + ifeq ($(MAKECMDGOALS),nogui) +-CFLAGS = -D NOGUI -I/usr/X11R6/include +-LIBS = -L/usr/lib -L/usr/X11R6/lib -lXmu -lXt -lSM -lICE -lXext -lX11 ++CFLAGS += -D NOGUI -I/usr/X11R6/include ++LIBS = -L/usr/GENTOOLIBDIR -L/usr/X11R6/lib -lXmu -lXt -lSM -lICE -lXext -lX11 + endif + + FIN = -lm -pthread #for RH9.0, ok for RH7.3 & RH8.0 +@@ -26,13 +26,13 @@ OBJS = PKINANGL.o PKINCRTL.o PKINCSBS.o PKINCSUB.o PKINCOUT.o PKINMENU.o PKINROT + # Commands specific to clients created by this Makefile + + prekin: $(OBJS) +- cc -o prekin $(CFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) ++ cc -o prekin $(CFLAGS) $(LDFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) + + debug: $(OBJS) +- cc -o prekin $(CFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) ++ cc -o prekin $(CFLAGS) $(LDFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) + + nogui: $(OBJS) +- cc -o prekin $(CFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) ++ cc -o prekin $(CFLAGS) $(LDFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) + + clean: + rm *.o diff --git a/sci-chemistry/prekin/files/6.51.081122-overflow.patch b/sci-chemistry/prekin/files/6.51.081122-overflow.patch new file mode 100644 index 000000000000..27bc01d61a52 --- /dev/null +++ b/sci-chemistry/prekin/files/6.51.081122-overflow.patch @@ -0,0 +1,28 @@ +diff --git a/PKIN.h b/PKIN.h +index 6cb6670..c9c6b89 100755 +--- a/PKIN.h ++++ b/PKIN.h +@@ -533,8 +533,8 @@ EXTERN float xnext,ynext,znext,onext,Bnext,Uvalnext; + EXTERN char aspectstrnext[MAXaspects+3]; /*in parens: (XXXX)*/ + + /* possible overlap with earlier PREKIN variables */ +-EXTERN char word[256],texts[256],temps[256]; +-EXTERN char alertstr[256],alertstr2[256],alertstr3[256]; ++EXTERN char word[256],texts[256],temps[512]; ++EXTERN char alertstr[1024],alertstr2[256],alertstr3[256]; + EXTERN char oldstr[256],olderstr[256],newstr[256],InfoStr[256],MolNameStr[16]; + EXTERN char NameStr[256],OutfileStr[256],ScriptinStr[256],ShortNameStr[256]; + EXTERN char DirStr[256],PDBfileStr[256],helpoutStr[256]; /*040425 helpout*/ +diff --git a/PKINCOUT.c b/PKINCOUT.c +index af8eb24..a9f3a5f 100755 +--- a/PKINCOUT.c ++++ b/PKINCOUT.c +@@ -17,7 +17,7 @@ static float VRMLx=0,VRMLy=0,VRMLz=0; + void writeoutput() + { + char cntl[5]; /* 4 actual characters */ +- char kol[20],extra[256],aname[13]; ++ char kol[20],extra[256],aname[32]; + char chain[32],atoms[32],cpks[32],hygen[32],hbond[32]; + char subname[32],allstr[32]; + char mastername[32]; /*051128*/ diff --git a/sci-chemistry/prekin/metadata.xml b/sci-chemistry/prekin/metadata.xml new file mode 100644 index 000000000000..9ac9ffdb3a41 --- /dev/null +++ b/sci-chemistry/prekin/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild new file mode 100644 index 000000000000..9e0521c7dbcc --- /dev/null +++ b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit toolchain-funcs eutils multilib + +MY_P=${PN}.${PV} + +DESCRIPTION="Prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/prekin.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${MY_P}.src.tgz" + +LICENSE="richardson" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="X" + +RDEPEND="x11-libs/libXext + x11-libs/libXmu + x11-libs/libX11 + x11-libs/libXt + X? ( >=x11-libs/motif-2.3:0 )" +DEPEND="${RDEPEND}" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-Makefile.patch \ + "${FILESDIR}"/${PV}-overflow.patch + sed \ + -e 's:cc:$(CC):g' \ + -e "s:GENTOOLIBDIR:$(get_libdir):g" \ + "${S}"/Makefile.linux > Makefile || die +} + +src_compile() { + local mytarget + + if use X; then + mytarget="${PN}" + else + mytarget="nogui" + fi + + emake CC="$(tc-getCC)" ${mytarget} || die +} + +src_install() { + dobin "${S}"/prekin || die +} diff --git a/sci-chemistry/probe/Manifest b/sci-chemistry/probe/Manifest new file mode 100644 index 000000000000..f5dd9226d404 --- /dev/null +++ b/sci-chemistry/probe/Manifest @@ -0,0 +1,2 @@ +DIST probe.2.12.110413.src.zip 262460 SHA256 90cd0a693683958a8ac05d13a47c2b464f2939df24369bf5c568f59913756de4 SHA512 ac6a92f1666d1819c0dede5ea97113c9e03271c42b829d88a2b65041dec7f853441fc61e94e48782078884a9a69c1043432ca3576768d31bfe9190d3ea1da4c8 WHIRLPOOL f6e6ec43016d14114ae5cbfdbfd1cdb5bdf0c6a1c34742b0fef0cfe5ee39409a41b4b2127fbefe526d66d99c33b91ef5e3ea4c9de33784f9ea493700e8bc8784 +DIST probe.2.13.110909.src.zip 131063 SHA256 df14b76d27a7c43b2b57c315d0ad71cdf6acc7943c43195a797162be7816fa71 SHA512 5efa066873d0e139da66bf8edb541fe42df94e99cab171ad8d06a8a6f5caada982ef5b18481e748b224dbed86f63c99237d04ecd107c82855b44de91fb6d2b16 WHIRLPOOL 12f6fefe1b03b71268f39fa3aa7ad796230c76c2e029b8dc86955abd43c8e3f09f7591f84cd79c7ba11037d5b323c922ddf36abf6911d556981f5cc21378912f diff --git a/sci-chemistry/probe/files/2.12.110413-as-needed.patch b/sci-chemistry/probe/files/2.12.110413-as-needed.patch new file mode 100644 index 000000000000..95368625505d --- /dev/null +++ b/sci-chemistry/probe/files/2.12.110413-as-needed.patch @@ -0,0 +1,38 @@ + Makefile | 13 ++++++------- + 1 files changed, 6 insertions(+), 7 deletions(-) + +diff --git a/Makefile b/Makefile +index e6a740e..8f74d6a 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,14 +1,12 @@ +-MACHINEFLAGS = +-CFLAGS = $(MACHINEFLAGS) +-LFLAGS = -lm $(MACHINEFLAGS) ++LIBS = -lm + OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \ +- parse.o atomprops.o stdconntable.o autobondrot.o ++ parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o + + .c.o: +- cc -c $*.c $(CFLAGS) ++ $(CC) $(CFLAGS) -c $*.c + + probe: probe.o $(OBJLIST) +- cc -o $@ probe.o $(OBJLIST) $(LFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ probe.o $(OBJLIST) $(LIBS) + + clean: + @rm -f *.o *.ckp +@@ -30,9 +28,10 @@ parse.o: ./parse.h ./utility.h parse.c + probe.o: ./abin.h ./atomprops.h ./autobondrot.h ./dots.h ./geom3d.h \ + ./parse.h ./probe.h ./readPDBrecs.h ./select.h \ + ./stdconntable.h ./utility.h probe.c +-readPDBrecs.o: ./geom3d.h ./readPDBrecs.h ./utility.h readPDBrecs.c ++readPDBrecs.o: ./geom3d.h ./readPDBrecs.h ./utility.h ./hybrid_36_c.h readPDBrecs.c + select.o: ./abin.h ./atomprops.h ./geom3d.h ./parse.h ./select.h \ + ./stdconntable.h ./utility.h select.c + stdconntable.o: ./stdconntable.h stdconntable.c + utility.o: utility.c ++hybrid_36_c.o: ./hybrid_36_c.h hybrid_36_c.c + # DO NOT DELETE THIS 2nd LINE -- make depend uses it diff --git a/sci-chemistry/probe/files/as-needed.patch b/sci-chemistry/probe/files/as-needed.patch new file mode 100644 index 000000000000..9ddecf5f569e --- /dev/null +++ b/sci-chemistry/probe/files/as-needed.patch @@ -0,0 +1,21 @@ +diff --git a/Makefile b/Makefile +index 68d7469..bcb821c 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,6 +1,6 @@ + MACHINEFLAGS = + CFLAGS = $(MACHINEFLAGS) +-LFLAGS = -lm $(MACHINEFLAGS) ++LFLAGS = -lm + OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \ + parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o + +@@ -8,7 +8,7 @@ OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \ + cc -c $*.c $(CFLAGS) + + probe: probe.o $(OBJLIST) +- cc -o $@ probe.o $(OBJLIST) $(LFLAGS) ++ cc $(MACHINEFLAGS) -o $@ probe.o $(OBJLIST) $(LFLAGS) + + clean: + @rm -f *.o *.ckp diff --git a/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch b/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch new file mode 100644 index 000000000000..df7040c3ba1d --- /dev/null +++ b/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch @@ -0,0 +1,25 @@ + Makefile | 8 +++----- + 1 files changed, 3 insertions(+), 5 deletions(-) + +diff --git a/Makefile b/Makefile +index 9031bd0..8f74d6a 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,14 +1,12 @@ +-MACHINEFLAGS = +-CFLAGS = $(MACHINEFLAGS) +-LFLAGS = -static -lm $(MACHINEFLAGS) ++LIBS = -lm + OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \ + parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o + + .c.o: +- cc -c $*.c $(CFLAGS) ++ $(CC) $(CFLAGS) -c $*.c + + probe: probe.o $(OBJLIST) +- cc -o $@ probe.o $(OBJLIST) $(LFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ probe.o $(OBJLIST) $(LIBS) + + clean: + @rm -f *.o *.ckp diff --git a/sci-chemistry/probe/metadata.xml b/sci-chemistry/probe/metadata.xml new file mode 100644 index 000000000000..e42d0af60f42 --- /dev/null +++ b/sci-chemistry/probe/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/probe/probe-2.12.110413.ebuild b/sci-chemistry/probe/probe-2.12.110413.ebuild new file mode 100644 index 000000000000..bb0a36a232de --- /dev/null +++ b/sci-chemistry/probe/probe-2.12.110413.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_P="${PN}.${PV}" + +DESCRIPTION="Evaluates atomic packing within or between molecules" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/probe.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/probe/${MY_P}.src.zip" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}"/trunk + +src_prepare() { + epatch "${FILESDIR}"/${PV}-as-needed.patch + # Respect CC + sed -i \ + -e 's:cc:$(CC):g' \ + "${S}"/Makefile || die + tc-export CC +} + +src_install() { + dobin "${S}"/probe + dodoc "${S}"/README* +} diff --git a/sci-chemistry/probe/probe-2.13.110909.ebuild b/sci-chemistry/probe/probe-2.13.110909.ebuild new file mode 100644 index 000000000000..a841b16de30f --- /dev/null +++ b/sci-chemistry/probe/probe-2.13.110909.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_P="${PN}.${PV}" + +DESCRIPTION="Evaluates atomic packing within or between molecules" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/probe.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/probe/${MY_P}.src.zip" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}"/${MY_P}.src + +src_prepare() { + epatch "${FILESDIR}"/${P}-as-needed.patch + tc-export CC +} + +src_install() { + dobin "${S}"/probe + dodoc "${S}"/README* +} diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest new file mode 100644 index 000000000000..c50c49d67536 --- /dev/null +++ b/sci-chemistry/procheck/Manifest @@ -0,0 +1,3 @@ +DIST procheck-3.5.4-README 6585 SHA256 202d5b4d9ffaebdad19c368e6e6fd8ab54744c511609b1c609ef46c21fa0ffa0 SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a WHIRLPOOL 53a618978a9285e8a8f09c7ebd3e34951a8c1056c0894c1f4e4c11f73ad3127829322c9c7597fc6dea98f1fa4c40552e6caf383eed15aaeef0594cf93887d196 +DIST procheck-3.5.4-manual.tar.gz 517840 SHA256 3c2faa505be05102ccbe23473abdddc1cd4dc87c6b5e74222b7ea5c27b18db5a +DIST procheck-3.5.4.tar.gz 522013 SHA256 4923fe5a7b86d5369fd639d0c77cfb866e574f076ec8c52424d746e843a404f4 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc WHIRLPOOL 2732981bdbb5269567019a645b401009bd48d782ab20b4f68bd213a90f7248a9fa3f46ab3a026aa0515a677a99826040d4c3f5464816ed4390b5091a6a98b375 diff --git a/sci-chemistry/procheck/files/3.5.4-ldflags.patch b/sci-chemistry/procheck/files/3.5.4-ldflags.patch new file mode 100644 index 000000000000..453aebe3211f --- /dev/null +++ b/sci-chemistry/procheck/files/3.5.4-ldflags.patch @@ -0,0 +1,49 @@ +diff --git a/Makefile b/Makefile +index c5bb58f..0394b0a 100644 +--- a/Makefile ++++ b/Makefile +@@ -35,31 +35,31 @@ distrib : + # Individual executables + # ---------------------- + anglen : anglen.o +- $(F77) $(FOPTS) -o $@ anglen.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ anglen.o + clean : clean.o +- $(F77) $(FOPTS) -o $@ clean.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ clean.o + rmsdev : rmsdev.o +- $(F77) $(FOPTS) -o $@ rmsdev.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ rmsdev.o + secstr : secstr.o +- $(F77) $(FOPTS) -o $@ secstr.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ secstr.o + gfac2pdb : gfac2pdb.o ps.o +- $(F77) $(FOPTS) -o $@ gfac2pdb.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ gfac2pdb.o ps.o + pplot : pplot.o ps.o +- $(F77) $(FOPTS) -o $@ pplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ pplot.o ps.o + bplot : bplot.o ps.o +- $(F77) $(FOPTS) -o $@ bplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ bplot.o ps.o + tplot : tplot.o ps.o +- $(F77) $(FOPTS) -o $@ tplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ tplot.o ps.o + mplot : mplot.o ps.o +- $(F77) $(FOPTS) -o $@ mplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ mplot.o ps.o + vplot : vplot.o ps.o +- $(F77) $(FOPTS) -o $@ vplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ vplot.o ps.o + viol2pdb : viol2pdb.o ps.o +- $(F77) $(FOPTS) -o $@ viol2pdb.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ viol2pdb.o ps.o + wirplot : wirplot.o ps.o +- $(F77) $(FOPTS) -o $@ wirplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ wirplot.o ps.o + nb : nb.c +- $(CC) $(COPTS) -o nb nb.c $(CLIBS) ++ $(CC) $(COPTS) $(LDFLAGS) -o nb nb.c $(CLIBS) + + # Individual rules for FORTRAN files with .inc files + # -------------------------------------------------- diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch new file mode 100644 index 000000000000..16a0658e654d --- /dev/null +++ b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch @@ -0,0 +1,35 @@ +diff --git a/pplot.f b/pplot.f +index 7e06e68..c86b2b2 100644 +--- a/pplot.f ++++ b/pplot.f +@@ -4720,6 +4720,7 @@ C---- Initialise variables + SCORE(IDIST) = 0.0 + 50 CONTINUE + ++ REWIND(3) + C---- If the required residue is of a greater number than that required, + C read through the file until come to it + IF (IRESID.GT.INRES) THEN +diff --git a/ps.f b/ps.f +index b652a7d..858b8e5 100644 +--- a/ps.f ++++ b/ps.f +@@ -1705,12 +1705,14 @@ CVAX - CARRIAGECONTROL='LIST', + C---- If this is an existing file, then read through all its records until + C get to the end of file + IF (.NOT.NEWFIL) THEN ++ CLOSE(14) ++ OPEN(14, file=fname, status='old', position='append', err=900) + + C---- Loop through the file until reach the end +- 100 CONTINUE +- READ(14,110,END=500) IREC +- 110 FORMAT(A) +- GO TO 100 ++C 100 CONTINUE ++C READ(14,110,END=500) IREC ++C 110 FORMAT(A) ++C GO TO 100 + + C---- If this is a new file, then write the header records to it + ELSE
\ No newline at end of file diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml new file mode 100644 index 000000000000..b3618ba38c1c --- /dev/null +++ b/sci-chemistry/procheck/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/procheck/procheck-3.5.4-r1.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r1.ebuild new file mode 100644 index 000000000000..855c2badf4d0 --- /dev/null +++ b/sci-chemistry/procheck/procheck-3.5.4-r1.ebuild @@ -0,0 +1,87 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 multilib toolchain-funcs versionator + +DESCRIPTION="Checks the stereochemical quality of a protein structure" +HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html" +SRC_URI=" + ${P}.tar.gz ${P}-README + doc? ( ${P}-manual.tar.gz )" + +LICENSE="procheck" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="doc" + +RDEPEND="app-shells/tcsh" +DEPEND="${RDEPEND}" + +RESTRICT="fetch" + +S="${WORKDIR}/${PN}" + +pkg_nofetch() { + elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html" + elog "And follow the instruction for downloading." + elog "Files should be stored in following way" + elog "${PN}.tar.gz -> ${DISTDIR}/${P}.tar.gz" + elog "README -> ${DISTDIR}/${P}-README" + if use doc; then + elog "manual.tar.gz -> ${DISTDIR}/${P}-manual.tar.gz" + fi +} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-ldflags.patch +} + +src_compile() { + emake \ + F77=$(tc-getFC) \ + CC=$(tc-getCC) \ + COPTS="${CFLAGS}" \ + FOPTS="${FFLAGS}" +} + +src_install() { + for i in *.scr; do + newbin ${i} ${i%.scr} + done + + exeinto /usr/$(get_libdir)/${PN}/ + doexe \ + anglen \ + clean \ + rmsdev \ + secstr \ + gfac2pdb \ + pplot \ + bplot \ + tplot \ + mplot \ + vplot \ + viol2pdb \ + wirplot \ + nb + dodoc "${DISTDIR}"/${P}-README + + insinto /usr/$(get_libdir)/${PN}/ + doins *.dat *.prm + newins resdefs.dat resdefs.data + + cat >> "${T}"/30${PN} <<- EOF + prodir="${EPREFIX}/usr/$(get_libdir)/${PN}/" + EOF + + doenvd "${T}"/30${PN} + + if use doc; then + pushd "${WORKDIR}" + dohtml -r manual + popd + fi +} diff --git a/sci-chemistry/procheck/procheck-3.5.4-r2.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r2.ebuild new file mode 100644 index 000000000000..0c4683e03a72 --- /dev/null +++ b/sci-chemistry/procheck/procheck-3.5.4-r2.ebuild @@ -0,0 +1,88 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils fortran-2 multilib toolchain-funcs versionator + +DESCRIPTION="Checks the stereochemical quality of a protein structure" +HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html" +SRC_URI=" + ${P}.tar.gz ${P}-README + doc? ( ${P}-manual.tar.gz )" + +LICENSE="procheck" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc" + +RDEPEND="app-shells/tcsh" +DEPEND="${RDEPEND}" + +RESTRICT="fetch" + +S="${WORKDIR}/${PN}" + +pkg_nofetch() { + elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html" + elog "And follow the instruction for downloading." + elog "Files should be stored in following way" + elog "${PN}.tar.gz -> ${DISTDIR}/${P}.tar.gz" + elog "README -> ${DISTDIR}/${P}-README" + use doc && elog "manual.tar.gz -> ${DISTDIR}/${P}-manual.tar.gz" +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-ldflags.patch \ + "${FILESDIR}"/${P}-close.patch +} + +src_compile() { + emake \ + F77=$(tc-getFC) \ + CC=$(tc-getCC) \ + COPTS="${CFLAGS}" \ + FOPTS="${FFLAGS} -std=legacy" +} + +src_install() { + for i in *.scr; do + newbin ${i} ${i%.scr} + done + + exeinto /usr/libexec/${PN}/ + doexe \ + anglen \ + clean \ + rmsdev \ + secstr \ + gfac2pdb \ + pplot \ + bplot \ + tplot \ + mplot \ + vplot \ + viol2pdb \ + wirplot \ + nb + dodoc "${DISTDIR}"/${P}-README + + insinto /usr/libexec/${PN}/ + doins *.dat *.prm + newins resdefs.dat resdefs.data + + cat >> "${T}"/30${PN} <<- EOF + prodir="${EPREFIX}/usr/libexec/${PN}/" + EOF + + doenvd "${T}"/30${PN} + + if use doc; then + pushd "${WORKDIR}" > /dev/null + docinto html + dodoc -r manual + popd > /dev/null + fi +} diff --git a/sci-chemistry/prodecomp/Manifest b/sci-chemistry/prodecomp/Manifest new file mode 100644 index 000000000000..ffead0387fc2 --- /dev/null +++ b/sci-chemistry/prodecomp/Manifest @@ -0,0 +1 @@ +DIST prodecomp-3.0.tar.bz2 18377446 SHA256 097b97aa6503ff1aecd4147a6e3ef9997807773a7ef58aab8b10baf73b65e457 SHA512 8d23f174e125d4c7776432a37b063d2f39af8497050bd7f7ff358c67d509b1eef2c2865596efae632855fd583fb52c233b67d0e667c6c2a03ba6f5a2f2ac9b0d WHIRLPOOL c06f4bf32e3d5ff4f2b5f1b1c4fd03d7a5b734651707e6fc101ce0ea5ba17c9377edb60166c4e9313b616b37bd580febea01bf62a71e15389174b301c4d70738 diff --git a/sci-chemistry/prodecomp/metadata.xml b/sci-chemistry/prodecomp/metadata.xml new file mode 100644 index 000000000000..a91e9092dc52 --- /dev/null +++ b/sci-chemistry/prodecomp/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> + PRODECOMP (PROjection DECOMPosition) is a software tool for + decomposition of 2D projections of high-dimensional NMR spectra to a set + of components (defined in turn by one-dimensional "shapes"). + Simultaneous analysis of projections from one or several + high-dimensional experiments provide unambigous chemical shifts for + large spin systems. The latter can be used for backbone and side-chain + assignments as well as structural studies of proteins + (Malmodin and Billeter 2005; 2006; Staykova et al. 2008a,b). +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/prodecomp/prodecomp-3.0.ebuild b/sci-chemistry/prodecomp/prodecomp-3.0.ebuild new file mode 100644 index 000000000000..28791c9108ba --- /dev/null +++ b/sci-chemistry/prodecomp/prodecomp-3.0.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit python-single-r1 + +DESCRIPTION="Decomposition-based analysis of NMR projections" +HOMEPAGE="http://www.lundberg.gu.se/nmr/software.php?program=PRODECOMP" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND="sci-libs/scipy[${PYTHON_USEDEP}]" +DEPEND="" + +S="${WORKDIR}"/NMRProjAnalys + +src_install() { + if use examples; then + insinto /usr/share/${PN} + doins -r ExampleData Results + fi + + dodoc ProjTools/Manual.pdf + rm -rf ProjTools/Manual.pdf ProdecompOutput || die + + python_moduleinto ${PN} + python_domodule ProjTools/. + python_optimize + + cat >> "${T}"/${PN} <<- EOF + #!/bin/bash + ${PYTHON} -O "${EPREFIX}"/$(python_get_sitedir)/${PN}/ProjAnalys.py $@ + EOF + dobin "${T}"/${PN} + + dosym ../../../../share/doc/${PF}/Manual.pdf $(python_get_sitedir)/${PN}/Manual.pdf +} diff --git a/sci-chemistry/propka/Manifest b/sci-chemistry/propka/Manifest new file mode 100644 index 000000000000..5f7630e69501 --- /dev/null +++ b/sci-chemistry/propka/Manifest @@ -0,0 +1 @@ +DIST propka-3.1_p140511.tar.xz 151284 SHA256 42b4f6b98bbbefa11fba5e603aa33f1747362746c1170c9958ad408dc34e39af SHA512 c2938af41ed386e267cd045b14e34779889b3c206016d747b68c400f2c8b37bd50cc3b74d055d931476065ac6817a2dd2cb87d68de9911adfff1c8e34a667fc3 WHIRLPOOL 0553ef5f519d41af508885f1900a68627fcf3fb2f901c5d1cef54fe6a5774ef08caf42bf5e80f08cba4c76c9e330be89502e648cf5604aca411c168d4ecda6fa diff --git a/sci-chemistry/propka/metadata.xml b/sci-chemistry/propka/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/propka/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/propka/propka-3.1_p140511.ebuild b/sci-chemistry/propka/propka-3.1_p140511.ebuild new file mode 100644 index 000000000000..d390752866d6 --- /dev/null +++ b/sci-chemistry/propka/propka-3.1_p140511.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Prediction of the pKa values of ionizable groups in proteins and protein-ligand complexes" +HOMEPAGE="http://propka.ki.ku.dk/" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="all-rights-reserved" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]" + +RESTRICT="mirror bindist" + +python_prepare_all() { + sed -e "/exclude/s:scripts:\', \'Tests:g" \ + -i setup.py || die + distutils-r1_python_prepare_all +} + +python_test() { + cd Tests || die + ${PYTHON} runtest.py || die +} + +python_install_all() { + dosym ${PN}31 /usr/bin/${PN} + distutils-r1_python_install_all +} diff --git a/sci-chemistry/psi/Manifest b/sci-chemistry/psi/Manifest new file mode 100644 index 000000000000..c7fb8a8d6271 --- /dev/null +++ b/sci-chemistry/psi/Manifest @@ -0,0 +1 @@ +DIST psi-3.4.0.tar.gz 7413072 SHA256 c87a7f63cb4e34bfd1a8b3731474eb417d9933338327143415a985bcedb619d4 SHA512 b13d2464502545cceec3a3b6048b505b918da26730c1614617b04ee6c1d637c9f799ef7fd92ad9554fa2db87617004aa810a6a81400a04df3c06787d51654ca6 WHIRLPOOL 9c0b9de2c9fbed298eaf958f0c135cadff16eac8754d4064dba0ac2275aabd36204bcad92f90236030bc62ef9917b967653ec608e40ad631e70a0ce1c16f2127 diff --git a/sci-chemistry/psi/files/3.4.0-destdir.patch b/sci-chemistry/psi/files/3.4.0-destdir.patch new file mode 100644 index 000000000000..45db9529aa4d --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-destdir.patch @@ -0,0 +1,41 @@ +diff --git a/Makefile.in b/Makefile.in +index aca5a16..2e49f0a 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -8,6 +8,7 @@ subdirs = lib include src + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ ++datarootdir = @datarootdir@ + VPATH = @srcdir@ + top_objdir = . + +diff --git a/lib/ruby/Makefile.in b/lib/ruby/Makefile.in +index b31ce7f..e099e1b 100644 +--- a/lib/ruby/Makefile.in ++++ b/lib/ruby/Makefile.in +@@ -29,10 +29,10 @@ ccenergy.rb cclambda.rb chkpt.rb color.rb deriv2.rb frequ + cceom.rb ccsort.rb cints.rb cphf.rb detci.rb input.rb optking.rb psi3.rb testcases.rb + + install: $(RUBYSRC) +- $(MKDIRS) $(rubydatadir) ++ $(MKDIRS) $(DESTDIR)/$(rubydatadir) + for rbfile in $(RUBYSRC); \ + do \ +- ($(INSTALL_DATA) $(srcdir)/$${rbfile} $(rubydatadir)) || exit 1; \ ++ ($(INSTALL_DATA) $(srcdir)/$${rbfile} $(DESTDIR)/$(rubydatadir)) || exit 1; \ + done + + install_man: +diff --git a/src/bin/Makefile.in b/src/bin/Makefile.in +index e1abb46..4eddf8d 100644 +--- a/src/bin/Makefile.in ++++ b/src/bin/Makefile.in +@@ -65,6 +65,7 @@ targetclean: + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ ++datarootdir = @datarootdir@ + top_objdir = ../.. + + $(top_srcdir)/configure: $(top_srcdir)/configure.ac $(top_srcdir)/aclocal.m4 diff --git a/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch b/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch new file mode 100644 index 000000000000..0d65cee8a1a9 --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch @@ -0,0 +1,13 @@ +diff --git a/src/lib/Makefile.in b/src/lib/Makefile.in +index 42e025d..b098a36 100644 +--- a/src/lib/Makefile.in ++++ b/src/lib/Makefile.in +@@ -2,7 +2,7 @@ + .PHONY: default all install depend clean dclean targetclean + + subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd libutil \ +- liboptions libmoinfo libint libderiv libr12 libbasis libmints ++ liboptions libmoinfo libbasis libmints + + all: default + diff --git a/sci-chemistry/psi/files/3.4.0-fortify.patch b/sci-chemistry/psi/files/3.4.0-fortify.patch new file mode 100644 index 000000000000..5f098399ad3f --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-fortify.patch @@ -0,0 +1,58 @@ + src/bin/ccenergy/get_params.cc | 2 +- + src/bin/cclambda/get_params.cc | 2 +- + src/bin/ccresponse/get_params.cc | 2 +- + src/bin/ccsort/get_params.cc | 2 +- + 4 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/src/bin/ccenergy/get_params.cc b/src/bin/ccenergy/get_params.cc +index 53f4c83..a2fa932 100644 +--- a/src/bin/ccenergy/get_params.cc ++++ b/src/bin/ccenergy/get_params.cc +@@ -193,7 +193,7 @@ void get_params() + } + } + else if(params.local) { +- local.weakp = (char *) malloc(4 * sizeof(char)); ++ local.weakp = (char *) malloc(5 * sizeof(char)); + sprintf(local.weakp, "%s", "NONE"); + } + +diff --git a/src/bin/cclambda/get_params.cc b/src/bin/cclambda/get_params.cc +index 4a9d2c8..8a2ae17 100644 +--- a/src/bin/cclambda/get_params.cc ++++ b/src/bin/cclambda/get_params.cc +@@ -150,7 +150,7 @@ void get_params(void) + } + } + else if(params.local) { +- local.weakp = (char *) malloc(4 * sizeof(char)); ++ local.weakp = (char *) malloc(5 * sizeof(char)); + sprintf(local.weakp, "%s", "NONE"); + } + +diff --git a/src/bin/ccresponse/get_params.cc b/src/bin/ccresponse/get_params.cc +index a96db13..5c40aa0 100644 +--- a/src/bin/ccresponse/get_params.cc ++++ b/src/bin/ccresponse/get_params.cc +@@ -207,7 +207,7 @@ void get_params() + } + } + else if(params.local) { +- local.weakp = (char *) malloc(4 * sizeof(char)); ++ local.weakp = (char *) malloc(5 * sizeof(char)); + sprintf(local.weakp, "%s", "NONE"); + } + +diff --git a/src/bin/ccsort/get_params.cc b/src/bin/ccsort/get_params.cc +index ad7f0c3..6ee1993 100644 +--- a/src/bin/ccsort/get_params.cc ++++ b/src/bin/ccsort/get_params.cc +@@ -120,7 +120,7 @@ void get_params() + } + } + else if(params.local) { +- local.weakp = (char *) malloc(4 * sizeof(char)); ++ local.weakp = (char *) malloc(5 * sizeof(char)); + sprintf(local.weakp, "%s", "NONE"); + } + diff --git a/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch b/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch new file mode 100644 index 000000000000..8283e6d8d8ea --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch @@ -0,0 +1,293 @@ +diff --git a/src/bin/mcscf/block_matrix.cc b/src/bin/mcscf/block_matrix.cc +index fe1e131..3ad0bcd 100644 +--- a/src/bin/mcscf/block_matrix.cc ++++ b/src/bin/mcscf/block_matrix.cc +@@ -1,6 +1,7 @@ + #include "block_matrix.h" + #include "matrix_base.h" + #include "memory_manager.h" ++#include <cstdio> + + extern FILE* outfile; + +diff --git a/src/bin/mcscf/block_vector.cc b/src/bin/mcscf/block_vector.cc +index fb383c7..36f55d4 100644 +--- a/src/bin/mcscf/block_vector.cc ++++ b/src/bin/mcscf/block_vector.cc +@@ -1,6 +1,7 @@ + #include "block_vector.h" + #include "vector_base.h" + #include "memory_manager.h" ++#include <cstdio> + + extern FILE* outfile; + +diff --git a/src/bin/mcscf/sblock_matrix.cc b/src/bin/mcscf/sblock_matrix.cc +index 61aa7cc..4da4263 100644 +--- a/src/bin/mcscf/sblock_matrix.cc ++++ b/src/bin/mcscf/sblock_matrix.cc +@@ -1,4 +1,5 @@ + #include <cstdlib> ++#include <cstdio> + #include <psifiles.h> + #include "sblock_matrix.h" + +@@ -103,4 +104,4 @@ void SBlockMatrix::check(const char* cstr) + } + } + +-}} +\ No newline at end of file ++}} +diff --git a/src/bin/mcscf/sblock_vector.cc b/src/bin/mcscf/sblock_vector.cc +index 63c3926..f24fc5b 100644 +--- a/src/bin/mcscf/sblock_vector.cc ++++ b/src/bin/mcscf/sblock_vector.cc +@@ -1,4 +1,5 @@ + #include <cstdlib> ++#include <cstdio> + #include <psifiles.h> + + #include "sblock_vector.h" +@@ -58,4 +59,4 @@ void SBlockVector::check(const char* cstr) + } + } + +-}} +\ No newline at end of file ++}} +diff --git a/src/bin/mcscf/scf.cc b/src/bin/mcscf/scf.cc +index 77318fd..7d1e17f 100644 +--- a/src/bin/mcscf/scf.cc ++++ b/src/bin/mcscf/scf.cc +@@ -5,6 +5,7 @@ + + #include <iostream> + #include <cmath> ++#include <cstdio> + + extern FILE* outfile; + +diff --git a/src/bin/mcscf/scf_Feff.cc b/src/bin/mcscf/scf_Feff.cc +index 584aa83..8a99c3b 100644 +--- a/src/bin/mcscf/scf_Feff.cc ++++ b/src/bin/mcscf/scf_Feff.cc +@@ -1,4 +1,5 @@ + #include <liboptions/liboptions.h> ++#include <cstdio> + + #include "scf.h" + +diff --git a/src/bin/mcscf/scf_canonicalize_MO.cc b/src/bin/mcscf/scf_canonicalize_MO.cc +index a2b3915..96bb6cc 100644 +--- a/src/bin/mcscf/scf_canonicalize_MO.cc ++++ b/src/bin/mcscf/scf_canonicalize_MO.cc +@@ -1,6 +1,7 @@ + #include "scf.h" + + #include <liboptions/liboptions.h> ++#include <cstdio> + + namespace psi{ namespace mcscf{ + +diff --git a/src/bin/mcscf/scf_check_orthonormality.cc b/src/bin/mcscf/scf_check_orthonormality.cc +index 63fbbbb..a13436c 100644 +--- a/src/bin/mcscf/scf_check_orthonormality.cc ++++ b/src/bin/mcscf/scf_check_orthonormality.cc +@@ -1,5 +1,6 @@ + #include <iostream> + #include <cmath> ++#include <cstdio> + + #include "scf.h" + +diff --git a/src/bin/mcscf/scf_compute_energy.cc b/src/bin/mcscf/scf_compute_energy.cc +index fe7ee6d..20194eb 100644 +--- a/src/bin/mcscf/scf_compute_energy.cc ++++ b/src/bin/mcscf/scf_compute_energy.cc +@@ -1,4 +1,5 @@ + #include <iostream> ++#include <cstdio> + + #include "scf.h" + +diff --git a/src/bin/mcscf/scf_diis.cc b/src/bin/mcscf/scf_diis.cc +index 9bcde15..261492a 100644 +--- a/src/bin/mcscf/scf_diis.cc ++++ b/src/bin/mcscf/scf_diis.cc +@@ -1,4 +1,5 @@ + #include <iostream> ++#include <cstdio> + + #include <liboptions/liboptions.h> + +diff --git a/src/bin/mcscf/scf_iterate_scf_equations.cc b/src/bin/mcscf/scf_iterate_scf_equations.cc +index 9e96360..3a3acc3 100644 +--- a/src/bin/mcscf/scf_iterate_scf_equations.cc ++++ b/src/bin/mcscf/scf_iterate_scf_equations.cc +@@ -1,6 +1,7 @@ + #include <cstdlib> + #include <iostream> + #include <cmath> ++#include <cstdio> + + #include <liboptions/liboptions.h> + +diff --git a/src/bin/mcscf/scf_pairs.cc b/src/bin/mcscf/scf_pairs.cc +index b0a8c9d..af5fc35 100644 +--- a/src/bin/mcscf/scf_pairs.cc ++++ b/src/bin/mcscf/scf_pairs.cc +@@ -1,4 +1,5 @@ + #include <iostream> ++#include <cstdio> + + #include <libmoinfo/libmoinfo.h> + +diff --git a/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc b/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc +index 3aac92a..e28e9e3 100644 +--- a/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc ++++ b/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc +@@ -3,6 +3,7 @@ + #include <string> + #include <utility> + #include <algorithm> ++#include <cstdio> + + #include <libmoinfo/libmoinfo.h> + +diff --git a/src/bin/psimrcc/blas_algorithms.cc b/src/bin/psimrcc/blas_algorithms.cc +index bb36025..0a5a3e2 100644 +--- a/src/bin/psimrcc/blas_algorithms.cc ++++ b/src/bin/psimrcc/blas_algorithms.cc +@@ -1,5 +1,6 @@ + #include <libmoinfo/libmoinfo.h> + #include <libutil/libutil.h> ++#include <cstdio> + + #include "blas.h" + #include "memory_manager.h" +diff --git a/src/bin/psimrcc/blas_compatibile.cc b/src/bin/psimrcc/blas_compatibile.cc +index 8de6d73..7caf4f3 100644 +--- a/src/bin/psimrcc/blas_compatibile.cc ++++ b/src/bin/psimrcc/blas_compatibile.cc +@@ -1,6 +1,7 @@ + #include "blas.h" + #include <libutil/libutil.h> + #include <cstdlib> ++#include <cstdio> + + extern FILE *infile, *outfile; + +diff --git a/src/bin/psimrcc/blas_parser.cc b/src/bin/psimrcc/blas_parser.cc +index d211a24..78fe60a 100644 +--- a/src/bin/psimrcc/blas_parser.cc ++++ b/src/bin/psimrcc/blas_parser.cc +@@ -3,6 +3,7 @@ + #include "debugging.h" + #include <libutil/libutil.h> + #include <algorithm> ++#include <cstdio> + + namespace psi{ namespace psimrcc{ + +diff --git a/src/bin/psimrcc/blas_solve.cc b/src/bin/psimrcc/blas_solve.cc +index b138a5b..f5dcdfc 100644 +--- a/src/bin/psimrcc/blas_solve.cc ++++ b/src/bin/psimrcc/blas_solve.cc +@@ -1,6 +1,7 @@ + #include "blas.h" + #include "debugging.h" + #include <libmoinfo/libmoinfo.h> ++#include <cstdio> + + namespace psi{ namespace psimrcc{ + +diff --git a/src/bin/psimrcc/index.cc b/src/bin/psimrcc/index.cc +index 3465d88..68c2b77 100644 +--- a/src/bin/psimrcc/index.cc ++++ b/src/bin/psimrcc/index.cc +@@ -5,6 +5,7 @@ + ***************************************************************************/ + #include <iostream> + #include <algorithm> ++#include <cstdio> + + #include <libmoinfo/libmoinfo.h> + +diff --git a/src/bin/psimrcc/operation.cc b/src/bin/psimrcc/operation.cc +index edbaed5..f4e881f 100644 +--- a/src/bin/psimrcc/operation.cc ++++ b/src/bin/psimrcc/operation.cc +@@ -7,6 +7,7 @@ + #include "debugging.h" + #include "blas.h" + #include <libutil/libutil.h> ++#include <cstdio> + + namespace psi{ namespace psimrcc{ + +diff --git a/src/bin/psimrcc/operation_compute.cc b/src/bin/psimrcc/operation_compute.cc +index 7d2553c..72a1b39 100644 +--- a/src/bin/psimrcc/operation_compute.cc ++++ b/src/bin/psimrcc/operation_compute.cc +@@ -11,6 +11,7 @@ + #include "algebra_interface.h" + #include <libmoinfo/libmoinfo.h> + #include <cstdlib> ++#include <cstdio> + + extern FILE *infile, *outfile; + +diff --git a/src/bin/psimrcc/sort_out_of_core.cc b/src/bin/psimrcc/sort_out_of_core.cc +index 3f255c9..8fa31a3 100644 +--- a/src/bin/psimrcc/sort_out_of_core.cc ++++ b/src/bin/psimrcc/sort_out_of_core.cc +@@ -8,6 +8,7 @@ + #include "sort.h" + #include "matrix.h" + #include <libmoinfo/libmoinfo.h> ++#include <cstdio> + + extern FILE* outfile; + +diff --git a/src/lib/libmoinfo/moinfo_model_space.cc b/src/lib/libmoinfo/moinfo_model_space.cc +index 3bf2030..0a63cde 100644 +--- a/src/lib/libmoinfo/moinfo_model_space.cc ++++ b/src/lib/libmoinfo/moinfo_model_space.cc +@@ -1,6 +1,7 @@ + #include <iostream> + #include <cmath> + #include <cstdlib> ++#include <cstdio> + + #include <psifiles.h> + #include <liboptions/liboptions.h> +@@ -322,4 +323,4 @@ vector<string> MOInfo::get_matrix_names(std::string str) + return(names); + } + +-} +\ No newline at end of file ++} +diff --git a/src/lib/libmoinfo/moinfo_slaterdeterminant.cc b/src/lib/libmoinfo/moinfo_slaterdeterminant.cc +index 8831cd5..a046679 100644 +--- a/src/lib/libmoinfo/moinfo_slaterdeterminant.cc ++++ b/src/lib/libmoinfo/moinfo_slaterdeterminant.cc +@@ -1,4 +1,5 @@ + #include <iostream> ++#include <cstdio> + #include "moinfo.h" + + extern FILE *infile, *outfile; +diff --git a/src/lib/libutil/stl_string.cc b/src/lib/libutil/stl_string.cc +index 0ec247d..f719dcd 100644 +--- a/src/lib/libutil/stl_string.cc ++++ b/src/lib/libutil/stl_string.cc +@@ -2,6 +2,7 @@ + #include <cmath> + #include <iomanip> + #include <algorithm> ++#include <cstdio> + + #include "libutil.h" + diff --git a/sci-chemistry/psi/files/3.4.0-ldflags.patch b/sci-chemistry/psi/files/3.4.0-ldflags.patch new file mode 100644 index 000000000000..9d7f2767e8ec --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-ldflags.patch @@ -0,0 +1,21 @@ +Respect LDFLAGS + +--- configure.ac ++++ configure.ac +@@ -288,15 +288,13 @@ + ) + AC_SUBST(LDLIBS) + +-LDFLAGS= + LIBDIRS= + AC_ARG_WITH(libdirs, + [ --with-libdirs Specifies library directories (-Ldir1 -Ldir2).], + LIBDIRS=$withval +-LDFLAGS=$withval + AC_MSG_RESULT([Using extra library directories: $withval]) + ) +-AC_SUBST(LDFLAGS) ++AC_SUBST(LIBDIRS) + + AC_CHECK_PROGS(PERL,perl,perl) AC_SUBST(PERL) + diff --git a/sci-chemistry/psi/files/3.4.0-man_paths.patch b/sci-chemistry/psi/files/3.4.0-man_paths.patch new file mode 100644 index 000000000000..02cced160847 --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-man_paths.patch @@ -0,0 +1,25 @@ +Fix man paths + +http://bugs.gentoo.org/show_bug.cgi?id=326185 + +--- src/bin/nonbonded/Makefile.in ++++ src/bin/nonbonded/Makefile.in +@@ -19,5 +19,5 @@ + endif + + install_man:: nonbonded.1 +- $(MKDIRS) $(mandir)/man1 +- $(INSTALL_INCLUDE) $^ $(mandir)/man1 ++ $(MKDIRS) $(DESTDIR)$(mandir)/man1 ++ $(INSTALL_INCLUDE) $^ $(DESTDIR)$(mandir)/man1 +--- src/bin/intder/Makefile.in ++++ src/bin/intder/Makefile.in +@@ -21,6 +21,6 @@ + endif + + install_man:: intder.1 +- $(MKDIRS) $(mandir)/man1 +- $(INSTALL_INCLUDE) $^ $(mandir)/man1 ++ $(MKDIRS) $(DESTDIR)$(mandir)/man1 ++ $(INSTALL_INCLUDE) $^ $(DESTDIR)$(mandir)/man1 + diff --git a/sci-chemistry/psi/files/3.4.0-parallel_fix.patch b/sci-chemistry/psi/files/3.4.0-parallel_fix.patch new file mode 100644 index 000000000000..65234fb40dcb --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-parallel_fix.patch @@ -0,0 +1,400 @@ +--- Makefile.in ++++ Makefile.in +@@ -17,62 +17,19 @@ + INSTALL = @INSTALL@ + INSTALL_PROGRAM = @INSTALL_PROGRAM@ + +-all: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making in $${dir} && $(MAKE) all) || exit 1; \ +- done +- +-install: install_host +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making depend in $${dir} && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making clean in $${dir} && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making dclean in $${dir} && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs) tests doc; \ +- do \ +- (cd $${dir} && echo Making clean in $${dir} && $(MAKE) targetclean) || exit 1; \ +- done ++all clean install install_inc install_man depend dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + tests: +- (cd tests && echo Running test suite... && $(MAKE)) || exit 1; ++ $(MAKE) -C tests + + testsclean: +- (cd tests && echo Cleaning test suite... && $(MAKE) clean) || exit 1; ++ $(MAKE) -C tests clean + + doc: +- (cd doc && echo Building documentation... && $(MAKE)) || exit 1; ++ $(MAKE) -C doc + + $(top_srcdir)/configure: $(top_srcdir)/configure.ac $(top_srcdir)/aclocal.m4 + cd $(top_srcdir) && autoconf +--- lib/Makefile.in ++++ lib/Makefile.in +@@ -31,7 +31,7 @@ + $(INSTALL_DATA) $(srcdir)/psi.dat $(DESTDIR)$(pkgdatadir) + for dir in $(subdirs); \ + do \ +- (cd $${dir}; echo Making in $${dir}; $(MAKE) install) || exit 1; \ ++ $(MAKE) -C $$dir install; \ + done + + install_man: macro.psi +--- src/Makefile.in ++++ src/Makefile.in +@@ -6,53 +6,10 @@ + + default: all + +-all: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making in $${dir} && $(MAKE) all) || exit 1; \ +- done +- +-install: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making depend in $${dir} && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making clean in $${dir} && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making dclean in $${dir} && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making clean in $${dir} && $(MAKE) targetclean) || exit 1; \ +- done ++all clean install depend dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ +--- src/lib/Makefile.in ++++ src/lib/Makefile.in +@@ -4,56 +4,10 @@ + subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd libutil \ + liboptions libmoinfo libbasis libmints + +-all: default +- +-default: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \ +- done +- +-install: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \ +- done +- ++all clean install install_inc install_man depend dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + # + # keep the configuration information and makefile up-to-date +--- src/bin/Makefile.in ++++ src/bin/Makefile.in +@@ -13,55 +13,10 @@ + subdirs += psirb + endif + +-all: default +- +-default: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \ +- done +- +-install: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \ +- done ++all install depend clean dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ +--- src/samples/Makefile.in ++++ src/samples/Makefile.in +@@ -5,55 +5,10 @@ + + subdirs = mints + +-all: default +- +-default: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \ +- done +- +-install: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \ +- done ++all install depend clean dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ +--- src/util/Makefile.in ++++ src/util/Makefile.in +@@ -3,55 +3,10 @@ + + subdirs = tocprint psi2molden + +-all: default +- +-default: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \ +- done +- +-install: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \ +- done ++all install depend clean dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ +--- src/lib/libipv1/Makefile.in ++++ src/lib/libipv1/Makefile.in +@@ -58,4 +58,4 @@ + # in case DODEPEND is no + # + +-ip_read.o: y.tab.h ++ip_read.o: y.tab.c y.tab.h diff --git a/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch b/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch new file mode 100644 index 000000000000..2805cb195e24 --- /dev/null +++ b/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch @@ -0,0 +1,19 @@ +diff --git a/src/lib/libipv1/Makefile.in b/src/lib/libipv1/Makefile.in +index eafe8e2..141bf3b 100644 +--- a/src/lib/libipv1/Makefile.in ++++ b/src/lib/libipv1/Makefile.in +@@ -33,10 +33,12 @@ LIBOBJ = $(ALLCSRC:%.c=%.o) $(ALLCXXSRC:%.cc=%.o) + + include ../MakeRules + +-y.tab.c y.tab.h: parse.y ++y.tab.h: y.tab.c ++ ++y.tab.c: parse.y + $(YACC) -v -d $< + +-scan.c: scan.l ++scan.c: scan.l y.tab.h + $(LEX) -t $^ > scan.c + + install_inc:: $(ALLINCLUDE) diff --git a/sci-chemistry/psi/files/use-external-libint.patch b/sci-chemistry/psi/files/use-external-libint.patch new file mode 100644 index 000000000000..1d9ce91e3111 --- /dev/null +++ b/sci-chemistry/psi/files/use-external-libint.patch @@ -0,0 +1,37 @@ +--- psi3.orig/src/bin/cints/Makefile.in 2003-11-14 08:15:19.000000000 -0800 ++++ psi3/src/bin/cints/Makefile.in 2006-02-10 22:42:31.000000000 -0800 +@@ -51,25 +51,25 @@ + # and form the list of the libraries. Remember that libderiv and libr12 + # depend on libint, and hence need to come first for GNU ld to work. + # +-INTLIBS := -lPSI_int ++INTLIBS := -lint + ifeq ($(findstring MP2R12,$(SUBDIRS)),MP2R12) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring R12_Ints,$(SUBDIRS)),R12_Ints) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv1,$(SUBDIRS)),Default_Deriv1) +- ifneq ($(findstring -lPSI_deriv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv2,$(SUBDIRS)),Default_Deriv2) +- ifneq ($(findstring -lderiv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + diff --git a/sci-chemistry/psi/metadata.xml b/sci-chemistry/psi/metadata.xml new file mode 100644 index 000000000000..3774ad2a405f --- /dev/null +++ b/sci-chemistry/psi/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">psicode</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/psi/psi-3.4.0-r2.ebuild b/sci-chemistry/psi/psi-3.4.0-r2.ebuild new file mode 100644 index 000000000000..9a42b877dc16 --- /dev/null +++ b/sci-chemistry/psi/psi-3.4.0-r2.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools-utils fortran-2 multilib toolchain-funcs + +DESCRIPTION="Suite of ab initio quantum chemistry programs to compute various molecular properties" +HOMEPAGE="http://www.psicode.org/" +SRC_URI="mirror://sourceforge/psicode/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="static-libs test" + +RDEPEND=" + !sci-visualization/extrema + virtual/blas + virtual/lapack + >=sci-libs/libint-1.1.4" +DEPEND="${RDEPEND} + virtual/pkgconfig + test? ( dev-lang/perl )" + +S="${WORKDIR}/${PN}${PV:0:1}" + +PATCHES=( + "${FILESDIR}"/${PV}-dont-build-libint.patch + "${FILESDIR}"/use-external-libint.patch + "${FILESDIR}"/${PV}-gcc-4.3.patch + "${FILESDIR}"/${PV}-destdir.patch + "${FILESDIR}"/${P}-parallel-make.patch + "${FILESDIR}"/${PV}-man_paths.patch + "${FILESDIR}"/${PV}-ldflags.patch + "${FILESDIR}"/${PV}-parallel_fix.patch + "${FILESDIR}"/${PV}-fortify.patch + ) + +src_prepare() { + autotools-utils_src_prepare + # Broken test + sed \ + -e 's:scf-mvd-opt ::g' \ + -e 's:scf-mvd-opt-puream ::g' \ + -i tests/Makefile.in || die + + sed \ + -e "/LIBPATTERNS/d" \ + -i src/{bin,util,samples}/MakeVars.in || die + eautoreconf +} + +src_configure() { + # This variable gets set sometimes to /usr/lib/src and breaks stuff + unset CLIBS + + local myeconfargs=( + --with-opt="${CXXFLAGS}" + --datadir="${EPREFIX}"/usr/share/${PN} + --with-blas="$($(tc-getPKG_CONFIG) blas --libs)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile SCRATCH="${WORKDIR}/libint" DODEPEND="no" +} + +src_test() { + emake EXECDIR="${S}"/bin TESTFLAGS="" -j1 tests +} + +src_install() { + autotools-utils_src_install DODEPEND="no" + if ! use static-libs; then + rm -f "${ED}"/usr/$(get_libdir)/*.a || die + fi +} diff --git a/sci-chemistry/pymol-apbs-plugin/Manifest b/sci-chemistry/pymol-apbs-plugin/Manifest new file mode 100644 index 000000000000..b2d73f85090c --- /dev/null +++ b/sci-chemistry/pymol-apbs-plugin/Manifest @@ -0,0 +1,4 @@ +DIST pymol-apbs-plugin-0_p15.py 104351 SHA256 c5a259ddc1931f1ec4efe0ffc3ae9e9ac4a84a28c83a4f93a06ebb7c1bef0c1d +DIST pymol-apbs-plugin-0_p18.py 108766 SHA256 ec09c5a0903ac965cc29fcf0a3c1999bd939f9791d037915596092698855d12c +DIST pymol-apbs-plugin-2.1_p24.py 113049 SHA256 d51bb1bbbf641777ee36713c0c47696d7906179e42cac8cdd0e8e156ef081c9f SHA512 49141ea7e4a3a3430d342fb4fbb497d522ce6485c6d9e3527414519574eab7b8218fe240f26920013676528c40059a46341d58153bfe9d05bf747ead926b2cfd WHIRLPOOL 17a4f9ed9670b9a7f82395a9cf1ad465635f840b7389c10ad8c8eae3262c3696383bbacadf5aee9fed817eff7370008cc85a1666896fed56dffb0163e4c3d7e1 +DIST pymol-apbs-plugin-2.1_p26.py 113086 SHA256 552242b4f5b47f298eeb0616e0d51924b4a7649dc8a16e4809e923dbcb97738d SHA512 3561d077875a1880d6badccf835db3d17e0c45416accd6127cbef7c550711908b47ccb392563e3d29ecb7d6527c098584eeabb6490d1033720ed7efe751d0fb0 WHIRLPOOL dccd32b0193e74e505d69922b441323fb24b0ba30aa85f4d69b94663ab406a57b772985ca2c56146e2c4b929f73b321095c3ae2caf95f297f14d8b31671f475e diff --git a/sci-chemistry/pymol-apbs-plugin/files/pymol-apbs-plugin-2.1_p26-tcltk8.6.patch b/sci-chemistry/pymol-apbs-plugin/files/pymol-apbs-plugin-2.1_p26-tcltk8.6.patch new file mode 100644 index 000000000000..c3675cf4c0d0 --- /dev/null +++ b/sci-chemistry/pymol-apbs-plugin/files/pymol-apbs-plugin-2.1_p26-tcltk8.6.patch @@ -0,0 +1,176 @@ +--- pymol-apbs-plugin-2.1_p26.py.orig 2013-08-16 20:29:27.000000000 -0400 ++++ pymol-apbs-plugin-2.1_p26.py 2013-08-16 20:31:35.000000000 -0400 +@@ -560,7 +560,8 @@ + # Set up the Main page + page = self.notebook.add('Main') + group = Pmw.Group(page,tag_text='Main options') +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + self.selection = Pmw.EntryField(group.interior(), + labelpos='w', + label_text='Selection to use: ', +@@ -606,7 +607,8 @@ + page = self.notebook.add('Configuration') + + group = Pmw.Group(page,tag_text='Dielectric Constants') +- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) ++ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + group.grid(column=0, row=0) + self.interior_dielectric = Pmw.EntryField(group.interior(),labelpos='w', + label_text = 'Protein Dielectric:', +@@ -625,7 +627,8 @@ + #entry.pack(side='left',fill='both',expand=1,padx=4) # side-by-side + entry.pack(fill='x',expand=1,padx=4,pady=1) # vertical + group = Pmw.Group(page,tag_text='Other') +- group.pack(fill='both',expand=1, padx=4, pady=5) ++ #group.pack(fill='both',expand=1, padx=4, pady=5) ++ group.grid(padx=4, pady=5, sticky=(N, S, E, W)) + group.grid(column=1, row=1,columnspan=4) + self.max_mem_allowed = Pmw.EntryField(group.interior(),labelpos='w', + label_text = 'Maximum Memory Allowed (MB):', +@@ -683,7 +686,8 @@ + + + group = Pmw.Group(page,tag_text='Ions') +- group.pack(fill='both',expand=1, padx=4, pady=5) ++ #group.pack(fill='both',expand=1, padx=4, pady=5) ++ group.grid(padx=4, pady=5, sticky=(N, S, E, W)) + group.grid(column=0, row=1, ) + self.ion_plus_one_conc = Pmw.EntryField(group.interior(), + labelpos='w', +@@ -742,7 +746,8 @@ + entry.pack(fill='x',expand=1,padx=4) + + group = Pmw.Group(page,tag_text = 'Coarse Mesh Length') +- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) ++ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + group.grid(column = 1, row = 0) + for coord in 'x y z'.split(): + setattr(self,'grid_coarse_%s'%coord,Pmw.EntryField(group.interior(), +@@ -757,7 +762,8 @@ + + + group = Pmw.Group(page,tag_text = 'Fine Mesh Length') +- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) ++ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + group.grid(column = 2, row = 0) + for coord in 'x y z'.split(): + setattr(self,'grid_fine_%s'%coord,Pmw.EntryField(group.interior(), +@@ -772,7 +778,8 @@ + + + group = Pmw.Group(page,tag_text = 'Grid Center') +- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) ++ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + group.grid(column = 3, row = 0) + for coord in 'x y z'.split(): + setattr(self,'grid_center_%s'%coord,Pmw.EntryField(group.interior(), +@@ -786,7 +793,8 @@ + getattr(self,'grid_center_%s'%coord).pack(fill='x', expand=1, padx=4, pady=1) + + group = Pmw.Group(page,tag_text = 'Grid Points') +- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) ++ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + group.grid(column = 4, row = 0) + for coord in 'x y z'.split(): + setattr(self,'grid_points_%s'%coord,Pmw.EntryField(group.interior(), +@@ -804,7 +812,8 @@ + page.grid_columnconfigure(5,weight=1) + page = self.notebook.add('Program Locations') + group = Pmw.Group(page,tag_text='Locations') +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + def quickFileValidation(s): + if s == '': return Pmw.PARTIAL + elif os.path.isfile(s): return Pmw.OK +@@ -867,7 +876,8 @@ + + page = self.notebook.add('Temp File Locations') + group = Pmw.Group(page,tag_text='Locations') +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(), + labelpos = 'w', + label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename), +@@ -915,17 +925,20 @@ + page = self.notebook.add('Visualization (1)') + group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1) + self.visualization_group_1 = group +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + + page = self.notebook.add('Visualization (2)') + group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2) + self.visualization_group_2 = group +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + + # Create a couple of other empty pages + page = self.notebook.add('About') + group = Pmw.Group(page, tag_text='About PyMOL APBS Tools') +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/). + + Documentation may be found at +@@ -2158,7 +2171,8 @@ + self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0) + self.update_buttonbox.pack(side=LEFT) + self.update_buttonbox.add('Update',command=self.refresh) +- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) ++ #self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) ++ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + + self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface') + self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0) +@@ -2209,7 +2223,8 @@ + bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high) + Pmw.alignlabels(bars) + for bar in bars: bar.pack(side=LEFT) +- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ #self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ self.ms_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + + self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines') + self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0) +@@ -2224,7 +2239,8 @@ + text = """Follows same coloring as surface.""", + ) + label.pack() +- self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) ++ #self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) ++ self.fl_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + + self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface') + self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0) +@@ -2243,7 +2259,8 @@ + entryfield_validate = {'validator' : 'real', 'min':0} + ) + self.pos_surf_val.pack(side=LEFT) +- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ #self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ self.pi_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + + self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface') + self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0) +@@ -2262,7 +2279,8 @@ + entryfield_validate = {'validator' : 'real', 'max':0} + ) + self.neg_surf_val.pack(side=LEFT) +- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ #self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + + + diff --git a/sci-chemistry/pymol-apbs-plugin/metadata.xml b/sci-chemistry/pymol-apbs-plugin/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/pymol-apbs-plugin/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-0_p15.ebuild b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-0_p15.ebuild new file mode 100644 index 000000000000..8609778501ce --- /dev/null +++ b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-0_p15.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" +SUPPORT_PYTHON_ABIS="1" + +inherit python + +MY_PV="${PV##*_p}" + +DESCRIPTION="APBS plugin for pymol" +HOMEPAGE="http://sourceforge.net/projects/pymolapbsplugin/" +SRC_URI="http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py?revision=${MY_PV} -> ${P}.py" + +SLOT="0" +KEYWORDS="~amd64 ~ppc x86 ~amd64-linux ~x86-linux" +LICENSE="pymol" +IUSE="" + +RDEPEND=" + sci-chemistry/apbs + sci-chemistry/pdb2pqr + !<sci-chemistry/pymol-1.2.2-r1" +DEPEND="${RDEPEND}" +RESTRICT_PYTHON_ABIS="3.*" + +src_unpack() { + mkdir "${S}" + cp "${DISTDIR}"/${P}.py "${S}"/ + python_copy_sources +} + +src_install() { + installation() { + sed \ + -e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \ + -e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/\":g" \ + -e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \ + -i ${P}.py + + insinto $(python_get_sitedir)/pmg_tk/startup/ + newins ${P}.py apbs_tools.py || die + } + python_execute_function -s installation +} + +pkg_postinst() { + python_mod_optimize pmg_tk/startup/apbs_tools.py +} + +pkg_postrm() { + python_mod_cleanup pmg_tk/startup/apbs_tools.py +} diff --git a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-0_p18.ebuild b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-0_p18.ebuild new file mode 100644 index 000000000000..11596fe54cbf --- /dev/null +++ b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-0_p18.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" +SUPPORT_PYTHON_ABIS="1" + +inherit python + +MY_PV="${PV##*_p}" + +DESCRIPTION="APBS plugin for pymol" +HOMEPAGE="http://sourceforge.net/projects/pymolapbsplugin/" +SRC_URI="http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py?revision=${MY_PV} -> ${P}.py" + +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +LICENSE="pymol" +IUSE="" + +RDEPEND=" + sci-chemistry/apbs + sci-chemistry/pdb2pqr + !<sci-chemistry/pymol-1.2.2-r1" +DEPEND="${RDEPEND}" +RESTRICT_PYTHON_ABIS="3.*" + +src_unpack() { + mkdir "${S}" + cp "${DISTDIR}"/${P}.py "${S}"/ + python_copy_sources +} + +src_install() { + installation() { + sed \ + -e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \ + -e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/\":g" \ + -e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \ + -i ${P}.py + + insinto $(python_get_sitedir)/pmg_tk/startup/ + newins ${P}.py apbs_tools.py || die + } + python_execute_function -s installation +} + +pkg_postinst() { + python_mod_optimize pmg_tk/startup/apbs_tools.py +} + +pkg_postrm() { + python_mod_cleanup pmg_tk/startup/apbs_tools.py +} diff --git a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-2.1_p24.ebuild b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-2.1_p24.ebuild new file mode 100644 index 000000000000..627780c1ff39 --- /dev/null +++ b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-2.1_p24.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" +SUPPORT_PYTHON_ABIS="1" + +inherit python + +MY_PV="${PV##*_p}" + +DESCRIPTION="APBS plugin for pymol" +HOMEPAGE="http://sourceforge.net/projects/pymolapbsplugin/" +SRC_URI="http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py?revision=${MY_PV} -> ${P}.py" + +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +LICENSE="pymol" +IUSE="" + +RDEPEND=" + sci-chemistry/apbs + sci-chemistry/pdb2pqr + !<sci-chemistry/pymol-1.2.2-r1" +DEPEND="${RDEPEND}" +RESTRICT_PYTHON_ABIS="3.*" + +src_unpack() { + mkdir "${S}" + cp "${DISTDIR}"/${P}.py "${S}"/ + python_copy_sources +} + +src_install() { + installation() { + sed \ + -e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \ + -e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/\":g" \ + -e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \ + -i ${P}.py + + insinto $(python_get_sitedir)/pmg_tk/startup/ + newins ${P}.py apbs_tools.py || die + } + python_execute_function -s installation +} + +pkg_postinst() { + python_mod_optimize pmg_tk/startup/apbs_tools.py +} + +pkg_postrm() { + python_mod_cleanup pmg_tk/startup/apbs_tools.py +} diff --git a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-2.1_p26-r1.ebuild b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-2.1_p26-r1.ebuild new file mode 100644 index 000000000000..819687b121bc --- /dev/null +++ b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-2.1_p26-r1.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 + +MY_PV="${PV##*_p}" + +DESCRIPTION="APBS plugin for pymol" +HOMEPAGE="http://sourceforge.net/projects/pymolapbsplugin/" +SRC_URI="http://sourceforge.net/p/pymolapbsplugin/code/${MY_PV}/tree/trunk/src/apbsplugin.py?format=raw -> ${P}.py" + +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +LICENSE="pymol" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + sci-chemistry/apbs + sci-chemistry/pdb2pqr + !<sci-chemistry/pymol-1.2.2-r1" +DEPEND="${RDEPEND}" + +src_unpack() { + mkdir "${S}" + cp "${DISTDIR}"/${P}.py "${S}"/ +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-tcltk8.6.patch + python_copy_sources +} + +src_install() { + installation() { + cd "${BUILD_DIR}" || die + sed \ + -e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \ + -e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"$(python_get_sitedir)/pdb2pqr/\":g" \ + -e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \ + ${P}.py > apbs_tools.py || die + + python_moduleinto pmg_tk/startup + python_domodule apbs_tools.py + python_optimize + } + python_parallel_foreach_impl installation +} diff --git a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-2.1_p26.ebuild b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-2.1_p26.ebuild new file mode 100644 index 000000000000..5f4c1affc3de --- /dev/null +++ b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-2.1_p26.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 + +MY_PV="${PV##*_p}" + +DESCRIPTION="APBS plugin for pymol" +HOMEPAGE="http://sourceforge.net/projects/pymolapbsplugin/" +SRC_URI="http://sourceforge.net/p/pymolapbsplugin/code/${MY_PV}/tree/trunk/src/apbsplugin.py?format=raw -> ${P}.py" + +SLOT="0" +KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +LICENSE="pymol" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + sci-chemistry/apbs + sci-chemistry/pdb2pqr + !<sci-chemistry/pymol-1.2.2-r1" +DEPEND="${RDEPEND}" + +src_unpack() { + mkdir "${S}" + cp "${DISTDIR}"/${P}.py "${S}"/ +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-tcltk8.6.patch + python_copy_sources +} + +src_install() { + installation() { + cd "${BUILD_DIR}" || die + sed \ + -e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \ + -e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/\":g" \ + -e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \ + ${P}.py > apbs_tools.py + + python_moduleinto pmg_tk/startup + python_domodule apbs_tools.py || die + python_optimize + } + python_parallel_foreach_impl installation +} diff --git a/sci-chemistry/pymol-plugins-bni-tools/Manifest b/sci-chemistry/pymol-plugins-bni-tools/Manifest new file mode 100644 index 000000000000..532cf761f73b --- /dev/null +++ b/sci-chemistry/pymol-plugins-bni-tools/Manifest @@ -0,0 +1,2 @@ +DIST bni-tools-0.251.zip 32596 SHA256 79f77ecb5797de49249c571eda958a97647f34f456bcda952e4b63ffd0c412d2 SHA512 0d28433679fff1d4473469078ef3b9091f4ed13ccf414d4c54afadcde2f120768f26c0aaee378f04fd9cc71159f21ad7f9281a163a365106dadc3f641b743b76 WHIRLPOOL 4f869b2a357b6c1be6077f478b7356e4bba14ae7a4ef7c17357f6729888439d4c3b09cb27271585258024f39f2fe2437016dd7bec3301e849de453add25330d9 +DIST bni-tools-027.zip 33753 SHA256 9ddb9785146b12c5c2ff03d34262fec8ff04bfaa9c56ec4665bac5e33879cd7c SHA512 9c0ef1ca5bbb3040192ab2668f354f947e93d42c91a0cfdde5d05be273e6ba9f29ec3c6ee86367f18d87316282b4e0141183b8d6259bd36d44010b7bbb7666e5 WHIRLPOOL 7e14a2ef86009237f53e28f6ac95b56687dd7275e8bd8a856c4d408a6c57cffb7131cb9a505d01da7b2f58bf20bae9b400e478d994bb04f9e799ecf09a60edd3 diff --git a/sci-chemistry/pymol-plugins-bni-tools/metadata.xml b/sci-chemistry/pymol-plugins-bni-tools/metadata.xml new file mode 100644 index 000000000000..c4982f1db5fb --- /dev/null +++ b/sci-chemistry/pymol-plugins-bni-tools/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher (jlec)</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bni-tools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.25.1.ebuild b/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.25.1.ebuild new file mode 100644 index 000000000000..640cf969c61e --- /dev/null +++ b/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.25.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" +SUPPORT_PYTHON_ABIS="1" + +inherit python versionator + +MY_PN="${PN#pymol-plugins-}" +MY_P="${MY_PN}-$(delete_version_separator 2)" + +DESCRIPTION="Gives Pymol additional functionalities and presets to the PyMOL GUI" +HOMEPAGE="http://bni-tools.sourceforge.net/" +SRC_URI="mirror://sourceforge/${MY_PN}/${MY_P}.zip" + +LICENSE="CNRI" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="sci-chemistry/pymol" +DEPEND="app-arch/unzip" +RESTRICT_PYTHON_ABIS="2.4 3.*" + +src_install(){ + installation() { + insinto $(python_get_sitedir)/pmg_tk/startup/ + doins bni-tools.py || die "Failed to install ${P}" + } + python_execute_function installation + dodoc readme.txt || die "No dodoc" +} + +pkg_postinst(){ + python_mod_optimize pmg_tk/startup +} + +pkg_postrm() { + python_mod_cleanup pmg_tk/startup +} diff --git a/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild b/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild new file mode 100644 index 000000000000..8ade4b32c540 --- /dev/null +++ b/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 versionator + +MY_PN="${PN#pymol-plugins-}" +MY_P="${MY_PN}-$(delete_version_separator 1)" +MY_P_DOT="${MY_PN}-${PV}" + +DESCRIPTION="Gives Pymol additional functionalities and presets to the PyMOL GUI" +HOMEPAGE="http://bni-tools.sourceforge.net/" +SRC_URI="mirror://sourceforge/${MY_PN}/${MY_PN}/${MY_P_DOT}/${MY_P}.zip" + +LICENSE="CNRI" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="app-arch/unzip" + +S="${WORKDIR}" + +src_install(){ + python_moduleinto pmg_tk/startup + python_parallel_foreach_impl python_domodule bni-tools.py + python_parallel_foreach_impl python_optimize + dodoc readme.txt + dohtml ShortCommandDescription.html +} diff --git a/sci-chemistry/pymol-plugins-caver/Manifest b/sci-chemistry/pymol-plugins-caver/Manifest new file mode 100644 index 000000000000..ecfe07a54c4b --- /dev/null +++ b/sci-chemistry/pymol-plugins-caver/Manifest @@ -0,0 +1 @@ +DIST Caver2_1_2_pymol_plugin.zip 5698331 SHA256 1dcc61ba13247c05710c4cd68491d0c867ce1d0c11c824be85a516250b2874e3 SHA512 9d28e059bb20f30cf6a0d25ed2eb080dcf9dbb753e9d4578d95e293b31c5cf5fe23d5177dccdb79c192ab3e65bb484b6eb22b26c267637b125404f871e01a52c WHIRLPOOL 33e6893d2114b5ce197fc098d09dfc67ce88f38741e30f1fa574873836c636b5e0c180301849fd98f1f93de5ce51554d2245d0bd615b938d39a802e91e68ebb9 diff --git a/sci-chemistry/pymol-plugins-caver/metadata.xml b/sci-chemistry/pymol-plugins-caver/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/pymol-plugins-caver/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild b/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild new file mode 100644 index 000000000000..a07aef903771 --- /dev/null +++ b/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit multilib python-r1 eutils versionator java-utils-2 + +MY_PV="$(replace_all_version_separators _)" +MY_P="Caver${MY_PV}_pymol_plugin" + +DESCRIPTION="Calculation of pathways from buried cavities to outside solvent in protein structures" +HOMEPAGE="http://loschmidt.chemi.muni.cz/caver/" +SRC_URI="${MY_P}.zip" + +LICENSE="CAVER" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=virtual/jre-1.6 + sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="app-arch/unzip" + +RESTRICT="fetch" + +S="${WORKDIR}/${MY_P}"/linux_mac + +pkg_nofetch() { + elog "Download ${A}" + elog "from ${HOMEPAGE}. This requires registration." + elog "Place tarballs in ${DISTDIR}." +} + +src_install() { + java-pkg_dojar Caver${MY_PV}/*.jar + + java-pkg_jarinto /usr/share/${PN}/lib/lib/ + java-pkg_dojar Caver${MY_PV}/lib/*.jar + + installation() { + sed \ + -e "s:directory/where/jar/with/plugin/is/located:${EPREFIX}/usr/share/${PN}/lib/:g" \ + -i Caver${MY_PV}.py || die + + python_moduleinto pmg_tk/startup/ + python_domodule Caver${MY_PV}.py + python_optimize + } + python_foreach_impl installation +} diff --git a/sci-chemistry/pymol-plugins-dssp/Manifest b/sci-chemistry/pymol-plugins-dssp/Manifest new file mode 100644 index 000000000000..026f06f2be36 --- /dev/null +++ b/sci-chemistry/pymol-plugins-dssp/Manifest @@ -0,0 +1 @@ +DIST pymol-plugins-dssp-110430.py.xz 6836 SHA256 8be8da803f5b3908b5918c8fd355bd7e37785d2eada3a92d6de15b362b9e3868 SHA512 521e0a32ca6d2c8c21c690815b0654bb44303bd7fb9a1eb76227030b2ad7311fadb0d748e49b8bbc16cd5e69acba375b5353de7bffef1ff69686e62021fe64f4 WHIRLPOOL bfe0edc2307b3879668095dbe8a9bb242a58c5f6e449f1a08d3a655e9383c7b5a273d7cae65d3067f8f06a0a9d251565cd7f047d741349876bbfdfd366ffe2a5 diff --git a/sci-chemistry/pymol-plugins-dssp/metadata.xml b/sci-chemistry/pymol-plugins-dssp/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/pymol-plugins-dssp/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild b/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild new file mode 100644 index 000000000000..bc129c005d87 --- /dev/null +++ b/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +DESCRIPTION="DSSP Plugin for PyMOL" +HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/dssp_pymol/dssp_pymol.html" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.py.xz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD pymol" +IUSE="" + +RDEPEND=" + sci-chemistry/dssp + sci-biology/stride + sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="" + +S="${WORKDIR}" + +src_prepare() { + sed \ + -e "s:GENTOO_DSSP:${EPREFIX}/usr/bin/dssp:g" \ + -e "s:GENTOO_STRIDE:${EPREFIX}/usr/bin/stride:g" \ + -i ${P}.py || die +} + +src_install() { + python_moduleinto pmg_tk/startup + python_parallel_foreach_impl python_domodule ${P}.py + python_parallel_foreach_impl python_optimize +} diff --git a/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430.ebuild b/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430.ebuild new file mode 100644 index 000000000000..4bdb53a1019e --- /dev/null +++ b/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" +SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.* *-jython" + +inherit python + +DESCRIPTION="DSSP Plugin for PyMOL" +HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/dssp_pymol/dssp_pymol.html" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.py.xz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD pymol" +IUSE="" + +RDEPEND=" + sci-chemistry/dssp + sci-biology/stride + sci-chemistry/pymol" +DEPEND="" + +src_prepare() { + sed \ + -e "s:GENTOO_DSSP:${EPREFIX}/usr/bin/dssp:g" \ + -e "s:GENTOO_STRIDE:${EPREFIX}/usr/bin/stride:g" \ + -i ${P}.py || die +} + +src_install() { + installation() { + insinto $(python_get_sitedir)/pmg_tk/startup + doins ${P}.py + } + python_execute_function installation +} + +pkg_postinst() { + python_mod_optimize pmg_tk/startup/${P}.py +} + +pkg_postrm() { + python_mod_cleanup pmg_tk/startup/${P}.py +} diff --git a/sci-chemistry/pymol-plugins-dynamics/Manifest b/sci-chemistry/pymol-plugins-dynamics/Manifest new file mode 100644 index 000000000000..a607e37c50b4 --- /dev/null +++ b/sci-chemistry/pymol-plugins-dynamics/Manifest @@ -0,0 +1 @@ +DIST pymol-plugins-dynamics-1.2.0.tar.gz 725163 SHA256 edf9bddbbce41ee5319bfd0b28d6e0b0eba56e8b2d8a300d510be8ff5894704f SHA512 7e8d62ea58cb88348136fccd132d9a1faaa3474c0a0f821e729ced777620e2083b1b0606d79fc75802755c96c5eb0b90e08b00e5c865ecbaaee2b837f56987de WHIRLPOOL 07061d3b0840fef0025be55b90fca013afc1ea58308d6ee11a8b74321de4f1c24760b1cf141b0a86678c5cf652c8890cdf2c4e0da60403c8454e04b003e20aaa diff --git a/sci-chemistry/pymol-plugins-dynamics/metadata.xml b/sci-chemistry/pymol-plugins-dynamics/metadata.xml new file mode 100644 index 000000000000..78402e14de8d --- /dev/null +++ b/sci-chemistry/pymol-plugins-dynamics/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <upstream> + <remote-id type="github">tomaszmakarewicz/Dynamics</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-1.2.0.ebuild b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-1.2.0.ebuild new file mode 100644 index 000000000000..3959b0bedcac --- /dev/null +++ b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-1.2.0.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +MY_PN="Dynamics" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Molecular dynamics in Pymol" +HOMEPAGE="https://github.com/tomaszmakarewicz/Dynamics" +SRC_URI="https://github.com/tomaszmakarewicz/Dynamics/archive/v1.2.0.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS}" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${MY_P} + +DOCS=( manual.odt ) + +src_prepare() { + sed \ + -e "/sys.path.insert/d" \ + -e "s:import dynamics_pymol_plugin:from pmg_tk.startup import dynamics_pymol_plugin:g" \ + -i pydynamics* || die +} + +src_install() { + python_moduleinto pmg_tk/startup + python_parallel_foreach_impl python_domodule dynamics_pymol_plugin.py + python_parallel_foreach_impl python_doscript pydynamics* +} diff --git a/sci-chemistry/pymol-plugins-emovie/Manifest b/sci-chemistry/pymol-plugins-emovie/Manifest new file mode 100644 index 000000000000..26303adeb07b --- /dev/null +++ b/sci-chemistry/pymol-plugins-emovie/Manifest @@ -0,0 +1 @@ +DIST eMovie_package.zip 22840 RMD160 1576bbf2007f82f6d06b0a79d45ee634d1d28be5 SHA1 4a3ed376cfe612f515c9d0390d5c4b0dead8de72 SHA256 a899d08f43902f803a797ddbd1052c687db03add53b2f815c91ae83223cc7f82 diff --git a/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch b/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch new file mode 100644 index 000000000000..a9a77e5055dd --- /dev/null +++ b/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch @@ -0,0 +1,22 @@ +diff --git a/eMovie.py b/eMovie.py +index a865732..8b5b068 100644 +--- a/eMovie.py ++++ b/eMovie.py +@@ -931,7 +931,7 @@ class Story(tkSimpleDialog.Dialog): + + if self.parent is not None: + self.geometry("+%d+%d" % (parent.winfo_rootx()+50,parent.winfo_rooty()+50)) +- self.initial_focus.focus_set() ++ self.initial_focus.focus_set() + + self.wait_window(self) + +@@ -2041,7 +2041,7 @@ class AddMorph(tkSimpleDialog.Dialog): + + if self.parent is not None: + self.geometry("+%d+%d" % (parent.winfo_rootx()+50,parent.winfo_rooty()+50)) +- self.initial_focus.focus_set() ++ self.initial_focus.focus_set() + + self.wait_window(self) + diff --git a/sci-chemistry/pymol-plugins-emovie/metadata.xml b/sci-chemistry/pymol-plugins-emovie/metadata.xml new file mode 100644 index 000000000000..18330bb401f1 --- /dev/null +++ b/sci-chemistry/pymol-plugins-emovie/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +<maintainer> + <email>jlec@gentoo.org</email> +</maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild b/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild new file mode 100644 index 000000000000..38a48fd485fe --- /dev/null +++ b/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +SUPPORT_PYTHON_ABIS="1" + +inherit eutils python + +DESCRIPTION="eMovie is a plug-in tool for the molecular visualization program PyMOL" +SRC_URI="http://www.weizmann.ac.il/ISPC/eMovie_package.zip" +HOMEPAGE="http://www.weizmann.ac.il/ISPC/eMovie.html" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~x86 ~amd64 ~x86-linux ~amd64-linux" +IUSE="" + +RDEPEND=">sci-chemistry/pymol-0.99" +DEPEND="app-arch/unzip" +#RESTRICT_PYTHON_ABIS="3.*" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-indent.patch + + mkdir ${P} + mv e* ${P}/ + + python_copy_sources + + conversion() { + [[ "${PYTHON_ABI}" == 2.* ]] && return + + 2to3-${PYTHON_ABI} -w eMovie.py > /dev/null + } + python_execute_function --action-message 'Applying patches for Python ${PYTHON_ABI}' --failure-message 'Applying patches for Python ${PYTHON_ABI} failed' -s conversion +} + +src_install(){ + installation() { + insinto $(python_get_sitedir)/pmg_tk/startup/ + doins eMovie.py || die + } + python_execute_function -s installation +} + +pkg_postinst(){ + python_mod_optimize pmg_tk/startup +} + +pkg_postrm() { + python_mod_cleanup pmg_tk/startup +} diff --git a/sci-chemistry/pymol-plugins-msms/Manifest b/sci-chemistry/pymol-plugins-msms/Manifest new file mode 100644 index 000000000000..d4d6fb620908 --- /dev/null +++ b/sci-chemistry/pymol-plugins-msms/Manifest @@ -0,0 +1 @@ +DIST pymol-plugins-msms-100415.py 62320 SHA256 1452acdcf8b13f5af22da563d44d51aca9f8fdd108dd7a0548ec41941cb463a5 SHA512 924d89836f92d0be52d7534cbe6dc9338dac1c2263a51900ab62dbe96e4f54f565dbaa6bdf51236d8ea8e9042aa09283a117f5285561b252177a5a32f3876489 WHIRLPOOL c5889b3543ac554083b76c38bb53fad1f001bd46f6686b0cdc36c1a7e576de3dc9a9bba0b459e0d928e30aec21ab09b98a0a8eb128fa64fc5b4228ca9ad7c0e4 diff --git a/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch new file mode 100644 index 000000000000..0d26fb31c5f1 --- /dev/null +++ b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch @@ -0,0 +1,33 @@ + pymol-plugins-msms-100415.py | 18 ++++++++++-------- + 1 files changed, 10 insertions(+), 8 deletions(-) + +diff --git a/pymol-plugins-msms-100415.py b/pymol-plugins-msms-100415.py +index 725934d..7ea00bf 100644 +--- a/pymol-plugins-msms-100415.py ++++ b/pymol-plugins-msms-100415.py +@@ -99,15 +99,17 @@ class MSMSPlugin: + self.cleanup_saved_pymol_sel.set(True) # by default, clean up + + self.pdb_fn.set('') +- if 'MSMS_BIN' in os.environ: +- if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN'] +- self.msms_bin.set(os.environ['MSMS_BIN']) +- else: +- if VERBOSE: print 'MSMS_BIN not found in environmental variables.' +- self.msms_bin.set('') ++ self.msms_bin.set('GENTOOMSMS') ++## if 'MSMS_BIN' in os.environ: ++## if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN'] ++## self.msms_bin.set(os.environ['MSMS_BIN']) ++## else: ++## if VERBOSE: print 'MSMS_BIN not found in environmental variables.' ++## self.msms_bin.set('') + ## self.pdb2xyzr_bin.set('') +- if 'PDB2XYZRN' in os.environ: self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN']) +- else: self.pdb2xyzrn_bin.set('') ++ self.pdb2xyzrn_bin.set('GENTOOXYZRN') ++## if 'PDB2XYZRN' in os.environ: self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN']) ++## else: self.pdb2xyzrn_bin.set('') + self.tmp_dir.set('/tmp') + self.cleanup_msms_output = Tkinter.BooleanVar() + self.cleanup_msms_output.set(True) # by default, clean up msms output diff --git a/sci-chemistry/pymol-plugins-msms/metadata.xml b/sci-chemistry/pymol-plugins-msms/metadata.xml new file mode 100644 index 000000000000..c6f92c968349 --- /dev/null +++ b/sci-chemistry/pymol-plugins-msms/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +MSMS is an excellent tool for computing protein solvent excluded surface (SES). +MSMS Plugin for PyMOL provides a graphical user interface for running MSMS and +displaying its results in PyMOL. + +1. Citation for this plugin: + Hongbo Zhu. MSMS plugin for PyMOL, 2010, Biotechnology Center (BIOTEC), TU Dresden. +2. Citation for PyMOL can be found at: http://pymol.sourceforge.net/faq.html#CITE +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild new file mode 100644 index 000000000000..d90a27f98ca8 --- /dev/null +++ b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 + +DESCRIPTION="GUI for MSMS and displaying its results in PyMOL" +HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/msms_pymol.html" +SRC_URI="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/pymol_script/msms_pymol.py -> ${P}.py" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD pymol" +IUSE="" + +RDEPEND=" + sci-chemistry/msms-bin + sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND}" + +src_unpack() { + mkdir "${S}" || die + cp "${DISTDIR}"/${A} "${S}/" || die +} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-msms.patch + sed \ + -e "s:GENTOOMSMS:${EPREFIX}/opt/bin/msms:g" \ + -e "s:GENTOOXYZRN:${EPREFIX}/usr/bin/pdb_to_xyzrn:g" \ + -i ${A} || die +} + +src_install() { + python_moduleinto pmg_tk/startup + python_parallel_foreach_impl python_domodule ${P}.py + python_parallel_foreach_impl python_optimize +} diff --git a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415.ebuild b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415.ebuild new file mode 100644 index 000000000000..e226003f8560 --- /dev/null +++ b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" +SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.* *-jython" + +inherit eutils python + +DESCRIPTION="GUI for MSMS and displaying its results in PyMOL" +HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/msms_pymol.html" +SRC_URI="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/pymol_script/msms_pymol.py -> ${P}.py" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD pymol" +IUSE="" + +RDEPEND=" + sci-chemistry/msms-bin + sci-chemistry/pymol" +DEPEND="${RDEPEND}" + +src_unpack() { + mkdir "${S}" + cp "${DISTDIR}"/${A} "${S}/" +} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-msms.patch + sed \ + -e "s:GENTOOMSMS:${EPREFIX}/opt/bin/msms:g" \ + -e "s:GENTOOXYZRN:${EPREFIX}/usr/bin/pdb_to_xyzrn:g" \ + -i ${A} || die +} + +src_install() { + installation() { + insinto $(python_get_sitedir)/pmg_tk/startup + doins ${P}.py + } + python_execute_function installation +} + +pkg_postinst() { + python_mod_optimize pmg_tk/startup/${P}.py +} + +pkg_postrm() { + python_mod_cleanup pmg_tk/startup/${P}.py +} diff --git a/sci-chemistry/pymol-plugins-promol/Manifest b/sci-chemistry/pymol-plugins-promol/Manifest new file mode 100644 index 000000000000..30b2014c9f2f --- /dev/null +++ b/sci-chemistry/pymol-plugins-promol/Manifest @@ -0,0 +1 @@ +DIST pymol-plugins-promol-3.0.2.zip 2219295 SHA256 4281131ab5fc5568c1e3984aec4a7022b515334c66adfbc2682df5f0e6a4c2d6 SHA512 e40e9c08e2cb1b223390d751bb1f32069924f1c23aa2b4bdafb6689254e6aa673d4412aca587792f660869f97a389db8a9183033d8b2394c998d0f911104d8d7 WHIRLPOOL 83a3122aaa60b3d81ca8f19dcc4c8bce32190861893c712e517d48053d65009ff001b7bb1bb89b7bbd2504f1cea38999655ddd164defcba0231e805a5c590728 diff --git a/sci-chemistry/pymol-plugins-promol/metadata.xml b/sci-chemistry/pymol-plugins-promol/metadata.xml new file mode 100644 index 000000000000..4a00a64b40ae --- /dev/null +++ b/sci-chemistry/pymol-plugins-promol/metadata.xml @@ -0,0 +1,7 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild new file mode 100644 index 000000000000..e2d6430c01e1 --- /dev/null +++ b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +DESCRIPTION="Fast and accurate regognition of active sites" +HOMEPAGE="http://www.rit.edu/cos/ezviz/ProMOL_dl.html" +SRC_URI="http://www.rit.edu/cos/ezviz/ProMOL.zip -> ${P}.zip" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +LICENSE="all-rights-reserved" +IUSE="" + +RESTRICT="mirror bindist" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + virtual/pmw[${PYTHON_USEDEP}] + sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="" + +S="${WORKDIR}/ProMOL Folder" + +src_prepare() { + python_copy_sources + preparation() { + cd "${BUILD_DIR}" || die + sed \ + -e "s:./modules/pmg_tk/startup:${EPREFIX}/$(python_get_sitedir)/pmg_tk/startup/ProMol:g" \ + -i ProMOL_302.py || die + } + python_foreach_impl preparation +} + +src_install(){ + dodoc *doc + dohtml -r Thanks.html EDMHelp.htm Help + + installation() { + cd "${BUILD_DIR}" || die + python_moduleinto pmg_tk/startup/ProMol + python_domodule PDB_List AminoPics Motifs *GIF pdb_entry_type.txt Master.txt Scripts + python_moduleinto pmg_tk/startup + python_domodule *.py + dosym ../../../../../../share/doc/${PF}/html/Help \ + $(python_get_sitedir)/pmg_tk/startup/ProMol/Help + dosym ../../../../../../share/doc/${PF}/html/Thanks.html \ + $(python_get_sitedir)/pmg_tk/startup/ProMol/Thanks.html + dosym ../../../../../../share/doc/${PF}/html/EDMHelp.htm \ + $(python_get_sitedir)/pmg_tk/startup/ProMol/EDMHelp.htm + } + python_foreach_impl installation +} diff --git a/sci-chemistry/pymol-plugins-psico/Manifest b/sci-chemistry/pymol-plugins-psico/Manifest new file mode 100644 index 000000000000..0484184b2dd1 --- /dev/null +++ b/sci-chemistry/pymol-plugins-psico/Manifest @@ -0,0 +1 @@ +DIST pymol-plugins-psico-3.1.tar.gz 76136 SHA256 07bfb0cfc1ca4720180de0b462a8c210e933bfc75cec9823d8c89fa2007ce651 SHA512 b0f57049ea6fc290a5abd48e0c98d4fda3c3f947898597b80e11cb3ab9ac14038aade0a016b21a525bf0ab4cf68e3be35c64b8ec34422268058414c20a755b0e WHIRLPOOL 7f64fc7fbded6a5eeb1940725b7ab3488e9c94a1587040a8f072a5e38319a640fbcf9d71cb57d97cdd7ca83de0298a0d839221f3a850601785db869a0ce2e2ea diff --git a/sci-chemistry/pymol-plugins-psico/metadata.xml b/sci-chemistry/pymol-plugins-psico/metadata.xml new file mode 100644 index 000000000000..3eff7c70cfe7 --- /dev/null +++ b/sci-chemistry/pymol-plugins-psico/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <upstream> + <remote-id type="github">speleo3/pymol-psico</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild new file mode 100644 index 000000000000..2b4d116b04fd --- /dev/null +++ b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 vcs-snapshot + +DESCRIPTION="Pymol ScrIpt COllection" +HOMEPAGE="https://github.com/speleo3/pymol-psico/" +SRC_URI="https://github.com/speleo3/pymol-psico/tarball/${PV} -> ${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD-2" +IUSE="minimal" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-biology/biopython[${PYTHON_USEDEP}] + sci-libs/mmtk[${PYTHON_USEDEP}] + sci-chemistry/pymol[${PYTHON_USEDEP}] + !minimal? ( + media-libs/qhull + media-video/mplayer + sci-biology/stride + sci-chemistry/ccp4-apps[${PYTHON_USEDEP}] + sci-chemistry/dssp + sci-chemistry/mm-align + sci-chemistry/pdbmat + sci-chemistry/theseus + sci-chemistry/tm-align + sci-mathematics/diagrtb + )" + +pkg_postinst() { + if ! use minimal; then + elog "For full functionality you need to get DynDom from" + elog "http://fizz.cmp.uea.ac.uk/dyndom/dyndomMain.do" + fi +} diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest new file mode 100644 index 000000000000..3e0a1ca939e5 --- /dev/null +++ b/sci-chemistry/pymol/Manifest @@ -0,0 +1,4 @@ +DIST pymol-1.7.0.0.png.xz 5392 SHA256 4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105 WHIRLPOOL 395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b +DIST pymol-1.7.0.1.tar.xz 6550492 SHA256 e8c6f6a465aec78171daf5cd981ebd1614dfa5e014e13c85a044cfbb591841c8 SHA512 a09277cd827f832c4f4e307f6117613d2ee8250643d129a5c34a30ceab2bfe8cea195c71a138fff09b6c69e9427153b917d7d3a7262d154ada5f323ec9635087 WHIRLPOOL 1803b55ade1b04de5963fd4a3bbe1354cda8759e15254c644952e25d7dcc904bc7b9fd91da75fdb8c6a96fd118a5a21bec9c8bba368744b44436747faca5cd9c +DIST pymol-1.7.4.0.tar.xz 6528964 SHA256 5a732aeb8a02797a185f54c3bd8bb477a1a11976eb9f982f6cf79ce887ce3a4a SHA512 fa53e90413cb1e02797a30b21b4254901504edc029104567fd2d4c5ef630eb8c2eb9f5065b2b9e65f657aaa30ca8ac85c3314c6c7fbb89148d89a9a0964de3cf WHIRLPOOL 1467a9746abe60e371162e6065253fbb23453f80a4757a18936f5b6509f63657b7073ee5e118c7e4faf333371cd38c78917e1f4b0a3a684b4807972546180d69 +DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b11111e9d3aeda0b6035d55d WHIRLPOOL 3582cc846695ca580a4bcd31db8079f32d3cb0d84b8fa1afeb0b210d7004642bf58eab42cafd552f360a5e20b546e554cf5420b7dd2e8cefa5b956a9453215e2 diff --git a/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch b/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch new file mode 100644 index 000000000000..cd4650bbf4e0 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch @@ -0,0 +1,11 @@ +--- contrib/uiuc/plugins/molfile_plugin/src/maeffplugin_orig.cpp 2014-02-07 19:50:50.132261610 -0800 ++++ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp 2014-02-07 19:52:12.527797099 -0800 +@@ -1983,7 +1983,7 @@ + } + } + catch (std::exception &e) { +- fprintf(stderr, e.what()); ++ fprintf(stderr, "%s", e.what()); + return MOLFILE_ERROR; + } + return MOLFILE_SUCCESS; diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml new file mode 100644 index 000000000000..ace2d8e58ce8 --- /dev/null +++ b/sci-chemistry/pymol/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <use> + <flag name="apbs">Install the apbs plugin</flag> + <flag name="web">Install Pymodule needed for web app support</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/pymol/pymol-1.7.0.1.ebuild b/sci-chemistry/pymol/pymol-1.7.0.1.ebuild new file mode 100644 index 000000000000..fbd2fd858c86 --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.7.0.1.ebuild @@ -0,0 +1,101 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit distutils-r1 fdo-mime versionator + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="http://www.pymol.org/" +SRC_URI=" + http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz + http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz +" +# mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2 + +LICENSE="PSF-2.2" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="apbs web" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + media-libs/freeglut + media-libs/freetype:2 + media-libs/glew + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib + virtual/pmw[${PYTHON_USEDEP}] + apbs? ( + sci-chemistry/apbs + sci-chemistry/pdb2pqr + sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] + ) + web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${P}/${PN} + +python_prepare_all() { + sed \ + -e "s:\"/usr:\"${EPREFIX}/usr:g" \ + -e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \ + -e "/import/s:argparse:argparseX:g" \ + -i setup.py || die + + rm ./modules/pmg_tk/startup/apbs_tools.py || die + + sed \ + -e "s:/opt/local:${EPREFIX}/usr:g" \ + -e '/ext_comp_args/s:\[.*\]:[]:g' \ + -i setup.py || die + + distutils-r1_python_prepare_all +} + +python_install() { + distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol" +} + +python_install_all() { + distutils-r1_python_install_all + + python_export python2_7 EPYTHON + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF + PYMOL_PATH="$(python_get_sitedir)/${PN}" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png + make_desktop_entry ${PN} PyMol ${PN} \ + "Graphics;Education;Science;Chemistry;" \ + "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" + + if ! use web; then + rm -rf "${D}/$(python_get_sitedir)/web" || die + fi + + rm -f "${ED}"/usr/share/${PN}/LICENSE || die +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update +} + +pkg_postrm() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update +} diff --git a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild new file mode 100644 index 000000000000..20f49ba45a55 --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit distutils-r1 fdo-mime versionator + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="http://www.pymol.org/" +SRC_URI=" + http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz + http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz +" +# mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2 +# git archive -v --prefix=${P}/ master -o ${P}.tar.xz + +LICENSE="PSF-2.2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="apbs web" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + media-libs/freeglut + media-libs/freetype:2 + media-libs/glew + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib + virtual/pmw[${PYTHON_USEDEP}] + apbs? ( + sci-chemistry/apbs[${PYTHON_USEDEP}] + sci-chemistry/pdb2pqr[${PYTHON_USEDEP}] + sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] + ) + web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${P}/${PN} + +PATCHES=( + "${FILESDIR}"/${PN}-1.7.3.1-maeffplugin.cpp.patch + ) + +python_prepare_all() { + sed \ + -e "s:\"/usr:\"${EPREFIX}/usr:g" \ + -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ + -e "/import/s:argparse:argparseX:g" \ + -i setup.py || die + + rm ./modules/pmg_tk/startup/apbs_tools.py || die + + sed \ + -e "s:/opt/local:${EPREFIX}/usr:g" \ + -e '/ext_comp_args/s:\[.*\]:[]:g' \ + -i setup.py || die + + distutils-r1_python_prepare_all +} + +python_install() { + distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol" +} + +python_install_all() { + distutils-r1_python_install_all + + python_export python2_7 EPYTHON + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF + PYMOL_PATH="$(python_get_sitedir)/${PN}" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png + make_desktop_entry ${PN} PyMol ${PN} \ + "Graphics;Education;Science;Chemistry;" \ + "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" + + if ! use web; then + rm -rf "${D}/$(python_get_sitedir)/web" || die + fi + + rm -f "${ED}"/usr/share/${PN}/LICENSE || die +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update +} + +pkg_postrm() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update +} diff --git a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild new file mode 100644 index 000000000000..d3ec32637cee --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild @@ -0,0 +1,113 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit distutils-r1 fdo-mime flag-o-matic versionator + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="http://www.pymol.org/" +SRC_URI=" + http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz + http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz +" +# mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2 +# git archive -v --prefix=${P}/ master -o ${P}.tar.xz + +LICENSE="PSF-2.2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="apbs web" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + media-libs/freeglut + media-libs/freetype:2 + media-libs/glew + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib + virtual/pmw[${PYTHON_USEDEP}] + apbs? ( + sci-chemistry/apbs[${PYTHON_USEDEP}] + sci-chemistry/pdb2pqr[${PYTHON_USEDEP}] + !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] + ) + web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${P}/${PN} + +python_prepare_all() { + sed \ + -e "s:\"/usr:\"${EPREFIX}/usr:g" \ + -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ + -e "/import/s:argparse:argparseX:g" \ + -i setup.py || die + + sed \ + -e "s:/opt/local:${EPREFIX}/usr:g" \ + -e '/ext_comp_args/s:\[.*\]:[]:g' \ + -i setup.py || die + + append-cxxflags -std=c++0x + + distutils-r1_python_prepare_all +} + +python_install() { + distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol" + + sed \ + -e '1d' \ + -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ + -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ + -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die +} + +python_install_all() { + distutils-r1_python_install_all + + sed \ + -e '1i#!/usr/bin/env python' \ + "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die + + python_foreach_impl python_doscript "${T}"/${PN} + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF + PYMOL_PATH="${EPREFIX}/usr/share/pymol" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png + make_desktop_entry ${PN} PyMol ${PN} \ + "Graphics;Education;Science;Chemistry;" \ + "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" + + if ! use web; then + rm -rf "${D}/$(python_get_sitedir)/web" || die + fi + + rm -f "${ED}"/usr/share/${PN}/LICENSE || die +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update +} + +pkg_postrm() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update +} diff --git a/sci-chemistry/rasmol/Manifest b/sci-chemistry/rasmol/Manifest new file mode 100644 index 000000000000..7a21a40c5d2b --- /dev/null +++ b/sci-chemistry/rasmol/Manifest @@ -0,0 +1 @@ +DIST rasmol-2.7.5.2-13May11.tar.gz 9768769 SHA256 b975e6e69d5c6b161a81f04840945d2f220ac626245c61bcc6c56181b73a5718 SHA512 c4fd149c002a34d8ce7620a7eed37aa6020acd83fc352a4c16697eb94e6a0377c55455cb6da5fb3f492f879248a6707f677f4b35572f2295b23fc924ddf3128f WHIRLPOOL 261c5351e32a67807d2979b73fbdf83b947aa641568c08fd2f2b0e06115330541a56f7bbd8f05313c86554c321e59cfe11bf5ee613c09249b9e149411c61d5ca diff --git a/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch b/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch new file mode 100644 index 000000000000..10705165ad47 --- /dev/null +++ b/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch @@ -0,0 +1,80 @@ +diff --git a/src/Imakefile b/src/Imakefile +index 03be00e..a0c68f9 100755 +--- a/src/Imakefile ++++ b/src/Imakefile +@@ -176,7 +176,7 @@ XFORMSLIB_DIR = /usr/local + #endif + endif + XFORMSLIB_INCLUDE_DIR = $(XFORMSLIB_DIR)/include +-XFORMSLIB_LDLIB = -lXpm -L$(XFORMSLIB_DIR)/lib -lforms ++XFORMSLIB_LDLIB = -lXpm -L$(XFORMSLIB_DIR)/lib + #endif + #endif + #endif +@@ -281,17 +281,10 @@ RASMOLDIR = $(USRLIBDIR)/rasmol/ + + #ifndef USE_XFORMSLIB + DEFINES = $(GTKCFLAGS) $(GUIDEF) -DRASMOLDIR=\"$(RASMOLDIR)\" $(DEPTHDEF) $(LOCALEDEF) \ +- -D_USE_RASMOL_H_ $(GUIOPTION) -I$(CBFLIB_INCLUDE_DIR) \ +- -I$(CQRLIB_INCLUDE_DIR) \ +- -I$(CVECTOR_INCLUDE_DIR) \ +- -I$(NEARTREE_INCLUDE_DIR) ++ -D_USE_RASMOL_H_ $(GUIOPTION) -I@GENTOO_PORTAGE_EPREFIX@/usr/include -I@GENTOO_PORTAGE_EPREFIX@/usr/include/cbflib + #else + DEFINES = $(GTKCFLAGS) $(GUIDEF) -DRASMOLDIR=\"$(RASMOLDIR)\" $(DEPTHDEF) $(LOCALEDEF) \ +- -D_USE_RASMOL_H_ $(GUIOPTION) -I$(CBFLIB_INCLUDE_DIR) \ +- -I$(CQRLIB_INCLUDE_DIR) \ +- -I$(CVECTOR_INCLUDE_DIR) \ +- -I$(NEARTREE_INCLUDE_DIR) \ +- -I$(XFORMSLIB_INCLUDE_DIR) ++ -D_USE_RASMOL_H_ $(GUIOPTION) -I@GENTOO_PORTAGE_EPREFIX@/usr/include -I@GENTOO_PORTAGE_EPREFIX@/usr/include/cbflib + #endif + + +@@ -317,11 +310,11 @@ OBJS = rasmol.o molecule.o abstree.o cmndline.o command.o transfor.o \ + # Additional RS6000 AIX MITSHM Library + # LDLIBS = -lm -lXi -lXextSam $(XLIB) + +-LDLIBS = -lm -lXi $(XLIB) $(EXTRA_LIBRARIES) $(XFORMSLIB) $(GTKLIBS) \ +- $(CBFLIB_LDLIB) \ +- $(CQRLIB_LDLIB) \ +- $(CVECTOR_LDLIB) \ +- $(NEARTREE_LDLIB) $(XFORMSLIB_LDLIB) ++LDLIBS = -lm -lXi $(XLIB) $(EXTRA_LIBRARIES) $(GTKLIBS) \ ++ -lcbf \ ++ -lCQRlib \ ++ -lCVector \ ++ -lCNearTree -lgfortran + + + # +@@ -425,11 +418,11 @@ $(NEARTREE_DIR): + $(NEARTREE_DIR)/CNearTree.c: $(NEARTREE_DIR) + #endif + +-$(OBJS): $(EXTPKGDIR) $(CBFLIB_OBJDEP) \ +- $(CQRLIB_OBJDEP) \ +- $(CVECTOR_OBJDEP) \ +- $(NEARTREE_OBJDEP) \ +- $(XFORMSLIB_OBJDEP) ++# $(OBJS): $(EXTPKGDIR) $(CBFLIB_OBJDEP) \ ++# $(CQRLIB_OBJDEP) \ ++# $(CVECTOR_OBJDEP) \ ++# $(NEARTREE_OBJDEP) \ ++# $(XFORMSLIB_OBJDEP) + + + gtkwin.c: gtkui.h +diff --git a/src/Makefile.in b/src/Makefile.in +index fc6d0af..bad90fc 100755 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -165,7 +165,7 @@ $(CBFLIBDIR)/lib/libcbf.a: $(CBFLIBDIR) + + all: postdownload rasmol rastxt + +-rasmol: postdownload $(X11OBJS) $(CBFLIBDIR)/lib/libcbf.a ++rasmol: postdownload $(X11OBJS) + $(CC) -o rasmol $(LFLAGS) $(X11OBJS) $(X11LIBS) + chmod 755 rasmol + diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch new file mode 100644 index 000000000000..22eb229d8a3d --- /dev/null +++ b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch @@ -0,0 +1,39 @@ +diff -urp RasMol-2.7.5.2/src/command.c RasMol-2.7.5.2_sprintf/src/command.c +--- RasMol-2.7.5.2/src/command.c 2011-05-15 01:23:49.000000000 +0700 ++++ RasMol-2.7.5.2_sprintf/src/command.c 2014-02-12 18:02:24.633489549 +0700 +@@ -1286,7 +1286,7 @@ void ShowRecordCommand( void ) { + if (record_on[1]) WriteString("record appearance on\n"); + else WriteString("record apperance off\n"); + if (RecordMaxMS == 1.) { +- sprintf(param,RecordTemplate); ++ sprintf(param, "%s", RecordTemplate); + } else{ + sprintf(param,RecordTemplate,millisec<0?0:millisec); + } +@@ -1381,7 +1381,7 @@ void ShowPlayCommand( void ) { + WriteString(param); + } + if (PlayMaxMS == 1.) { +- sprintf(param,PlayTemplate); ++ sprintf(param, "%s", PlayTemplate); + } else{ + sprintf(param,PlayTemplate,millisec<0?0:millisec); + } +@@ -1469,7 +1469,7 @@ void WriteMovieFrame( void ) { + RecordPause = True; + } else { + if (RecordMaxMS == 1.) { +- sprintf(param,RecordTemplate); ++ sprintf(param, "%s", RecordTemplate); + } else{ + sprintf(param,RecordTemplate,millisec); + } +@@ -1505,7 +1505,7 @@ static int PlayMovieFrame( void ) { + for (play_frame[1] = 0;play_frame[1]<=millisec; play_frame[1]++) + { + if (RecordMaxMS == 1.) { +- sprintf(param,PlayTemplate); ++ sprintf(param, "%s", PlayTemplate); + } else{ + sprintf(param,PlayTemplate,millisec-play_frame[1]); + } diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch new file mode 100644 index 000000000000..69c19dae5e8d --- /dev/null +++ b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch @@ -0,0 +1,31 @@ + src/egg-macros.h | 3 ++- + src/eggfileformatchooser.c | 2 ++ + 2 files changed, 4 insertions(+), 1 deletions(-) + +diff --git a/src/egg-macros.h b/src/egg-macros.h +index 9a7caad..1a6bce0 100644 +--- a/src/egg-macros.h ++++ b/src/egg-macros.h +@@ -9,7 +9,8 @@ + #ifndef _EGG_MACROS_H_ + #define _EGG_MACROS_H_ + +-#include <glib/gmacros.h> ++#include <glib.h> ++#include <glib/gprintf.h> + + G_BEGIN_DECLS + +diff --git a/src/eggfileformatchooser.c b/src/eggfileformatchooser.c +index 32ce2ab..febfc2e 100644 +--- a/src/eggfileformatchooser.c ++++ b/src/eggfileformatchooser.c +@@ -19,6 +19,8 @@ + #include "eggfileformatchooser.h" + #include "egg-macros.h" + ++#include <glib.h> ++#include <glib/gprintf.h> + #include <glib/gi18n.h> + #include <gtk/gtk.h> + #include <string.h> diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch new file mode 100644 index 000000000000..3cff0fa2f98f --- /dev/null +++ b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch @@ -0,0 +1,12 @@ +diff -urp rasmol-2.7.5-23Jul09/src/rasmol.h rasmol-2.7.5-23Jul09-64b/src/rasmol.h +--- rasmol-2.7.5-23Jul09/src/rasmol.h 2009-07-20 21:08:43.000000000 +0700 ++++ rasmol-2.7.5-23Jul09-64b/src/rasmol.h 2013-02-22 14:40:00.378574163 +0700 +@@ -125,6 +125,8 @@ + #define VECTOR_FAR + #endif + ++#define _LONGLONG ++ + /*========================*/ + /* Default User Options! */ + /*========================*/ diff --git a/sci-chemistry/rasmol/metadata.xml b/sci-chemistry/rasmol/metadata.xml new file mode 100644 index 000000000000..b06ec8f7a2fa --- /dev/null +++ b/sci-chemistry/rasmol/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">openrasmol</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild b/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild new file mode 100644 index 000000000000..642a2641fd59 --- /dev/null +++ b/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild @@ -0,0 +1,107 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils fortran-2 multilib prefix toolchain-funcs + +MY_P="RasMol_${PV}" +VERS="13May11" + +DESCRIPTION="Molecular Graphics Visualisation Tool" +HOMEPAGE="http://www.openrasmol.org/" +#SRC_URI="http://www.rasmol.org/software/${MY_P}.tar.gz" +SRC_URI="mirror://sourceforge/open${PN}/RasMol/RasMol_2.7.5/${P}-${VERS}.tar.gz" +#SRC_URI="mirror://sourceforge/open${PN}/RasMol/RasMol_2.7.5/RasMol.tar.gz" + +LICENSE="|| ( GPL-2 RASLIC )" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-libs/cvector + dev-util/gtk-builder-convert + >=sci-libs/cbflib-0.9.2 + >=sci-libs/cqrlib-1.1.2 + >=sci-libs/neartree-3.1.1 + x11-libs/cairo + x11-libs/gtk+:2 + x11-libs/libXext + x11-libs/libXi + x11-libs/vte:0" +DEPEND="${RDEPEND} + app-text/rman + x11-misc/imake + x11-proto/inputproto + x11-proto/xextproto" + +#S="${WORKDIR}/${PN}-2.7.5-${VERS}" +S="${WORKDIR}/RasMol-${PV}" + +src_prepare() { + cd src || die + + epatch \ + "${FILESDIR}"/${P}-glib.h.patch \ + "${FILESDIR}"/${P}-format-security.patch \ + "${FILESDIR}"/${P}-longlong.patch + + if use amd64 || use amd64-linux; then + mv rasmol.h rasmol_amd64_save.h && \ + echo "#define _LONGLONG"|cat - rasmol_amd64_save.h > rasmol.h + fi + + sed \ + -e 's:-traditional::g' \ + -i Makefile* || die + + cat > Imakefile <<- EOF + #define PIXELDEPTH 32 + #define GTKWIN + EOF + + cat Imakefile_base >> Imakefile || die + epatch "${FILESDIR}"/2.7.5-bundled-lib.patch + + eprefixify Imakefile + + sed \ + -e 's:vector.c:v_ector.c:g' \ + -e 's:vector.o:v_ector.o:g' \ + -e 's:vector.h:v_ector.h:g' \ + -i *akefile* || die + + sed \ + -e 's:vector.h:v_ector.h:g' \ + -i *.c *.h || die + + mv vector.c v_ector.c || die + mv vector.h v_ector.h || die + + xmkmf -DGTKWIN || die "xmkmf failed with ${myconf}" +} + +src_compile() { + emake -C src clean + emake \ + -C src \ + DEPTHDEF=-DTHIRTYTWOBIT \ + CC="$(tc-getCC)" \ + CDEBUGFLAGS="${CFLAGS}" \ + EXTRA_LDOPTIONS="${LDFLAGS}" +} + +src_install () { + libdir=$(get_libdir) + insinto /usr/${libdir}/${PN} + doins doc/rasmol.hlp + dobin src/rasmol + dodoc PROJECTS {README,TODO}.txt doc/*.{ps,pdf}.gz doc/rasmol.txt.gz + doman doc/rasmol.1 + insinto /usr/${libdir}/${PN}/databases + doins data/* + + dohtml -r *html doc/*.html html_graphics +} diff --git a/sci-chemistry/raster3d/Manifest b/sci-chemistry/raster3d/Manifest new file mode 100644 index 000000000000..fbf2feb05ff4 --- /dev/null +++ b/sci-chemistry/raster3d/Manifest @@ -0,0 +1,2 @@ +DIST Raster3D_3.0-2.tar 1743034 SHA256 a89bdfda61fae8d189820941f1b5685b40743b817128f57bc1225f983a47d984 SHA512 f8f73cc91eae521839a9db8ee1a7a9d8727ed510cb574116d89e918480700d844691a6fc3c4a28cb54312b0133cc610422e55d99716803cf3e8bb5d9d934e37f WHIRLPOOL 58fc31cc438538715b1f0ea17a28b44294d78db32e40fa16f8ab5a5781e26198227c534f06b8d25072e6c6101a4c9255fa906b9fee57b128d0e767bc0e04db83 +DIST Raster3D_3.0-3.tar 1729356 SHA256 1e7d02cf17f2d14855b8d241269948b37ed4d3ae6395914b66ff9f95c3a7fecf SHA512 bd372c4ba8d40db38e19f520883ca71ab7c5ef7a451b67150894e229b45167dfe00b77c19e118afc6abdb9ac07800cc16de5d2dc82c3ef9baa751200490e40fa WHIRLPOOL ad7c11cfd42543845420dcffbc87024c60b3058a51663076ace63b2e2fc0fec81a342f7b4e54f535e03de14fb9e76eace65259cdd2e83a6e0e83810ac8280c10 diff --git a/sci-chemistry/raster3d/files/2.9.1-as-needed.patch b/sci-chemistry/raster3d/files/2.9.1-as-needed.patch new file mode 100644 index 000000000000..2139804c8962 --- /dev/null +++ b/sci-chemistry/raster3d/files/2.9.1-as-needed.patch @@ -0,0 +1,41 @@ +diff --git a/Makefile b/Makefile +index e75ffcf..bcdd05c 100644 +--- a/Makefile ++++ b/Makefile +@@ -188,7 +188,7 @@ avs2ps: avs2ps.c + $(CC) $(CFLAGS) $(FLAGS) $(LDFLAGS) -o avs2ps avs2ps.c -lm + + balls: balls.f +- $(FC) $(FFLAGS) -o balls balls.f ++ $(FC) $(LDFLAGS) $(FFLAGS) -o balls balls.f + + local.o: Makefile.incl local.c + $(CC) $(CFLAGS) $(FLAGS) -c local.c +@@ -201,21 +201,18 @@ ribbon: ribbon.f ribbon1.f modsubs.f + ribbon.f ribbon1.f modsubs.f -o ribbon + + rastep: rastep.f quadric.o suv.o +- $(FC) $(FFLAGS) \ +- rastep.f quadric.o suv.o $(LDFLAGS) \ +- -o rastep ++ $(FC) $(FFLAGS) $(LDFLAGS) -o rastep \ ++ rastep.f quadric.o suv.o + + render: render.o local.o quadric.o parse.o r3dtops.o ungz.o qinp.o +- $(FC) $(FFLAGS) \ ++ $(FC) $(FFLAGS) $(LDFLAGS) -o render \ + render.o local.o quadric.o parse.o r3dtops.o ungz.o \ + qinp.o \ +- $(LIBS) $(LDFLAGS) \ +- -o render ++ $(LIBS) + + normal3d: normal3d.o quadric.o qinp.o ungz.o parameters.incl +- $(FC) $(FFLAGS) \ +- normal3d.o quadric.o ungz.o qinp.o $(LDFLAGS) \ +- -o normal3d ++ $(FC) $(FFLAGS) $(LDFLAGS) -o normal3d \ ++ normal3d.o quadric.o ungz.o qinp.o + + stereo3d: + diff --git a/sci-chemistry/raster3d/files/3.0.2-as-needed.patch b/sci-chemistry/raster3d/files/3.0.2-as-needed.patch new file mode 100644 index 000000000000..9e0961952535 --- /dev/null +++ b/sci-chemistry/raster3d/files/3.0.2-as-needed.patch @@ -0,0 +1,50 @@ +diff --git a/Makefile b/Makefile +index 1a1c549..4d74dd0 100644 +--- a/Makefile ++++ b/Makefile +@@ -58,7 +58,7 @@ linux: + @echo OSDEFS = -DLINUX -DNETWORKBYTEORDER >> Makefile.incl + @echo include Makefile.package >> Makefile.incl + @echo >> Makefile.incl +- @echo qinp.o: qinp.f >> Makefile.incl ++ @echo qinp.o: qinp.f normal3d.o render.o >> Makefile.incl + @echo " \$$(FC) -g -O0 -Wall -Wtabs -c -o qinp.o qinp.f" >> Makefile.incl + @echo >> Makefile.incl + +@@ -214,20 +214,20 @@ ribbon: ribbon.f ribbon1.f modsubs.f + ribbon.f ribbon1.f modsubs.f -o ribbon + + rastep: rastep.f quadric.o suv.o +- $(FC) $(FFLAGS) \ +- rastep.f quadric.o suv.o $(LDFLAGS) \ ++ $(FC) $(FFLAGS) $(LDFLAGS) \ ++ rastep.f quadric.o suv.o \ + -o rastep + + render: render.o local.o quadric.o parse.o r3dtogd.o ungz.o qinp.o +- $(FC) $(FFLAGS) \ ++ $(FC) $(FFLAGS) $(LDFLAGS) \ + render.o local.o quadric.o parse.o r3dtogd.o ungz.o \ + qinp.o \ +- $(LIBS) $(LDFLAGS) \ +- -o render ++ -o render \ ++ $(LIBS) + + normal3d: normal3d.o quadric.o qinp.o ungz.o parameters.incl +- $(FC) $(FFLAGS) \ +- normal3d.o quadric.o ungz.o qinp.o $(LDFLAGS) \ ++ $(FC) $(FFLAGS) $(LDFLAGS) \ ++ normal3d.o quadric.o ungz.o qinp.o \ + -o normal3d + + stereo3d: +@@ -264,7 +264,7 @@ example1.png: render_small + ./render_small + + render_small: render_small.o local.o quadric.o parse_small.o r3dtogd.o ungz.o qinp_small.o +- $(FC) $(FFLAGS) $^ $(LIBS) $(LDFLAGS) -o $@ ++ $(FC) $(FFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) + + .SUFFIXES: .incl + SMALL=10 diff --git a/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch b/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch new file mode 100644 index 000000000000..19b6cac3a6fe --- /dev/null +++ b/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch @@ -0,0 +1,24 @@ +diff --git a/Makefile.template b/Makefile.template +index 59de553..0ed283d 100644 +--- a/Makefile.template ++++ b/Makefile.template +@@ -8,15 +8,15 @@ include VERSION + # + # Where to install the program, data files, and manuals + # +-prefix = /usr/local ++prefix = @GENTOO_PORTAGE_EPREFIX@/usr/ + bindir = $(prefix)/bin + datadir = $(prefix)/share/Raster3D/materials + mandir = $(prefix)/man/manl +-htmldir = $(prefix)/share/Raster3D/html ++htmldir = $(prefix)/share/doc/MYPF/html + examdir = $(prefix)/share/Raster3D/examples + +-INCDIRS = -I/usr/include -I/usr/local/include +-LIBDIRS = -L/usr/local/lib ++INCDIRS = -I@GENTOO_PORTAGE_EPREFIX@/usr/include ++LIBDIRS = -L@GENTOO_PORTAGE_EPREFIX@/usr/MYLIB + + # + # TIFF support (enabled by default) diff --git a/sci-chemistry/raster3d/files/raster3d-gcc-4.1-gentoo.patch b/sci-chemistry/raster3d/files/raster3d-gcc-4.1-gentoo.patch new file mode 100644 index 000000000000..4525f5fdc8ba --- /dev/null +++ b/sci-chemistry/raster3d/files/raster3d-gcc-4.1-gentoo.patch @@ -0,0 +1,74 @@ +diff -Naur Raster3D_2.7c/normal3d.f Raster3D_2.7c.new/normal3d.f +--- Raster3D_2.7c/normal3d.f 2003-10-20 18:50:11.000000000 -0400 ++++ Raster3D_2.7c.new/normal3d.f 2007-09-08 10:23:08.000000000 -0400 +@@ -443,7 +443,8 @@ + READ (INPUT,'(A)',ERR=101) TITLE + IF (TITLE(1:1).EQ.'#') GOTO 100 + GOTO 102 +- 101 WRITE (NOISE,'(A,A)') ' >> Cannot open or read file ',TITLE(2:132) ++ 101 WRITE (NOISE,'(A,A)') ' >> Cannot open or read file ', ++ * TITLE(2:132) + CALL EXIT(-1) + 102 CONTINUE + ENDIF +diff -Naur Raster3D_2.7c/parse.f Raster3D_2.7c.new/parse.f +--- Raster3D_2.7c/parse.f 2003-10-20 18:50:11.000000000 -0400 ++++ Raster3D_2.7c.new/parse.f 2007-09-08 10:23:48.000000000 -0400 +@@ -4,7 +4,8 @@ + COMMON /OPTIONS/ FONTSCALE, GAMMA, ZOOM, NSCHEME, SHADOWFLAG, XBG, + & NAX, NAY, OTMODE, QUALITY, INVERT, LFLAG + REAL FONTSCALE, GAMMA, ZOOM +- INTEGER NSCHEME, SHADOWFLAG, XBG ++ INTEGER NSCHEME, SHADOWFLAG ++ INTEGER*8 XBG + INTEGER*2 NAX, NAY, OTMODE, QUALITY + LOGICAL*2 INVERT, LFLAG + c +diff -Naur Raster3D_2.7c/rastep.f Raster3D_2.7c.new/rastep.f +--- Raster3D_2.7c/rastep.f 2004-02-12 12:01:31.000000000 -0500 ++++ Raster3D_2.7c.new/rastep.f 2007-09-08 10:23:08.000000000 -0400 +@@ -133,7 +133,7 @@ + c + c Support for validation of similarity of bonded atoms + logical suvflag +- integer suvlun, suvbad ++ integer suvlun, suvbad, defcols + real anisov(6) + c + c Default to CPK colors and VDW radii +diff -Naur Raster3D_2.7c/render.f Raster3D_2.7c.new/render.f +--- Raster3D_2.7c/render.f 2003-10-20 18:50:11.000000000 -0400 ++++ Raster3D_2.7c.new/render.f 2007-09-08 10:23:08.000000000 -0400 +@@ -792,9 +792,9 @@ + * Get background colour + READ (INPUT,*,ERR=104) BKGND + if (XBG.NE.0) then +- BKGND(3) = FLOAT(iand(XBG,'00FF'X)) / 255. +- BKGND(2) = FLOAT(iand(XBG,'FF00'X)/256) / 255. +- BKGND(1) = FLOAT(iand(XBG,'FF0000'X)/65536) / 255. ++ BKGND(3) = REAL(iand(XBG,'00FF'X)) / 255. ++ BKGND(2) = REAL(iand(XBG,'FF00'X)/256) / 255. ++ BKGND(1) = REAL(iand(XBG,'FF0000'X)/65536) / 255. + BKGND(3) = BKGND(3)**2 + BKGND(2) = BKGND(2)**2 + BKGND(1) = BKGND(1)**2 +@@ -3679,7 +3679,7 @@ + FRAC = DETAIL(K+8) + INEXT = INDTOP + 1 + IF (TYPE(INEXT).EQ.VERTEXRGB) INEXT = INEXT + 1 +- CALL ASSERT(TYPE(INEXT).EQ.VERTRANSP,'lost vertex transp') ++ CALL ASSERT(TYPE(INEXT).EQ.VERTRANSP,'lost vertex transp') + K = LIST(INEXT) + CLRITY = FRAC*DETAIL(K+1) + (1.-FRAC)*DETAIL(K+2) + ELSE IF (TYPE(INDTOP).EQ.TRIANG) THEN +diff -Naur Raster3D_2.7c/rings3d.f Raster3D_2.7c.new/rings3d.f +--- Raster3D_2.7c/rings3d.f 2003-10-20 18:50:11.000000000 -0400 ++++ Raster3D_2.7c.new/rings3d.f 2007-09-08 10:23:08.000000000 -0400 +@@ -16,7 +16,6 @@ + integer input, output, noise + parameter (input=5, output=6, noise=0) + integer iargc, narg +- external iargc + character*64 options + logical bflag, pflag, sflag + c diff --git a/sci-chemistry/raster3d/metadata.xml b/sci-chemistry/raster3d/metadata.xml new file mode 100644 index 000000000000..2a6e4b56f965 --- /dev/null +++ b/sci-chemistry/raster3d/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <upstream> + <changelog>http://skuld.bmsc.washington.edu/raster3d/CHANGELOG</changelog> + </upstream> + <use> + <flag name="gd">libgd support for PNG and JPEG output</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/raster3d/raster3d-3.0.2.ebuild b/sci-chemistry/raster3d/raster3d-3.0.2.ebuild new file mode 100644 index 000000000000..380f207260e1 --- /dev/null +++ b/sci-chemistry/raster3d/raster3d-3.0.2.ebuild @@ -0,0 +1,107 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 flag-o-matic multilib toolchain-funcs versionator prefix + +MY_PN="Raster3D" +MY_PV=$(replace_version_separator 2 -) +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Generation high quality raster images of proteins or other molecules" +HOMEPAGE="http://www.bmsc.washington.edu/raster3d/raster3d.html" +SRC_URI="http://www.bmsc.washington.edu/${PN}/${MY_P}.tar.gz -> ${MY_P}.tar" + +LICENSE="Artistic-2" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="gd tiff" + +RDEPEND=" + tiff? ( media-libs/tiff:0 ) + gd? ( media-libs/gd[jpeg,png] )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-as-needed.patch \ + "${FILESDIR}"/${PV}-gentoo-prefix.patch + + sed \ + -e "s:MYPF:${PF}:" \ + -e "s:MYLIB:$(get_libdir):g" \ + -i Makefile.template || \ + die "Failed to patch makefile.template" + + if ! use gd; then + sed \ + -e "/GDLIBS/s:^:#:g" \ + -e "/GDDEFS/s:^:#:g" \ + -i Makefile.template || die + fi + + if ! use tiff; then + sed \ + -e "/TLIBS/s:^:#:g" \ + -e "/TDEFS/s:^:#:g" \ + -i Makefile.template || die + fi + + if [[ $(tc-getFC) =~ gfortran ]]; then + append-cflags -Dgfortran + fi + + append-fflags -ffixed-line-length-132 + + eprefixify Makefile.template + cp Makefile.template Makefile.incl || die +} + +src_compile() { + local target + local i + + if [[ $(tc-getFC) =~ gfortran ]]; then + target="linux" + else + target="linux-$(tc-getFC)" + fi + + for i in render.o ${target} all; do + emake \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + FFLAGS="${FFLAGS}" \ + CC="$(tc-getCC)"\ + FC="$(tc-getFC)" \ + INCDIRS="-I${EPREFIX}/usr/include" \ + LIBDIRS="-L${EPREFIX}/usr/$(get_libdir)" \ + ${i} + done +} + +src_install() { + emake prefix="${ED}"/usr \ + bindir="${ED}"/usr/bin \ + datadir="${ED}"/usr/share/Raster3D/materials \ + mandir="${ED}"/usr/share/man/man1 \ + htmldir="${ED}"/usr/share/doc/${PF}/html \ + examdir="${ED}"/usr/share/Raster3D/examples \ + install + + dodir /etc/env.d + echo -e "R3D_LIB=${EPREFIX}/usr/share/${NAME}/materials" > \ + "${ED}"/etc/env.d/10raster3d || \ + die "Failed to install env file." +} + +pkg_postinst() { + elog "Add following line:" + elog "<delegate decode=\"r3d\" command='\"render\" < \"%i\" > \"%o\"' />" + elog "to ${EPREFIX}/usr/$(get_libdir)/ImageMagick-6.5.8/config/delegates.xml" + elog "to make imagemagick use raster3d for .r3d files" +} diff --git a/sci-chemistry/raster3d/raster3d-3.0.3.ebuild b/sci-chemistry/raster3d/raster3d-3.0.3.ebuild new file mode 100644 index 000000000000..d66a807cbbf8 --- /dev/null +++ b/sci-chemistry/raster3d/raster3d-3.0.3.ebuild @@ -0,0 +1,107 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils fortran-2 flag-o-matic multilib toolchain-funcs versionator prefix + +MY_PN="Raster3D" +MY_PV=$(replace_version_separator 2 -) +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Generation high quality raster images of proteins or other molecules" +HOMEPAGE="http://www.bmsc.washington.edu/raster3d/raster3d.html" +SRC_URI="http://www.bmsc.washington.edu/${PN}/${MY_P}.tar.gz -> ${MY_P}.tar" + +LICENSE="Artistic-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="gd tiff" + +RDEPEND=" + tiff? ( media-libs/tiff:0 ) + gd? ( media-libs/gd[jpeg,png] )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/3.0.2-as-needed.patch \ + "${FILESDIR}"/3.0.2-gentoo-prefix.patch + + sed \ + -e "s:MYPF:${PF}:" \ + -e "s:MYLIB:$(get_libdir):g" \ + -i Makefile.template || \ + die "Failed to patch makefile.template" + + if ! use gd; then + sed \ + -e "/GDLIBS/s:^:#:g" \ + -e "/GDDEFS/s:^:#:g" \ + -i Makefile.template || die + fi + + if ! use tiff; then + sed \ + -e "/TLIBS/s:^:#:g" \ + -e "/TDEFS/s:^:#:g" \ + -i Makefile.template || die + fi + + if [[ $(tc-getFC) =~ gfortran ]]; then + append-cflags -Dgfortran + fi + + append-fflags -ffixed-line-length-132 + + eprefixify Makefile.template + cp Makefile.template Makefile.incl || die +} + +src_compile() { + local target + local i + + if [[ $(tc-getFC) =~ gfortran ]]; then + target="linux" + else + target="linux-$(tc-getFC)" + fi + + for i in render.o ${target} all; do + emake \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + FFLAGS="${FFLAGS}" \ + CC="$(tc-getCC)"\ + FC="$(tc-getFC)" \ + INCDIRS="-I${EPREFIX}/usr/include" \ + LIBDIRS="-L${EPREFIX}/usr/$(get_libdir)" \ + ${i} + done +} + +src_install() { + emake prefix="${ED}"/usr \ + bindir="${ED}"/usr/bin \ + datadir="${ED}"/usr/share/Raster3D/materials \ + mandir="${ED}"/usr/share/man/man1 \ + htmldir="${ED}"/usr/share/doc/${PF}/html \ + examdir="${ED}"/usr/share/Raster3D/examples \ + install + + dodir /etc/env.d + echo -e "R3D_LIB=${EPREFIX}/usr/share/${NAME}/materials" > \ + "${ED}"/etc/env.d/10raster3d || \ + die "Failed to install env file." +} + +pkg_postinst() { + elog "Add following line:" + elog "<delegate decode=\"r3d\" command='\"render\" < \"%i\" > \"%o\"' />" + elog "to ${EPREFIX}/usr/$(get_libdir)/ImageMagick-6.5.8/config/delegates.xml" + elog "to make imagemagick use raster3d for .r3d files" +} diff --git a/sci-chemistry/reduce/Manifest b/sci-chemistry/reduce/Manifest new file mode 100644 index 000000000000..06e2812c62a9 --- /dev/null +++ b/sci-chemistry/reduce/Manifest @@ -0,0 +1,3 @@ +DIST reduce.3.13.080428.src.tgz 4387407 SHA256 6290dad33e395c5a40fe3634db86fb6035ea88ce19c3f25b80fb6378507ac066 +DIST reduce.3.14.080821.src.tgz 5199731 SHA256 0c32f3e9f818b976e0996f088639a194cde63f227eff32c35e14526ec05c930a SHA512 9c8d72983b376b1f741afeb08630ad69b6888f526aac0ad72c658e96a6c2d6f17df60dfbf03a35a217be254bbb858f99bd2088aba8877e504a45270371dbad44 WHIRLPOOL aac80449eeceae8afbc5ec8d4ea53152c4f0bff7080fc36d7d74d8e0aaad8e6cb3e5750d67dcab6c7669f58a5f09910a3253db6371828257d03832f1ccbc3418 +DIST reduce.3.16.111118.src.zip 20342632 SHA256 a9f45dd31eb7022e056cdab1efbbed17fd8be7453396313904c95c839d41dbb3 SHA512 f7b4d8d91f1f57e9e96c91139fa919c570aebd07f3a440faf3df54bf5deb3a05ad998996a24b5fe9aff6280e00329c9914e338cbfe802c047c055f52ce8312a9 WHIRLPOOL 5d5e3c988e39986888eb23907e87ad180a2a441cf236c53406fc43f1cddd25e9e9051ae41d287f35bcf17f3882d720f9cee4c925cbae32139de5848c1fbcccdd diff --git a/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch new file mode 100644 index 000000000000..7daa5336f689 --- /dev/null +++ b/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch @@ -0,0 +1,22 @@ +diff --git a/reduce_src/Makefile b/reduce_src/Makefile +index 598e367..067ace4 100644 +--- a/reduce_src/Makefile ++++ b/reduce_src/Makefile +@@ -12,7 +12,7 @@ PROG_FLGS = -DAROMATICS_ACCEPT_HBONDS \ + # -DDEBUGMOVABLENODE -DDEBUGDOTCOUNTS + # -DMINPREDEFINED -DMAXPREDEFINED\ + +-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC)\ ++CXXFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC)\ + -I$(PDBHOME) -I$(TOOLHOME) + # -Wall + +@@ -26,7 +26,7 @@ OBJLIST = GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o A + CXX = g++ + + .cpp.o: +- $(CXX) -c $*.cpp $(CFLAGS) ++ $(CXX) -c $*.cpp $(CXXFLAGS) + + OPT = -O3 + DEBUG = $(CXXDEBUGFLAGS) diff --git a/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch new file mode 100644 index 000000000000..bcee1a9fe8f3 --- /dev/null +++ b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch @@ -0,0 +1,11 @@ +--- reduce_src/Makefile 2009-08-09 10:11:29.000000000 +0200 ++++ reduce_src/Makefile.new 2009-08-09 10:13:31.000000000 +0200 +@@ -34,7 +34,7 @@ + all: reduce + + reduce: $(OBJLIST) +- $(CXX) -o $@ $(OBJLIST) $(LFLAGS) ++ $(CXX) $(LDFLAGS) -o $@ $(OBJLIST) $(LFLAGS) + + clean: + @rm -rf *.o *.ckp ii_files diff --git a/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch b/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch new file mode 100644 index 000000000000..8294c8ca385d --- /dev/null +++ b/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch @@ -0,0 +1,22 @@ +diff --git a/reduce_src/Makefile b/reduce_src/Makefile +index 598e367..067ace4 100644 +--- a/reduce_src/Makefile ++++ b/reduce_src/Makefile +@@ -12,7 +12,7 @@ PROG_FLGS = -DAROMATICS_ACCEPT_HBONDS \ + # -DDEBUGMOVABLENODE -DDEBUGDOTCOUNTS + # -DMINPREDEFINED -DMAXPREDEFINED\ + +-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\ ++CXXFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\ + -I$(PDBHOME) -I$(TOOLHOME) + # -Wall + +@@ -26,7 +26,7 @@ OBJLIST = GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o A + CXX = g++ + + .cpp.o: +- $(CXX) -c $*.cpp $(CFLAGS) ++ $(CXX) -c $*.cpp $(CXXFLAGS) + + OPT = -O3 + DEBUG = $(CXXDEBUGFLAGS) diff --git a/sci-chemistry/reduce/metadata.xml b/sci-chemistry/reduce/metadata.xml new file mode 100644 index 000000000000..e42d0af60f42 --- /dev/null +++ b/sci-chemistry/reduce/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild b/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild new file mode 100644 index 000000000000..f2af6fcda84a --- /dev/null +++ b/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +inherit eutils toolchain-funcs + +MY_P="${PN}.${PV}.src" + +DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.tgz" + +LICENSE="richardson" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-LDFLAGS.patch \ + "${FILESDIR}"/${PV}-CFLAGS.patch +} + +src_compile() { + DICT_DIR="/usr/share/reduce" + DICT_FILE="reduce_het_dict.txt" + + emake \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + OPT="${CXXFLAGS}" \ + DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FILE}" \ + || die "make failed" +} + +src_install() { + dobin "${S}"/reduce_src/reduce || die + insinto ${DICT_DIR} + doins "${S}"/${DICT_FILE} "${S}"/reduce_wwPDB_het_dict.txt || die + dodoc README.usingReduce.txt || die +} + +pkg_postinst() { + elog "To use the PDBv3 dictionary instead of PDBv2, set the environment" + elog "variable REDUCE_HET_DICT to ${EPREFIX}/usr/share/reduce/reduce_wwPDB_het_dict.txt" +} diff --git a/sci-chemistry/reduce/reduce-3.14.080821.ebuild b/sci-chemistry/reduce/reduce-3.14.080821.ebuild new file mode 100644 index 000000000000..824ee735ef0f --- /dev/null +++ b/sci-chemistry/reduce/reduce-3.14.080821.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_P="${PN}.${PV}.src" + +DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.tgz" + +LICENSE="richardson" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/3.13.080428-LDFLAGS.patch \ + "${FILESDIR}"/${PV}-CFLAGS.patch +} + +src_compile() { + DICT_DIR="/usr/share/reduce" + DICT_FOLD="reduce_het_dict.txt" + DICT_FNEW="reduce_wwPDB_het_dict.txt" + + emake clean + emake \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + OPT="${CXXFLAGS}" \ + DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FNEW}" \ + DICT_OLD="${EPREFIX}/${DICT_DIR}/${DICT_FOLD}" +} + +src_install() { + dobin "${S}"/reduce_src/reduce + insinto ${DICT_DIR} + doins "${S}"/${DICT_FOLD} "${S}"/${DICT_FNEW} + dodoc README.usingReduce.txt +} diff --git a/sci-chemistry/reduce/reduce-3.16.111118.ebuild b/sci-chemistry/reduce/reduce-3.16.111118.ebuild new file mode 100644 index 000000000000..6871341758b8 --- /dev/null +++ b/sci-chemistry/reduce/reduce-3.16.111118.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_P="${PN}.${PV}.src" + +DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.zip" + +LICENSE="richardson" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}/" + +src_prepare() { + epatch \ + "${FILESDIR}"/3.13.080428-LDFLAGS.patch \ + "${FILESDIR}"/3.14.080821-CFLAGS.patch +} + +src_compile() { + DICT_DIR="/usr/share/reduce" + DICT_FOLD="reduce_het_dict.txt" + DICT_FNEW="reduce_wwPDB_het_dict.txt" + + emake clean + emake \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + OPT="${CXXFLAGS}" \ + DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FNEW}" \ + DICT_OLD="${EPREFIX}/${DICT_DIR}/${DICT_FOLD}" +} + +src_install() { + dobin "${S}"/reduce_src/reduce + insinto ${DICT_DIR} + doins "${S}"/${DICT_FOLD} "${S}"/${DICT_FNEW} + dodoc README.usingReduce.txt +} diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest new file mode 100644 index 000000000000..ba3def103020 --- /dev/null +++ b/sci-chemistry/refmac/Manifest @@ -0,0 +1,2 @@ +DIST refmac_5.5.0110.tar.gz 1326832 SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca SHA512 7e7fd1a7d2d11ef5f2e08cae61da62ecfe6978730ce4ca80f8b00be9bdad5e7d0ad493e1b8d57d64f1393f2017a87b8342e2607b08bc4018def798038a111728 WHIRLPOOL 587260eebd2df3115ba01ee03c11ab773d7316100a09af1f259f7795a139f978d94c569b8e4ab85982c2eeda628e643376231bdca5311fc8c7d2de5b65a033ac +DIST test-framework.tar.gz 130933173 SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605 SHA512 3ef8253f472c5a481f836291afb80746ad73858e130130b848851b6b5dc53ada3b78c9f853af1c46fa22f469f2ce2f3248f5f760950e118610922c0429a7da16 WHIRLPOOL 022c1b493ecd35e769b44d1e52a351b4883682ef9759626bac36e26cc61078d95de0ec2531ed706897c683c38727139fa7a13d06b64c597026817ed79612d16d diff --git a/sci-chemistry/refmac/files/5.5-test.log.patch b/sci-chemistry/refmac/files/5.5-test.log.patch new file mode 100644 index 000000000000..61858be357a0 --- /dev/null +++ b/sci-chemistry/refmac/files/5.5-test.log.patch @@ -0,0 +1,32 @@ +--- test-framework/refmac5/test_refmac5.py 2009-06-29 15:45:37.000000000 +0200 ++++ test-framework/refmac5/test_refmac5.py.new 2009-06-29 15:48:05.000000000 +0200 +@@ -88,7 +88,8 @@ + 'make hydr no', + 'labin IP=IMEAN SIGIP=SIGIMEAN FREE=FreeR_flag', + 'labout FC=FC PHIC=PHIC'], +- working_directory = self.test_dir) ++ working_directory = self.test_dir, ++ log_file = 'test_twinned_refinement.log') + + self.assertEqual(status, 0) + +@@ -123,7 +124,8 @@ + 'weight auto', + 'ncyc 20', + 'labout FC=FC PHIC=PHIC'], +- working_directory = self.test_dir) ++ working_directory = self.test_dir, ++ log_file = 'test_4_domain_tls.log') + + self.assertEqual(status, 0) + +@@ -156,7 +158,8 @@ + 'anomalous form SE -9.9 3.9', + 'anomalous wavelength 0.97966', + 'labout FC=FC PHIC=PHIC'], +- working_directory = self.test_dir) ++ working_directory = self.test_dir, ++ log_file = 'test_sad_refinement.log') + + self.assertEqual(status, 0) + diff --git a/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch new file mode 100644 index 000000000000..1efbaa04d9e6 --- /dev/null +++ b/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch @@ -0,0 +1,84 @@ +diff --git a/makefile b/makefile +index 66d4cee..5270677 100644 +--- a/makefile ++++ b/makefile +@@ -9,7 +9,7 @@ XFFLAGS = -fno-second-underscore -static + XCFLAGS = -DGFORTRAN -DPROTOTYPE + FFLAGS = $(FOPTIM) $(XFFLAGS) + CFLAGS = $(COPTIM) $(XCFLAGS) +-CPPFLAGS = $(CFLAGS) ++CPPFLAGS = $(CXXFLAGS) $(XCFLAGS) + + LLIBCIF = + LLIBCCP = $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a +diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 +index 371d84d..557077f 100644 +--- a/makefile_refmac.inc1 ++++ b/makefile_refmac.inc1 +@@ -68,9 +68,7 @@ messy_pdb.o \ + bridge.o \ + i0.o \ + i1.o \ +-chbevl.o \ +-$(LLIBCIF) \ +-$(LLIBLAPACK) ++chbevl.o + #$(LLIBCCP) \ + #crt0.o \ + #heavy.o \ +@@ -95,8 +93,7 @@ make_unix_ccp4.o \ + emin.o \ + libcheck_min.o \ + mol2_file.o \ +-sdf_files.o \ +-$(LLIBCCP) ++sdf_files.o + + SUBM = \ + main_makecif.o \ +@@ -116,9 +113,7 @@ make_rst2.o \ + make_PDB.o \ + makecif.o \ + make_unix_ccp4.o \ +-make_vdw.o \ +-$(LLIBCCP) \ +-$(LLIBCIF) ++make_vdw.o + + SUBT = \ + tlsgroups.o \ +@@ -142,9 +137,7 @@ make_refmac_dummy.o \ + inout_routines.o \ + errwrt_1.o \ + linalgebra.o \ +-subnumrec.o \ +-$(LLIBCCP) \ +-$(LLIBCIF) ++subnumrec.o + #-------------------------------------------------------------------------------- + + ed = echo 'g/^CMDW-5.0/s// /@w@q@' | tr "@" "\012" | ed -s +@@ -154,18 +147,19 @@ ed = echo 'g/^CMDW-5.0/s// /@w@q@' | tr "@" "\012" | ed -s + all: refmac libcheck makecif + + refmac: $(SUBR) +- $(FC) $(FFLAGS) $(LDFLAGF)-o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) + + libcheck: $(SUBL) +- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) + + makecif: $(SUBM) +- $(FC) $(FFLAGS) -o makecif${VERSION} $(SUBM) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o makecif${VERSION} $(SUBM) $(LLIBCCP) $(LLIBCIF) + + tlsgroups: $(SUBT) +- $(FC) $(FFLAGS) -o tlsgroups${VERSION} $(SUBT) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o tlsgroups${VERSION} $(SUBT) $(LLIBCCP) $(LLIBCIF) + + clean: + /bin/rm *.o + + bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h ++ $(CXX) $(CXXFLAGS) -c bridge.cpp diff --git a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch b/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch new file mode 100644 index 000000000000..3969cc9c8586 --- /dev/null +++ b/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch @@ -0,0 +1,17 @@ + hkon_secder_tch.f | 3 ++- + 1 files changed, 2 insertions(+), 1 deletions(-) + +diff --git a/hkon_secder_tch.f b/hkon_secder_tch.f +index 31794b0..86d2cdf 100644 +--- a/hkon_secder_tch.f ++++ b/hkon_secder_tch.f +@@ -3724,7 +3724,8 @@ c---External functions and subprutines + INTEGER NWORKSPACE + REAL*8 TOLER + REAL*8 WORKSPACE(300) +- REAL LSTLSQ,D2DF_WEIGHT ++ REAL*8 D2DF_WEIGHT ++ REAL LSTLSQ + C + INTEGER IBIN,IBIN_S + INTEGER I,J,K diff --git a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch new file mode 100644 index 000000000000..9998b759c664 --- /dev/null +++ b/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch @@ -0,0 +1,341 @@ + makefile_refmac.inc1 | 215 ++++++++++++++++++++++++-------------------------- + 1 files changed, 104 insertions(+), 111 deletions(-) + +diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 +index 0f8bd63..e59fbfb 100644 +--- a/makefile_refmac.inc1 ++++ b/makefile_refmac.inc1 +@@ -96,9 +96,7 @@ bridge.o \ + i0.o \ + i1.o \ + chbevl.o \ +-make_unix_ccp4.o \ +-$(LLIBCIF) \ +-$(LLIBLAPACK) ++make_unix_ccp4.o + + + SUBL = \ +@@ -133,9 +131,7 @@ cell_symm_subrs.o \ + iheap_sort.o \ + linalgebra.o \ + math_refmac.o \ +-subnumrec.o \ +-$(LLIBLAPACK) \ +-$(LLIBCCP) ++subnumrec.o + + SUB_FREE = \ + freer_twin.o \ +@@ -145,9 +141,7 @@ subnumrec.o \ + libT.o \ + iheap_sort.o \ + cell_symm_subrs.o \ +-math_refmac.o \ +-$(LLIBLAPACK) \ +-$(LLIBCCP) ++math_refmac.o + + SUB_HEADER = header2matr.o + #-------------------------------------------------------------------------------- +@@ -185,41 +179,41 @@ rharvest_mod.o: rharvest_mod.f90 + twin77mod.o: twin77mod.f + $(FC) $(FFLAGS) -c twin77mod.f + +-gibbs_gm_sampler.o: linalgebra_f90.f90 gibbs_gm_sampler.f90 +- $(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90 ++gibbs_gm_sampler.o: linalgebra_f90.o gibbs_gm_sampler.f90 ++ $(FC) $(FFLAGS) -c gibbs_gm_sampler.f90 + +-max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f ++max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c max_with_twins.f + +-merohedr_twin.o: restr_files.f90 merohedr_twin.f +- $(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f ++merohedr_twin.o: restr_files.o merohedr_twin.f ++ $(FC) $(FFLAGS) -c merohedr_twin.f + +-ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f ++ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c ls_scaling_twin_save.f + +-ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f ++ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c ml_params_refine.f + +-optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90 ++optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o ++ $(FC) $(FFLAGS) -c optimise_solvent_all.f90 + +-ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f ++ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o ++ $(FC) $(FFLAGS) -c ncs_rest.f + +-ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90 +- $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90 ++ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o ++ $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 + +-lsq_exp2.o: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 ++lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c lsq_exp2.f + +-vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f ++vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o ++ $(FC) $(FFLAGS) -c vdw_and_contacts.f + + dist_routines.o: dist_routines.f90 + $(FC) $(FFLAGS) -c dist_routines.f90 + +-ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90 ++ncs_simil.o: ncs_rest_mod.o ncs_simil.f90 ++ $(FC) $(FFLAGS) -c ncs_simil.f90 + + ridge.o: ridge.f90 + $(FC) $(FFLAGS) -c ridge.f90 +@@ -227,140 +221,138 @@ ridge.o: ridge.f90 + align_refmac.o: align_refmac.f90 + $(FC) $(FFLAGS) -c align_refmac.f90 + +-rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f ++rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o ++ $(FC) $(FFLAGS) -c rigid_allocate.f + +-tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f ++tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c tls_allocate.f + +-hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \ +- restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \ +- hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90 ++hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \ ++ restr_files.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c hkon_secder_tch.f + +-oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f ++oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o ++ $(FC) $(FFLAGS) -c oppro_allocate.f + +-read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f ++read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o ++ $(FC) $(FFLAGS) -c read_extra_restraints.f + +-coords.o: coords.f90 atomf77mod.f +- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90 ++coords.o: coords.f90 atomf77mod.o ++ $(FC) $(FFLAGS) -c coords.f90 + + +-ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90 ++ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c ls_scaling_double.f + +-fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 +- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90 ++fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o ++ $(FC) $(FFLAGS) -c fast_hessian_tabulation.f + +-calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 ++calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c calc_stats_twin.f + +-refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f ++refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c refpre_twin.f + + +-decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f +- $(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f ++decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f ++ $(FC) $(FFLAGS) -c decide_twin_opers_0.f + + automorphism.o: automorphism.f90 + $(FC) $(FFLAGS) -c automorphism.f90 + +-mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f ++mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o ++ $(FC) $(FFLAGS) -c mtz_write_twin.f + + filter_params.o: filter_params.f90 + $(FC) $(FFLAGS) -c filter_params.f90 + +-rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \ +- agreem.f90 rharvest_mod.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \ +- agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f ++rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \ ++ agreem.o rharvest_mod.o ncs_constr.o ++ $(FC) $(FFLAGS) -c rcard_tor1.f + +-inout_routines.o: restr_files.f90 inout_routines.f +- $(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f ++inout_routines.o: restr_files.o inout_routines.f ++ $(FC) $(FFLAGS) -c inout_routines.f + +-local_tls.o: local_tls.f90 linalgebra_f90.f90 +- $(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90 ++local_tls.o: local_tls.f90 linalgebra_f90.o ++ $(FC) $(FFLAGS) -c local_tls.f90 + + linalgebra_f90.o: linalgebra_f90.f90 + $(FC) $(FFLAGS) -c linalgebra_f90.f90 + +-make_refmac_dummy.o: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f ++make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c make_refmac_dummy.f + +-ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f ++ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c ml_scaling_double.f + +-refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f ++refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c refall_twin.f + +-rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f ++rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c rharvest_subr.f + +-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f ++solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o ++ $(FC) $(FFLAGS) -c solvent_contr_mask.f + +-subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f ++subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o ++ $(FC) $(FFLAGS) -c subag_scale_hessian.f + +-aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f ++aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o ++ $(FC) $(FFLAGS) -c aniso_ref_eigen.f + +-subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f ++subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c subcf_scale1.f + +-bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f +- $(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90 ++bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o ++ $(FC) $(FFLAGS) -c bvalue_routines.f90 + +-newentry_idealise.o:: newentry_idealise.f weights.f90 +- $(FC) $(FFLAGS) -c newentry_idealise.f weights.f90 ++newentry_idealise.o:: newentry_idealise.f weights.o ++ $(FC) $(FFLAGS) -c newentry_idealise.f + +-occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90 ++occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c occupancy_only_refine.f + +-refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 +- $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 ++refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90 ++ $(FC) $(FFLAGS) -c refmac_completeness.f90 + +-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f ++refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c refmac_xml.f + + hkl_pack.o: hkl_pack.f90 + $(FC) $(FFLAGS) -c hkl_pack.f90 + +-extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90 ++extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o ++ $(FC) $(FFLAGS) -c extra_eigen.f + +-subvag.o: subvag.f hkl_pack.f90 +- $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f ++subvag.o: subvag.f hkl_pack.o ++ $(FC) $(FFLAGS) -c subvag.f + +-make_PDB.o: make_PDB.f ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f ++make_PDB.o: make_PDB.f ncs_constr.o ++ $(FC) $(FFLAGS) -c make_PDB.f + +-make_CIF.o: make_CIF.f ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f ++make_CIF.o: make_CIF.f ncs_constr.o ++ $(FC) $(FFLAGS) -c make_CIF.f + + refmac: $(SUBR) +- $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) + +-mol2_file.o: mol2_file.f odb_files.f90 +- $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f ++mol2_file.o: mol2_file.f odb_files.o ++ $(FC) $(FFLAGS) -c mol2_file.f + +-odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f +- $(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90 ++odb_files.o: odb_files.f90 elements_module.o enerf77mod.o ++ $(FC) $(FFLAGS) -c odb_files.f90 + + elements_module.o: elements_module.f90 + $(FC) $(FFLAGS) -c elements_module.f90 + +-make_lib2.o: make_lib2.f odb_files.f90 +- $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f ++make_lib2.o: make_lib2.f odb_files.o ++ $(FC) $(FFLAGS) -c make_lib2.f + + pdb2libcheck.o: pdb2libcheck.f90 + $(FC) $(FFLAGS) -c pdb2libcheck.f90 + +-libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90 +- $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f ++libcheck.o: libcheck.f elements_module.o pdb2libcheck.o ++ $(FC) $(FFLAGS) -c libcheck.f + + header2matr.o: header2matr.f90 + $(FC) $(FFLAGS) -c header2matr.f90 +@@ -369,16 +361,17 @@ freer_twin.o: freer_twin.f90 + $(FC) $(FFLAGS) -c freer_twin.f90 + + libcheck: $(SUBL) +- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) + + free_twin: $(SUB_FREE) +- $(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK) + + + header2matr: $(SUB_HEADER) +- $(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER) + + clean: + /bin/rm *.o *.mod + + bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h ++ $(CXX) $(CXXFLAGS) -c bridge.cpp diff --git a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch new file mode 100644 index 000000000000..9998b759c664 --- /dev/null +++ b/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch @@ -0,0 +1,341 @@ + makefile_refmac.inc1 | 215 ++++++++++++++++++++++++-------------------------- + 1 files changed, 104 insertions(+), 111 deletions(-) + +diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 +index 0f8bd63..e59fbfb 100644 +--- a/makefile_refmac.inc1 ++++ b/makefile_refmac.inc1 +@@ -96,9 +96,7 @@ bridge.o \ + i0.o \ + i1.o \ + chbevl.o \ +-make_unix_ccp4.o \ +-$(LLIBCIF) \ +-$(LLIBLAPACK) ++make_unix_ccp4.o + + + SUBL = \ +@@ -133,9 +131,7 @@ cell_symm_subrs.o \ + iheap_sort.o \ + linalgebra.o \ + math_refmac.o \ +-subnumrec.o \ +-$(LLIBLAPACK) \ +-$(LLIBCCP) ++subnumrec.o + + SUB_FREE = \ + freer_twin.o \ +@@ -145,9 +141,7 @@ subnumrec.o \ + libT.o \ + iheap_sort.o \ + cell_symm_subrs.o \ +-math_refmac.o \ +-$(LLIBLAPACK) \ +-$(LLIBCCP) ++math_refmac.o + + SUB_HEADER = header2matr.o + #-------------------------------------------------------------------------------- +@@ -185,41 +179,41 @@ rharvest_mod.o: rharvest_mod.f90 + twin77mod.o: twin77mod.f + $(FC) $(FFLAGS) -c twin77mod.f + +-gibbs_gm_sampler.o: linalgebra_f90.f90 gibbs_gm_sampler.f90 +- $(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90 ++gibbs_gm_sampler.o: linalgebra_f90.o gibbs_gm_sampler.f90 ++ $(FC) $(FFLAGS) -c gibbs_gm_sampler.f90 + +-max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f ++max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c max_with_twins.f + +-merohedr_twin.o: restr_files.f90 merohedr_twin.f +- $(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f ++merohedr_twin.o: restr_files.o merohedr_twin.f ++ $(FC) $(FFLAGS) -c merohedr_twin.f + +-ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f ++ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c ls_scaling_twin_save.f + +-ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f ++ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c ml_params_refine.f + +-optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90 ++optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o ++ $(FC) $(FFLAGS) -c optimise_solvent_all.f90 + +-ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f ++ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o ++ $(FC) $(FFLAGS) -c ncs_rest.f + +-ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90 +- $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90 ++ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o ++ $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 + +-lsq_exp2.o: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 ++lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c lsq_exp2.f + +-vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f ++vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o ++ $(FC) $(FFLAGS) -c vdw_and_contacts.f + + dist_routines.o: dist_routines.f90 + $(FC) $(FFLAGS) -c dist_routines.f90 + +-ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90 ++ncs_simil.o: ncs_rest_mod.o ncs_simil.f90 ++ $(FC) $(FFLAGS) -c ncs_simil.f90 + + ridge.o: ridge.f90 + $(FC) $(FFLAGS) -c ridge.f90 +@@ -227,140 +221,138 @@ ridge.o: ridge.f90 + align_refmac.o: align_refmac.f90 + $(FC) $(FFLAGS) -c align_refmac.f90 + +-rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f ++rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o ++ $(FC) $(FFLAGS) -c rigid_allocate.f + +-tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f ++tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c tls_allocate.f + +-hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \ +- restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \ +- hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90 ++hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \ ++ restr_files.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c hkon_secder_tch.f + +-oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f ++oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o ++ $(FC) $(FFLAGS) -c oppro_allocate.f + +-read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f ++read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o ++ $(FC) $(FFLAGS) -c read_extra_restraints.f + +-coords.o: coords.f90 atomf77mod.f +- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90 ++coords.o: coords.f90 atomf77mod.o ++ $(FC) $(FFLAGS) -c coords.f90 + + +-ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90 ++ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c ls_scaling_double.f + +-fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 +- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90 ++fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o ++ $(FC) $(FFLAGS) -c fast_hessian_tabulation.f + +-calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 ++calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c calc_stats_twin.f + +-refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f ++refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c refpre_twin.f + + +-decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f +- $(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f ++decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f ++ $(FC) $(FFLAGS) -c decide_twin_opers_0.f + + automorphism.o: automorphism.f90 + $(FC) $(FFLAGS) -c automorphism.f90 + +-mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f ++mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o ++ $(FC) $(FFLAGS) -c mtz_write_twin.f + + filter_params.o: filter_params.f90 + $(FC) $(FFLAGS) -c filter_params.f90 + +-rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \ +- agreem.f90 rharvest_mod.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \ +- agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f ++rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \ ++ agreem.o rharvest_mod.o ncs_constr.o ++ $(FC) $(FFLAGS) -c rcard_tor1.f + +-inout_routines.o: restr_files.f90 inout_routines.f +- $(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f ++inout_routines.o: restr_files.o inout_routines.f ++ $(FC) $(FFLAGS) -c inout_routines.f + +-local_tls.o: local_tls.f90 linalgebra_f90.f90 +- $(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90 ++local_tls.o: local_tls.f90 linalgebra_f90.o ++ $(FC) $(FFLAGS) -c local_tls.f90 + + linalgebra_f90.o: linalgebra_f90.f90 + $(FC) $(FFLAGS) -c linalgebra_f90.f90 + +-make_refmac_dummy.o: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f ++make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c make_refmac_dummy.f + +-ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f ++ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c ml_scaling_double.f + +-refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f ++refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c refall_twin.f + +-rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f ++rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c rharvest_subr.f + +-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f ++solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o ++ $(FC) $(FFLAGS) -c solvent_contr_mask.f + +-subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f ++subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o ++ $(FC) $(FFLAGS) -c subag_scale_hessian.f + +-aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f ++aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o ++ $(FC) $(FFLAGS) -c aniso_ref_eigen.f + +-subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f ++subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c subcf_scale1.f + +-bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f +- $(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90 ++bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o ++ $(FC) $(FFLAGS) -c bvalue_routines.f90 + +-newentry_idealise.o:: newentry_idealise.f weights.f90 +- $(FC) $(FFLAGS) -c newentry_idealise.f weights.f90 ++newentry_idealise.o:: newentry_idealise.f weights.o ++ $(FC) $(FFLAGS) -c newentry_idealise.f + +-occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90 ++occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c occupancy_only_refine.f + +-refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 +- $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 ++refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90 ++ $(FC) $(FFLAGS) -c refmac_completeness.f90 + +-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f ++refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c refmac_xml.f + + hkl_pack.o: hkl_pack.f90 + $(FC) $(FFLAGS) -c hkl_pack.f90 + +-extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90 ++extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o ++ $(FC) $(FFLAGS) -c extra_eigen.f + +-subvag.o: subvag.f hkl_pack.f90 +- $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f ++subvag.o: subvag.f hkl_pack.o ++ $(FC) $(FFLAGS) -c subvag.f + +-make_PDB.o: make_PDB.f ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f ++make_PDB.o: make_PDB.f ncs_constr.o ++ $(FC) $(FFLAGS) -c make_PDB.f + +-make_CIF.o: make_CIF.f ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f ++make_CIF.o: make_CIF.f ncs_constr.o ++ $(FC) $(FFLAGS) -c make_CIF.f + + refmac: $(SUBR) +- $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) + +-mol2_file.o: mol2_file.f odb_files.f90 +- $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f ++mol2_file.o: mol2_file.f odb_files.o ++ $(FC) $(FFLAGS) -c mol2_file.f + +-odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f +- $(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90 ++odb_files.o: odb_files.f90 elements_module.o enerf77mod.o ++ $(FC) $(FFLAGS) -c odb_files.f90 + + elements_module.o: elements_module.f90 + $(FC) $(FFLAGS) -c elements_module.f90 + +-make_lib2.o: make_lib2.f odb_files.f90 +- $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f ++make_lib2.o: make_lib2.f odb_files.o ++ $(FC) $(FFLAGS) -c make_lib2.f + + pdb2libcheck.o: pdb2libcheck.f90 + $(FC) $(FFLAGS) -c pdb2libcheck.f90 + +-libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90 +- $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f ++libcheck.o: libcheck.f elements_module.o pdb2libcheck.o ++ $(FC) $(FFLAGS) -c libcheck.f + + header2matr.o: header2matr.f90 + $(FC) $(FFLAGS) -c header2matr.f90 +@@ -369,16 +361,17 @@ freer_twin.o: freer_twin.f90 + $(FC) $(FFLAGS) -c freer_twin.f90 + + libcheck: $(SUBL) +- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) + + free_twin: $(SUB_FREE) +- $(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK) + + + header2matr: $(SUB_HEADER) +- $(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER) + + clean: + /bin/rm *.o *.mod + + bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h ++ $(CXX) $(CXXFLAGS) -c bridge.cpp diff --git a/sci-chemistry/refmac/metadata.xml b/sci-chemistry/refmac/metadata.xml new file mode 100644 index 000000000000..c0432fefe855 --- /dev/null +++ b/sci-chemistry/refmac/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher (jlec)</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild new file mode 100644 index 000000000000..eb8e87018219 --- /dev/null +++ b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild @@ -0,0 +1,85 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 flag-o-matic toolchain-funcs versionator + +DESCRIPTION="Macromolecular crystallographic refinement program" +HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac" +SRC_URI=" + ${HOMEPAGE}/data/refmac_stable/refmac_${PV}.tar.gz + test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + sci-chemistry/makecif + >=sci-libs/ccp4-libs-6.1.3-r7 + sci-libs/mmdb + <sci-libs/monomer-db-1 + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +FORTRAN_STANDARD="77 90" + +S="${WORKDIR}" + +PATCHES=( + "${FILESDIR}"/${PV}-allow-dynamic-linking.patch + "${FILESDIR}"/${PV}-gcc4.6.patch + ) + +src_prepare() { + epatch ${PATCHES[@]} + + use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch + [[ ${FC} == *gfortran* ]] && \ + append-fflags -fno-second-underscore && \ + append-cflags -DGFORTRAN -DPROTOTYPE && \ + append-libs -lgfortran -lgfortranbegin -lstdc++ + [[ ${FC} == *ifort* ]] && \ + append-libs -lstdc++ +} + +src_compile() { + emake \ + FC=$(tc-getFC) \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + COPTIM="${CFLAGS}" \ + FOPTIM="${FFLAGS:- -O2}" \ + VERSION="" \ + XFFLAGS="" \ + XCFLAGS="" \ + LLIBCCP="-lccp4f -lccp4c -lccif $($(tc-getPKG_CONFIG) --libs mmdb)" \ + LLIBLAPACK="$($(tc-getPKG_CONFIG) --libs lapack blas)" \ + LLIBOTHERS="${LIBS}" \ + ${PN} libcheck +} + +src_test() { + einfo "Starting tests ..." + source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" + export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}" + export CCP4_TEST="${WORKDIR}"/test-framework + export CCP4_SCR="${T}" + ln -sf refmac "${S}"/refmac5 + sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb + ccp4-run-thorough-tests -v test_refmac5 || die +} + +src_install() { + exeinto /usr/libexec/ccp4/bin/ + doexe ${PN} + dosym refmac /usr/libexec/ccp4/bin/refmac5 + dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} + dosym refmac /usr/bin/refmac5 + dodoc refmac_keywords.pdf bugs_and_features.pdf +} diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest new file mode 100644 index 000000000000..789564f5ef98 --- /dev/null +++ b/sci-chemistry/relax/Manifest @@ -0,0 +1,5 @@ +DIST relax-3.3.4.src.tar.bz2 89206485 SHA256 03ecc20353126d155c7d5c9ab45e3bb146a87243472711c937befced2db333c0 SHA512 78ae5778ef0fe84fc3a26648dd2192d529fb1e5241728f7c06a5a2cec2ce849a2c75c19a931123a17d5c210acc4f4c2401574b10a1fbbe0307d2d9867567352d WHIRLPOOL 4fcdec36e8df412091ab1a99a6b017ebc72f8e5c400429e698221f22e4ef7ae35713a6e2a05f6f1b573e5223f8eccc7cb0d2a20b1171e5bc483fd3ef1a0242bc +DIST relax-3.3.5.src.tar.bz2 90164368 SHA256 d9e3668221dba7589ba1d12ab40df517b5b6f742ee413864cc87ab636546e2ef SHA512 c8c248abf0edb54af631c11b102b641d41a106036bbdb88d8f1563c9750d3c7d402ee150d7afd770b845d3a421e431afcf95e6222197f9dc1afec61ddcd0bf37 WHIRLPOOL d9070bed833ef063c22fec5e55b1968c65b672ee100247b1af9a25d3149eb57475aeb94a4f125fc3cd278d97ac248e7826b083c840b47f9db83bae7e1aaae710 +DIST relax-3.3.6.src.tar.bz2 90005292 SHA256 2b1994626a910036c63d67c609c49b3bde8c754b60763de62c2ac8f6c3f589c3 SHA512 cda773a4af259d25550e4e4dbd8500594afd9df051ba06130355058347f308b804726acafaa76957e062c78d1d8fb26f843b3ac97d5aecd534b53c1a5155cafb WHIRLPOOL 0bf0f51664a132653fbd981ee6776cb16dd6371504df2167658027325d632cda8a6f4a21d4a530c46dc75c93b3ffb87f5189d4986acadb344154cd7420361e0b +DIST relax-3.3.7.src.tar.bz2 90268061 SHA256 a32508bd55fa124f6472e08d89ec0fa9f3837efcceb2be681404eb998457381f SHA512 3724a51ef9177f9bd78b3c92add7b88d559f21f5166eaf62b865586c061d17ce0a1af61a794db324d0f792eece04d8f1d037f9e982c858768da1d3fc208e9270 WHIRLPOOL e4446c7ccbe1e8f3caa450a3d747fb8dfcc33d9d336386572b72481544101199150e7938b0e5319a70ef3a5a7f4ad53c143d4a6c01cc7553f435fbc0d00fe952 +DIST relax-3.3.8.src.tar.bz2 90271667 SHA256 176d4e9f0f1c6cf6e6c93b12070a50ff31e10c8dbe2c05cfc2b253e51425b12d SHA512 ddc9df4a8da4ec563403003ae5bc9ecdf5f3bb7341e2306c405fcf7953ab67cab93e9f64139465b05acfa2c842da1624d941b481ef77c20804cabe7c9df811f9 WHIRLPOOL 1a7f77fc9cd712b7ca459a1943dffde4e154fa2d5e06b77ec42568b012c4319dd43eb0b85cdfd6116b9ba2584e5bd58e1b0d8ea8524d462ab4e18e33d4fa315e diff --git a/sci-chemistry/relax/metadata.xml b/sci-chemistry/relax/metadata.xml new file mode 100644 index 000000000000..617e574f7c34 --- /dev/null +++ b/sci-chemistry/relax/metadata.xml @@ -0,0 +1,30 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +The program relax is a software package designed for the study of molecular +dynamics through the analysis of experimental NMR data. Organic molecules, +proteins, RNA, DNA, sugars, and other biomolecules are all supported. It +was originally written for the model-free analysis of protein dynamics, +though its scope has been significantly expanded. + +relax is a community driven project created by NMR spectroscopists for +NMR spectroscopists. It supports a diverse range of analyses: + +Model-free analysis - the Lipari and Szabo model-free analysis of NMR + relaxation data. +R1 and R2 - the exponential curve fitting for the calculation of the + Rx NMR relaxation rates. +NOE - the calculation of the steady-state NOE NMR relaxation data. +Consistency testing of multiple field NMR relaxation data. +RSDM - Reduced Spectral Density Mapping. +Frame order and N-state model - study of domain motions via the N-state + model and frame order dynamics theories using anisotropic + NMR parameters such as RDCs and PCSs. +Stereochemistry investigations. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/relax/relax-3.3.4.ebuild b/sci-chemistry/relax/relax-3.3.4.ebuild new file mode 100644 index 000000000000..e394217054c8 --- /dev/null +++ b/sci-chemistry/relax/relax-3.3.4.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +WX_GTK_VER="2.9" + +inherit eutils multiprocessing python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx + +DESCRIPTION="Molecular dynamics by NMR data analysis" +HOMEPAGE="http://www.nmr-relax.com/" +SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-python/Numdifftools[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/wxpython:${WX_GTK_VER}[${PYTHON_USEDEP}] + sci-chemistry/molmol + sci-chemistry/pymol[${PYTHON_USEDEP}] + sci-chemistry/vmd + >=sci-libs/bmrblib-1.0.3[${PYTHON_USEDEP}] + >=sci-libs/minfx-1.0.11[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-visualization/grace + sci-visualization/opendx + x11-libs/wxGTK:${WX_GTK_VER}[X]" +DEPEND="${RDEPEND} + media-gfx/pngcrush" + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_prepare() { + rm -rf minfx bmrblib extern/numdifftools || die + tc-export CC +} + +src_compile() { + escons +} + +src_test() { + VIRTUALX_COMMAND="${EPYTHON} ./${PN}.py -x --traceback" + virtualmake +} + +src_install() { + dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf} + + python_moduleinto ${PN} + python_domodule * + + rm ${PN} README || die + + make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@" +} diff --git a/sci-chemistry/relax/relax-3.3.5.ebuild b/sci-chemistry/relax/relax-3.3.5.ebuild new file mode 100644 index 000000000000..154bc9af2c0b --- /dev/null +++ b/sci-chemistry/relax/relax-3.3.5.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +WX_GTK_VER="2.9" + +inherit eutils multiprocessing python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx + +DESCRIPTION="Molecular dynamics by NMR data analysis" +HOMEPAGE="http://www.nmr-relax.com/" +SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-python/Numdifftools[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/wxpython:${WX_GTK_VER}[${PYTHON_USEDEP}] + sci-chemistry/molmol + sci-chemistry/pymol[${PYTHON_USEDEP}] + sci-chemistry/vmd + >=sci-libs/bmrblib-1.0.3[${PYTHON_USEDEP}] + >=sci-libs/minfx-1.0.11[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-visualization/grace + sci-visualization/opendx + x11-libs/wxGTK:${WX_GTK_VER}[X]" +DEPEND="${RDEPEND} + media-gfx/pngcrush" + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_prepare() { + rm -rf minfx bmrblib extern/numdifftools || die + tc-export CC +} + +src_compile() { + escons +} + +src_test() { + VIRTUALX_COMMAND="${EPYTHON} ./${PN}.py -x --traceback" + virtualmake +} + +src_install() { + dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf} + + python_moduleinto ${PN} + python_domodule * + + rm ${PN} README || die + + make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@" +} diff --git a/sci-chemistry/relax/relax-3.3.6.ebuild b/sci-chemistry/relax/relax-3.3.6.ebuild new file mode 100644 index 000000000000..b8a571cbdc2a --- /dev/null +++ b/sci-chemistry/relax/relax-3.3.6.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +WX_GTK_VER="2.9" + +inherit eutils multiprocessing python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx + +DESCRIPTION="Molecular dynamics by NMR data analysis" +HOMEPAGE="http://www.nmr-relax.com/" +SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-python/Numdifftools[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/wxpython:${WX_GTK_VER}[${PYTHON_USEDEP}] + sci-chemistry/molmol + sci-chemistry/pymol[${PYTHON_USEDEP}] + sci-chemistry/vmd + >=sci-libs/bmrblib-1.0.3[${PYTHON_USEDEP}] + >=sci-libs/minfx-1.0.11[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-visualization/grace + sci-visualization/opendx + x11-libs/wxGTK:${WX_GTK_VER}[X]" +DEPEND="${RDEPEND} + media-gfx/pngcrush + test? ( + ${RDEPEND} + ) + " + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_prepare() { + rm -rf minfx bmrblib extern/numdifftools || die + tc-export CC +} + +src_compile() { + escons +} + +src_test() { + VIRTUALX_COMMAND="${EPYTHON} ./${PN}.py -x --traceback" + virtualmake +} + +src_install() { + dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf} + + python_moduleinto ${PN} + python_domodule * + + rm ${PN} README || die + + make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@" +} diff --git a/sci-chemistry/relax/relax-3.3.7.ebuild b/sci-chemistry/relax/relax-3.3.7.ebuild new file mode 100644 index 000000000000..b8a571cbdc2a --- /dev/null +++ b/sci-chemistry/relax/relax-3.3.7.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +WX_GTK_VER="2.9" + +inherit eutils multiprocessing python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx + +DESCRIPTION="Molecular dynamics by NMR data analysis" +HOMEPAGE="http://www.nmr-relax.com/" +SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-python/Numdifftools[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/wxpython:${WX_GTK_VER}[${PYTHON_USEDEP}] + sci-chemistry/molmol + sci-chemistry/pymol[${PYTHON_USEDEP}] + sci-chemistry/vmd + >=sci-libs/bmrblib-1.0.3[${PYTHON_USEDEP}] + >=sci-libs/minfx-1.0.11[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-visualization/grace + sci-visualization/opendx + x11-libs/wxGTK:${WX_GTK_VER}[X]" +DEPEND="${RDEPEND} + media-gfx/pngcrush + test? ( + ${RDEPEND} + ) + " + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_prepare() { + rm -rf minfx bmrblib extern/numdifftools || die + tc-export CC +} + +src_compile() { + escons +} + +src_test() { + VIRTUALX_COMMAND="${EPYTHON} ./${PN}.py -x --traceback" + virtualmake +} + +src_install() { + dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf} + + python_moduleinto ${PN} + python_domodule * + + rm ${PN} README || die + + make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@" +} diff --git a/sci-chemistry/relax/relax-3.3.8.ebuild b/sci-chemistry/relax/relax-3.3.8.ebuild new file mode 100644 index 000000000000..5ffdf922756d --- /dev/null +++ b/sci-chemistry/relax/relax-3.3.8.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +WX_GTK_VER="2.9" + +inherit eutils multiprocessing python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx + +DESCRIPTION="Molecular dynamics by NMR data analysis" +HOMEPAGE="http://www.nmr-relax.com/" +SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-python/Numdifftools[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/wxpython:${WX_GTK_VER}[${PYTHON_USEDEP}] + sci-chemistry/molmol + sci-chemistry/pymol[${PYTHON_USEDEP}] + sci-chemistry/vmd + >=sci-libs/bmrblib-1.0.3[${PYTHON_USEDEP}] + >=sci-libs/minfx-1.0.11[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-visualization/grace + sci-visualization/opendx + x11-libs/wxGTK:${WX_GTK_VER}[X]" +DEPEND="${RDEPEND} + media-gfx/pngcrush + test? ( ${RDEPEND} ) + " + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_prepare() { + rm -rf minfx bmrblib extern/numdifftools || die + tc-export CC +} + +src_compile() { + escons +} + +src_test() { + VIRTUALX_COMMAND="${EPYTHON} ./${PN}.py -x --traceback" + virtualmake +} + +src_install() { + dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf} + + python_moduleinto ${PN} + python_domodule * + + rm ${PN} README || die + + make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@" +} diff --git a/sci-chemistry/scala/Manifest b/sci-chemistry/scala/Manifest new file mode 100644 index 000000000000..e03416a28733 --- /dev/null +++ b/sci-chemistry/scala/Manifest @@ -0,0 +1 @@ +DIST scala-3.3.20.tar.gz 368628 SHA256 0efb108923a4d21fdc75d7ee92567e4bac4ae409f8798fbabd8142b5b026e976 SHA512 9f9812527013d87c80101333baf7ee646f6b3c665cdb477bb4e633c0a1fa57b31b6327913cf712e961c4484a9d9edf1aab5f3cfc66e6834aca1e970a4e0ca898 WHIRLPOOL 7d6082872a9f2f992186a2626dbf7ccd9f827b1322d1399b41ebc1b07267a46cfed5f7ea085403415c01eba4fc44e9d51983080537db04b227469d6871f8f1f9 diff --git a/sci-chemistry/scala/files/3.3.18-gcc4.6.patch b/sci-chemistry/scala/files/3.3.18-gcc4.6.patch new file mode 100644 index 000000000000..0bb3d40d479a --- /dev/null +++ b/sci-chemistry/scala/files/3.3.18-gcc4.6.patch @@ -0,0 +1,17 @@ + scala.f | 3 ++- + 1 files changed, 2 insertions(+), 1 deletions(-) + +diff --git a/scala.f b/scala.f +index d7e1cbe..8ed6fd2 100644 +--- a/scala.f ++++ b/scala.f +@@ -3955,7 +3955,8 @@ c line buffer + character*40 key, value + character*200 realfilename + +- integer intfp, i2swap, lenstr ++ integer intfp, lenstr ++ integer*2 i2swap + external intfp, i2swap, lenstr + logical litend + external litend diff --git a/sci-chemistry/scala/files/Makefile.am b/sci-chemistry/scala/files/Makefile.am new file mode 100644 index 000000000000..49fd61180ef0 --- /dev/null +++ b/sci-chemistry/scala/files/Makefile.am @@ -0,0 +1,7 @@ + +LIBS = -lccp4f $(LAPACK_LIBS) + +bin_PROGRAMS = scala + +scala_SOURCES = scala.f + diff --git a/sci-chemistry/scala/files/configure.ac b/sci-chemistry/scala/files/configure.ac new file mode 100644 index 000000000000..35c4c7fdd194 --- /dev/null +++ b/sci-chemistry/scala/files/configure.ac @@ -0,0 +1,14 @@ +# -*- Autoconf -*- +# Process this file with autoconf to produce a configure script. + +AC_PREREQ(2.59) +AC_INIT(scala, https://bugs.gentoo.org/) +AC_CONFIG_SRCDIR([scala.f]) +AM_INIT_AUTOMAKE([foreign]) + +PKG_CHECK_MODULES([LAPACK],[lapack]) + +# Checks for programs. +AC_PROG_FC +AC_PROG_F77 +AC_OUTPUT([Makefile]) diff --git a/sci-chemistry/scala/metadata.xml b/sci-chemistry/scala/metadata.xml new file mode 100644 index 000000000000..2c9359ab3513 --- /dev/null +++ b/sci-chemistry/scala/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +This program scales together multiple observations of reflections from +Xray difraction experiments, and merges multiple observations into an +average intensity. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/scala/scala-3.3.20.ebuild b/sci-chemistry/scala/scala-3.3.20.ebuild new file mode 100644 index 000000000000..3555cc29a9d1 --- /dev/null +++ b/sci-chemistry/scala/scala-3.3.20.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools fortran-2 + +DESCRIPTION="Scale together multiple observations of reflections" +HOMEPAGE="http://www.ccp4.ac.uk/dist/html/scala.html" +SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + !<sci-chemistry/ccp4-6.1.2 + !dev-lang/scala-bin + !dev-lang/scala + sci-libs/ccp4-libs + virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + cp "${FILESDIR}"/{configure.ac,Makefile.am} "${S}" + eautoreconf +} + +src_install() { + exeinto /usr/libexec/ccp4/bin/ + doexe ${PN} + dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} + dodoc ${PN}.doc + dohtml ${PN}.html +} diff --git a/sci-chemistry/sfcheck/Manifest b/sci-chemistry/sfcheck/Manifest new file mode 100644 index 000000000000..77615cec106b --- /dev/null +++ b/sci-chemistry/sfcheck/Manifest @@ -0,0 +1 @@ +DIST sfcheck-7.03.18.tar.gz 535707 SHA256 def9ceec86fc50f35b9a729e6f84b45a83560e2c6c20a5105647182e10313148 SHA512 256aa1690e0f5ca6aca0483a7d00c1deeb7b77701d950771a134532a658f7c3189bc6abec620ea6da2af200fc879ac9ff07ef7f4ba8614b6cd4e8455a11bed93 WHIRLPOOL 7b9f99f1a8387c5bc63bdab2078d3fcfab4146046429c56503760ca12a1898e944b5aa3c42b358d303206487e5d493bdcb77fe1795490779e7bd79b8b66a2d7a diff --git a/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch b/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch new file mode 100644 index 000000000000..4163cb52ac1e --- /dev/null +++ b/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch @@ -0,0 +1,12 @@ +diff --git a/src/makefile b/src/makefile +index ab43d7d..37e469f 100755 +--- a/src/makefile ++++ b/src/makefile +@@ -60,6 +60,6 @@ main_sfcheck_ccp4.o: main_sfcheck_ccp4.f sfch_version.fh + $(MR_FORT) -c main_sfcheck_ccp4.f + + sfcheck: $(OBJS) +- $(MR_FORT) -o $(BIN)/sfcheck $(OBJSL) $(MR_LIBRARY) ++ $(MR_FORT) $(LDFLAGS) -o $(BIN)/sfcheck $(OBJSL) $(MR_LIBRARY) + + # ---------------------------------------- diff --git a/sci-chemistry/sfcheck/metadata.xml b/sci-chemistry/sfcheck/metadata.xml new file mode 100644 index 000000000000..9ac9ffdb3a41 --- /dev/null +++ b/sci-chemistry/sfcheck/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild b/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild new file mode 100644 index 000000000000..e18673d0923e --- /dev/null +++ b/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="Program for assessing the agreement between the atomic model and X-ray data or EM map" +HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/sfcheck.html" +#SRC_URI="http://www.ysbl.york.ac.uk/~alexei/downloads/sfcheck.tar.gz" +SRC_URI="mirror://gentoo/${P}.tar.gz" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="sci-libs/ccp4-libs" +DEPEND="${RDEPEND} + !<sci-chmistry/ccp4-apps-6.1.3" + +S="${WORKDIR}"/${PN} + +src_prepare() { + epatch "${FILESDIR}"/7.03.17-ldflags.patch + + emake -C src clean +} + +src_compile() { + MR_FORT="$(tc-getFC) ${FFLAGS}" \ + MR_LIBRARY="-lccp4f" \ + emake -C src all +} + +src_install() { + exeinto /usr/libexec/ccp4/bin/ + doexe bin/${PN} + dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} + dodoc readme ${PN}.com.gz doc/${PN}* +} diff --git a/sci-chemistry/shelx/Manifest b/sci-chemistry/shelx/Manifest new file mode 100644 index 000000000000..47f9ac8dd7ad --- /dev/null +++ b/sci-chemistry/shelx/Manifest @@ -0,0 +1,18 @@ +DIST anode_amd64.bz2 8758937 SHA256 01568fd23b0abe280de7a286b9885182f10f06829f139e46bac75846276f60c7 SHA512 6d9f0e506531e14956a95ed23c4c5ccfabaf79b92feba237923db2731e9f3861163f6039e556a6976d910075558fae120088c4805f09880ff33955eff86cc2e1 WHIRLPOOL af181735822c8d04187f98d06f3be2d563cb3e81571fb81139e384a38b54ca7cc83d10a10564456fffb6eead5ab52833f9002882632634fd5a2f8f450d99ca8c +DIST anode_x86.bz2 4310241 SHA256 520f96803bb0ae7d2e7411187968bb38edadad42f06c22af4f89ee2fd4c95886 SHA512 344e25564d4e0d94764c536625c9be3f4a4b8be74153f17f07254f798e9ebbfe416d069a082906187ba0ec7ab958adf8c7c1ec0afab7a6b146fe02a0b5b88505 WHIRLPOOL 3f349040d1ac9af4323cb091e1b2eb37aff6fe5a1202e65adc9119d1ed141406b5a6792852050061e06253411cb409aebc07c3eb50a26bfa5064ed897ba8da9f +DIST ciftab_amd64.bz2 1409694 SHA256 47c4b4349b2534e5d98d499fb92322bfc0ded5c893a7f6c58c58dbcfb84d1b86 SHA512 7f2439cf5d7afefaf9df0a2e0ab970076ea3f65d1e394aa0a81340e4cae0cbcbd25169a5e490c8269cfdc92fe9d1240d9d0a2949322b48c339f7556173e83428 WHIRLPOOL 68dc54ee8c1f8ab5b84f0857fd1e21afd6e5417c949bcae74e9b76e3e13aeae0318c200f5716f02759a8a9b45089d6810d6bba658f43e7f300a28c7f010c224f +DIST ciftab_x86.bz2 510941 SHA256 d27dd5b21e85f77508f01da71c7f8e2cdadc75169eed362324a697938c02e992 SHA512 185628c888e74e7f7ae69eccb3195d841eab83616449c3358dd3fb49605f6bb9e86e97959cf6d20b424037746b67332ad98b9a41ca2a7fae7e3cbe503bf71127 WHIRLPOOL c121e9350b8bbfcb8cf87c4404e9485b678603943702eebfd07627441c47af95a00d457a49440c8fd65ac8fe625e09e35bd1ce8ead6c12af900dc5fbc56188a7 +DIST shelxc_amd64.bz2 1512555 SHA256 e4da94ecc95a8636b28e50254497a7e519313628106f4fe92869e238f659019f SHA512 11b382c6a8440052ffaf136f5c4695d7f6d10e184334810d0f9b7ff25a782c424ae3509a0bbacabddb152b56e6fdfea7266f9c395d0a39994a8c02bd650625ca WHIRLPOOL f6a7f92278741f19e4a19d4a278588770d50d1d9eac30ba96a285ba10add72613532b1cd5f3ffa28e270e654f252e4cf12939abb1458c70d166569e1dd36fbd4 +DIST shelxc_x86.bz2 614564 SHA256 0e8a4fd16a73f28b77e53225d3d6f1038aae1971dca5910043fa04a5818c6e61 SHA512 5be05948e5b79a44e4ead25deba9b1b08857a4636e4c2f8cdc832f6bb2c2407122adff393035f91ce24b48b025191582b919771052f56ebd7a06aaf66dc82115 WHIRLPOOL 6292394d47017524ecd8d3b809ff87793f718e8e3303e6b221c6b27ae4c7da562cff9945d23dd4112509f34f7c3e83cd4d73728c6ee26ffb7efc7b85a3f19aa0 +DIST shelxd_amd64.bz2 8773698 SHA256 fa7c103c0156ad060e7b66b6f39de8982d660a715a07584d2c1a1853d171d3c0 SHA512 6cb881a937e461edf9c9e7736bfab164e6dc16c4df4291b8dce69b3abf98ce27fadb8079cc5142d2b77eb94ac42c0bb375f3ac21b45f590d535839cc7f8cd762 WHIRLPOOL c4b3b8b7f9d78e15153b4f3678ef8766cdc97cc3c03686b528a40b98d45233612c0104aaa3ec491cd20e787d834965056b10bfa3fc247fc1a4aaee4c0739162d +DIST shelxd_x86.bz2 4406371 SHA256 0b0da50c0907f97e93b46bbd01e63737c007b1b93aa3a79d471621d39557e74f SHA512 68d11983f98984bfaca089b839d38cc9607857d2bb6d2cff306d9efa2f34ea8d741220eb01a99d2ecdd832dde1794b4bb228ceae3fc0e87e3210dfa491e6a402 WHIRLPOOL 6cb3343aa878a5703a65b93f6dd1255ebc668afad92117441a785a91dd39d1736a10411655b08da7ff714bed7ed423e30555b8436c9a7df9f49f8ea3351f651e +DIST shelxe_amd64.bz2 8302570 SHA256 fac87ba983a454cb32f76076318dabbf6ae2f98415cf2428a0154765b3401915 SHA512 cbafde59ba1d9943f74e8c66cc012168f1f8062e978d2f9103adb4d130c9a024e3e8b170af5b5207168f23db4742b4a99ce3b550e897c59e1dfd3631d7d6c6ab WHIRLPOOL 0007c53e4a9bb8e546b625a2565a9e5d01d60b35c8565e34ab753033c16f1c1b61cdfbe2129ff4981cb595cf637f08342b0d77c22ea8836e08df6b671ac6d2e4 +DIST shelxe_x86.bz2 4177233 SHA256 b2bff78b9b51b72e545d23ce76f6b93e016c2cd583aee9d7236b99fd1722d280 SHA512 67d56beef36918ec6b5d86109d2e61a0dc5a34ed73174ba5cdf96e0db8d8d41cdf20bffdee138f6f177e30a9df32aa1494c18221139538e5c778d61d5f558c51 WHIRLPOOL d8e4be4f7b7a313f5586c23a3d5c94dc2b177b36b47025219c5d54985fd41d7ffb902db4d2a1060ae0ce0448d59032782309029096449af76b5df6253db52e81 +DIST shelxl_amd64.bz2 2985452 SHA256 7e7bf32d5dcfa0e8bb0390add8dcc1d0e722012188dd3d124f255ed9e9c13208 SHA512 0c5b5e4bf6041399221a2f321a3e8f3def952a6eb9af26652a8af04c4bedf5cb98aa529c11e84da20c061028701a49af960135ac697ae157609ca8ae8acde219 WHIRLPOOL a5f7a2e118d5582cafa76c1abea86b614e48e1e8ed217e1280b770124eb16f247ef668112031b5a7660af098b51be94b2f53d0fb506dc090e1615ec7204ce712 +DIST shelxl_x86.bz2 1610822 SHA256 b7a28fb6318cb16948c06e7aed8ee7a7c6a5d3a8863c57f657fbbd2007b25955 SHA512 deaeed15676f294088ce07dc3760e2eecca503f87a537e3e9598d1de6102e82f25b2bd46c080e5140a35046847c345845a88adf159197be640ba52b1a790cfec WHIRLPOOL 5998b3909232016e4cfb99a112090e07a926e36442d47e6c7aa09d50d830eeeb21d2732cd962d01672b76b120cca51df400532805e971ee6b2a6c9d13692582d +DIST shelxs_amd64.bz2 1606403 SHA256 9b180574ee2b828123f622d42e307778d8d4a1f4c32d5741ba065ad2b7751e60 SHA512 3d26e8bc10f0004ee52a564be567db0cdf41f7d05d457e66c12e117bb82550066bf7333830f8dcd56ea987de677f365db25a51f4c22efda9c911fda03d49086e WHIRLPOOL 7e02ede8528e752f1a01d3109064914d42d6c83e4d8c0e901e13e9e1345160d087f35568d1f7ff7f61f54fdbf838a6e8b2d8ab9482df27fd561cc7f4dad610d7 +DIST shelxs_x86.bz2 746352 SHA256 3eea6b363f7e2ff90965a01b65f3aa5d4ac5642a1528a7824c3ea8398c272d2b SHA512 9ecf1e8da8df2280a1982c210dea5418004492047fdd3ab004eade39d247199f3c757d00a56d179eadc7a1ce434c8019c39af865b641ae3c370a8461a950140c WHIRLPOOL 5120481aefcaa3871e61dc2f9230095506386de83741e3e5fc7cdf29f2835509ae369276b55252b981907a76b59f3829e0c4ab1738605e5c6f72ff58401157d2 +DIST shelxt_amd64.bz2 8862210 SHA256 519c695b8f6c0425f2635dc021be8138ef029761a43d64133a5d736cccc031b8 SHA512 49cb7b5e9f3a1cab153dd04ce4ab424f3331790df2e4acf0584263edcd28e20f6225a6f48161469e1569ae0d6eeed5389db0c9a66d7853ea34b798364a346e27 WHIRLPOOL 11a821502863cddedb14377f8881b7a7931970f8ce9da668106a5dee6e7113fa6f41f69c9381e7ea4c93aa21a6c3498ba4c836df9289db7295c54e6267faa92c +DIST shelxt_x86.bz2 4441488 SHA256 ca64d86718d306d8d5269f0d7ca92fc2921f1a199afa1bc181b5f6cc339a012c SHA512 83027d24d58863030a284e5e573df27db760ce61f7c8d7da5741471bd814256ae5ade1316aa3e262a54c4c4fb6ad231dacfcef043c3279d381d2969e0b73dd14 WHIRLPOOL ec91f0e6d192507854cbcc2baa751c17185df70f2220eab8f487a1db082bc055aefe2b5f437e144fbbf60c01f1d735057c07ff2f71ab77c88c13a1a19ffe7a65 +DIST shredcif_amd64.bz2 1371002 SHA256 eddf6237b70114bab99845c228d5ba6240a2a9e019bf59678f2222e2ddc52cfe SHA512 5846f7a14936ae4c710ead752a83dd8d73bbcd6037c38f2c566156f87678a84c1db3fd5d0a6e3c6dfb04a2ed7c96c8497c36faaf2bf2ca99ace74f98152ba3be WHIRLPOOL 11b82847cd4f3529c7708de7d0ae7da4e741a58da58ac01954e7136ca2f02c599a81485c70ff36916cdce97e86ab67efe61ec544231db9d7ad903edfd68e232b +DIST shredcif_x86.bz2 461442 SHA256 aa06e0b3f2b7face7f486029d4c83e9fd591c46b2a41db6ce8e3014f6a713d78 SHA512 8097b6285d3e9269989663e52a4d903b279f9cdd0a5650c91d605dd324c62361de619c0873968a3178d3c125f59a9b448465a09542e2582779fbb8cca1f9ebf7 WHIRLPOOL 37f9410d1fcf2881b3e83b752d5170859ebab2063da8124715d5f627a83b9ef2ba4694a2a77a213e8c1b92d474304a7aea83b1f03111fd2abbb3fcd13d054052 diff --git a/sci-chemistry/shelx/files/20060317-autotool.patch b/sci-chemistry/shelx/files/20060317-autotool.patch new file mode 100644 index 000000000000..b90fb0a921c1 --- /dev/null +++ b/sci-chemistry/shelx/files/20060317-autotool.patch @@ -0,0 +1,47 @@ +diff -urN unix.orig/configure.ac unix/configure.ac +--- unix.orig/configure.ac 1969-12-31 16:00:00.000000000 -0800 ++++ unix/configure.ac 2006-06-04 22:31:49.000000000 -0700 +@@ -0,0 +1,12 @@ ++# -*- Autoconf -*- ++# Process this file with autoconf to produce a configure script. ++ ++AC_PREREQ(2.59) ++AC_INIT(shelx, 20060317, https://bugs.gentoo.org/) ++AC_CONFIG_SRCDIR([ciftab.f]) ++AM_INIT_AUTOMAKE([foreign]) ++ ++# Checks for programs. ++AC_PROG_FC ++AC_PROG_F77 ++AC_OUTPUT([Makefile]) +diff -urN unix.orig/Makefile.am unix/Makefile.am +--- unix.orig/Makefile.am 1969-12-31 16:00:00.000000000 -0800 ++++ unix/Makefile.am 2006-06-04 23:06:39.000000000 -0700 +@@ -0,0 +1,27 @@ ++bin_PROGRAMS = \ ++ ciftab \ ++ shelxa \ ++ shelxc \ ++ shelxd \ ++ shelxe \ ++ shelxh \ ++ shelxl \ ++ shelxpro \ ++ shelxs \ ++ shelxwat ++ ++dist_pkgdata_DATA = \ ++ ciftab.def \ ++ ciftab.rta \ ++ ciftab.rtm ++ ++ciftab_SOURCES = ciftab.f ++shelxa_SOURCES = shelxa.f ++shelxc_SOURCES = shelxc.f ++shelxd_SOURCES = shelxd.f ++shelxe_SOURCES = shelxe.f ++shelxh_SOURCES = shelxh.f shelxlv.f ++shelxl_SOURCES = shelxl.f shelxlv.f ++shelxpro_SOURCES = shelxpro.f ++shelxs_SOURCES = shelxs.f shelxsv.f ++shelxwat_SOURCES = shelxwat.f diff --git a/sci-chemistry/shelx/files/20060317-gfortran.patch b/sci-chemistry/shelx/files/20060317-gfortran.patch new file mode 100644 index 000000000000..d414a8e45c31 --- /dev/null +++ b/sci-chemistry/shelx/files/20060317-gfortran.patch @@ -0,0 +1,20 @@ +--- unix.orig/ciftab.f 2006-10-12 11:44:46.000000000 -0700 ++++ unix/ciftab.f 2006-10-12 11:38:22.000000000 -0700 +@@ -377,7 +377,7 @@ + C systems. It enables a 'read-only' file to be opened for reading. + C + OPEN(LR,FILE=CIFDIR(1:K)//'ciftab.'//IS(1:L),STATUS='OLD', +- +READONLY,ERR=5) ++ +ERR=5) + GOTO 6 + 4 WRITE(*,'(/A)')' ** Cannot open file **' + GOTO 108 +@@ -1332,7 +1332,7 @@ + 6 FORMAT(3X,4('h k l Fo Fc s',5X),'h k l Fo Fc s', + +A1/A1) + 7 FORMAT(4(I4,2I3,2I5,I4,2X),I4,2I3,2I5,I4) +- 8 FORMAT($,1X,A) ++ 8 FORMAT(1X,A,$) + C + WRITE(LO,1)' '//ESC//AMP//'l0o5c1x'//ESC//'(0u'// + +ESC//'(s0p16.66h8.5v0s0b0T'//CR diff --git a/sci-chemistry/shelx/metadata.xml b/sci-chemistry/shelx/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/shelx/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/shelx/shelx-20141228.ebuild b/sci-chemistry/shelx/shelx-20141228.ebuild new file mode 100644 index 000000000000..dfd2eac4f5f3 --- /dev/null +++ b/sci-chemistry/shelx/shelx-20141228.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="Programs for crystal structure determination from single-crystal diffraction data" +HOMEPAGE="http://shelx.uni-ac.gwdg.de/SHELX/" +SRC_URI=" + amd64? ( + anode_amd64.bz2 + ciftab_amd64.bz2 + shelxc_amd64.bz2 + shelxd_amd64.bz2 + shelxe_amd64.bz2 + shelxl_amd64.bz2 + shelxs_amd64.bz2 + shelxt_amd64.bz2 + shredcif_amd64.bz2 + ) + x86? ( + anode_x86.bz2 + ciftab_x86.bz2 + shelxc_x86.bz2 + shelxd_x86.bz2 + shelxe_x86.bz2 + shelxl_x86.bz2 + shelxs_x86.bz2 + shelxt_x86.bz2 + shredcif_x86.bz2 + ) +" + +SLOT="0" +LICENSE="free-noncomm" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}" + +RESTRICT="fetch" + +QA_PREBUILT="opt/bin/*" + +pkg_nofetch() { + elog "Go to ${HOMEPAGE}" + elog "Fill out the application form, and send it in." + elog "Download ${A} and rename them to" + use amd64 && elog "*_amd64.bz2" + use x86 && elog "*_x86.bz2" + elog "and place renamed tarballs in ${DISTDIR}." +} + +src_install() { + local i + into /opt + for i in *; do + newbin ${i} ${i/_*/} + done +} diff --git a/sci-chemistry/solve-resolve-bin/Manifest b/sci-chemistry/solve-resolve-bin/Manifest new file mode 100644 index 000000000000..0d3b66530d29 --- /dev/null +++ b/sci-chemistry/solve-resolve-bin/Manifest @@ -0,0 +1,2 @@ +DIST solve-2.13-linux-64.tar.gz 74444830 SHA256 e03250bb550686fc6e5f59d4e885b83b88cd342dfb4975eb31ddf95d9515650e SHA512 8f20715c3fb73940f03ba8a4bb3528f89ba01520cacead001796609bc15259ab7ab7f2d4960ea97efc43029863bc31e630c9e93f528a233652928220dafe0b4d WHIRLPOOL 125efe76024148656f3bb357ad1bc78d17f51eb8268c83241f4da9a94356170d0259fe48fadf6bf1ffe4b10b57bb27ed79199063dc95d0eef8d9e22de653c84a +DIST solve-2.13-linux.tar.gz 71902534 SHA256 975466fe92d8f6256de20ea0b5101876f3e5a7e3093199946c9f4824236c79d3 diff --git a/sci-chemistry/solve-resolve-bin/metadata.xml b/sci-chemistry/solve-resolve-bin/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/solve-resolve-bin/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild b/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild new file mode 100644 index 000000000000..6deae178afdd --- /dev/null +++ b/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="Automated crystallographic structure solution for MIR, SAD, and MAD" +HOMEPAGE="http://www.solve.lanl.gov/index.html" +SRC_URI=" + x86? ( https://solve.lanl.gov/pub/solve/${PV}/solve-${PV}-linux.tar.gz ) + amd64? ( https://solve.lanl.gov/pub/solve/${PV}/solve-${PV}-linux-64.tar.gz )" + +SLOT="0" +LICENSE="solve" +KEYWORDS="-* x86 amd64" +IUSE="examples" + +RDEPEND="sci-libs/ccp4-libs" +DEPEND="" + +RESTRICT="mirror" + +S="${WORKDIR}"/solve-${PV} + +QA_PREBUILT="opt/solve-resolve/bin/*" + +src_install(){ + local IN_PATH="/opt/solve-resolve/" + + exeinto ${IN_PATH}bin/ + doexe bin/* + + insinto ${IN_PATH}lib/ + doins -r lib/{*sym,sym*,hist*,*dat,segments,patterns} + + docinto html + dodoc -r lib/html/* + + sed \ + -e 's:/usr/local/lib/solve/:${EPREFIX}/opt/solve-resolve/lib/:' \ + -i lib/examples_solve/p9/solve* || die + if use examples; then + sed \ + -e 's:/usr/local/lib/resolve/:${EPREFIX}/opt/solve-resolve/lib/:' \ + -i lib/examples_resolve/{resolve.csh,prime_and_switch.csh} || die + insinto /usr/share/${PF}/ + doins -r lib/examples_*solve + fi + + cat >> "${T}"/20solve-resolve <<- EOF + CCP4_OPEN="UNKNOWN" + SYMOP="${EPREFIX}/usr/share/ccp4/data/symop.lib" + SYMINFO="${EPREFIX}/usr/share/ccp4/data/syminfo.lib" + SOLVEDIR="${EPREFIX}/${IN_PATH}lib/" + PATH="${EPREFIX}/${IN_PATH}bin" + EOF + + doenvd "${T}"/20solve-resolve +} + +pkg_postinst(){ + einfo "Get a valid license key from" + einfo "http://solve.lanl.gov/license.html" + einfo "and place it in" + einfo "${EPREFIX}${IN_PATH}lib/" +} diff --git a/sci-chemistry/sparky/Manifest b/sci-chemistry/sparky/Manifest new file mode 100644 index 000000000000..1e8514f6cde8 --- /dev/null +++ b/sci-chemistry/sparky/Manifest @@ -0,0 +1 @@ +DIST sparky-source-3.115.tar.gz 4103686 SHA256 c187546aaec3d6489c533c3a778e1fe6fa634a931dcaf245c1e13f5720a002b6 SHA512 33b0fd368f15bf4d091d7152a189f57279aea54fb89a12f15314f2a1414b073f7bd282afedeb72e79192195b0b6ac212ca74da3def513592af5400c118ac8e89 WHIRLPOOL 8557a525eab51150da437f78cb8e404adad4f41ed0884498601887e832f78bb316e4847cc3b3a7147ec66bcddd4e06064323bb2ce76452b37d504a809feee7ff diff --git a/sci-chemistry/sparky/files/3.115-fpic.patch b/sci-chemistry/sparky/files/3.115-fpic.patch new file mode 100644 index 000000000000..37725aa029e2 --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-fpic.patch @@ -0,0 +1,42 @@ +diff --git a/c++/Makefile b/c++/Makefile +index 421ff77..7442ed3 100644 +--- a/c++/Makefile ++++ b/c++/Makefile +@@ -158,7 +158,7 @@ winsystem-$(PLATFORM).o: winsystem-$(PLATFORM).cc + $(CXX) $(CXXFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/winsystem-$(PLATFORM).cc + + python.o: python.cc +- $(CXX) $(CXXFLAGS) $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc ++ $(CXX) $(CXXFLAGS) -fPIC $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc + + _tkinter.so: _tkinter.o + $(CXX) $(LDSHARED) $(LDFLAGS) -o $@ _tkinter.o $(TKLIBS) +diff --git a/c++/Makefile b/c++/Makefile +index 353122d..84b0c24 100644 +--- a/c++/Makefile ++++ b/c++/Makefile +@@ -168,7 +168,7 @@ _tkinter.o: _tkinter.c + + Makefile.dep: force + cd $(SPARKY_SRC) ; \ +- $(CXX) $(DEPEND) $(CXXFLAGS) $(TKFLAGS) $(PYFLAGS) \ ++ $(CXX) $(DEPEND) $(CXXFLAGS) -fPIC $(TKFLAGS) $(PYFLAGS) \ + $(SPARKY_OBJS:.o=.cc) $(OTHER_OBJS:.o=.cc) > $@ + + TAGS: force +diff --git a/c++/Makefile b/c++/Makefile +index 84b0c24..933f347 100644 +--- a/c++/Makefile ++++ b/c++/Makefile +@@ -30,9 +30,9 @@ TCL_LIBNAME = tcl$(TCLTK_VERSION) + PLATFORM = unix + + CXX = g++ +-CXXFLAGS = ++CXXFLAGS += -fPIC + CC = gcc +-CFLAGS = ++CFLAGS += -fPIC + PYFLAGS = -I$(PYTHON_INC) -I$(PYTHON_LIB)/config + TKFLAGS = -I$(TK_PREFIX)/include + TKLIBS = -L$(TK_PREFIX)/lib -l$(TK_LIBNAME) -l$(TCL_LIBNAME) -lX11 diff --git a/sci-chemistry/sparky/files/3.115-ldflags.patch b/sci-chemistry/sparky/files/3.115-ldflags.patch new file mode 100644 index 000000000000..bd4020387682 --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-ldflags.patch @@ -0,0 +1,61 @@ +diff --git a/c++/Makefile b/c++/Makefile +index aeb4daa..5cab356 100644 +--- a/c++/Makefile ++++ b/c++/Makefile +@@ -131,28 +131,28 @@ $(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk: + chmod 755 $@ + + sparky-no-python$(EXE_SUFFIX): main.o $(SPARKY_OBJS) +- $(CXX) -o $@ main.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ main.o $(SPARKY_OBJS) $(LDLIBS) + + ucsfdata$(EXE_SUFFIX): ucsfdata.o $(NMR_OBJS) +- $(CXX) -o $@ ucsfdata.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ ucsfdata.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + pipe2ucsf$(EXE_SUFFIX): pipe2ucsf.o $(NMR_OBJS) +- $(CXX) -o $@ pipe2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ pipe2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + vnmr2ucsf$(EXE_SUFFIX): vnmr2ucsf.o $(NMR_OBJS) +- $(CXX) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + bruk2ucsf$(EXE_SUFFIX): bruk2ucsf.o $(NMR_OBJS) +- $(CXX) -o $@ bruk2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ bruk2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + peaks2ucsf$(EXE_SUFFIX): peaks2ucsf.o $(NMR_OBJS) +- $(CXX) -o $@ peaks2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ peaks2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + matrix2ucsf$(EXE_SUFFIX): matrix2ucsf.o $(NMR_OBJS) +- $(CXX) -o $@ matrix2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ matrix2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + spy.so: python.o $(SPARKY_OBJS) +- $(CXX) $(LDSHARED) -o $@ python.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS) ++ $(CXX) $(LDSHARED) $(LDFLAGS) -o $@ python.o $(SPARKY_OBJS) $(LDLIBS) + + winsystem-$(PLATFORM).o: winsystem-$(PLATFORM).cc + $(CXX) $(CXXFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/winsystem-$(PLATFORM).cc +@@ -161,7 +161,7 @@ python.o: python.cc + $(CXX) $(CXXFLAGS) $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc + + _tkinter.so: _tkinter.o +- $(CXX) $(LDSHARED) -o $@ _tkinter.o $(LDFLAGS) $(TKLIBS) ++ $(CXX) $(LDSHARED) $(LDFLAGS) -o $@ _tkinter.o $(TKLIBS) + + _tkinter.o: _tkinter.c + $(CC) $(CFLAGS) $(TKFLAGS) $(PYFLAGS) -c $(SPARKY_SRC)/_tkinter.c +@@ -188,8 +188,8 @@ PYLDFLAGS = -L$(PYTHON_LIB)/config -lpython$(PYTHON_VERSION) + PYIFLAGS = -I$(PYTHON_INC) + + debug-sparky: main-debug.o python.o _tkinter.o $(SPARKY_OBJS) +- $(CXX) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \ +- $(LDFLAGS) $(PYLDFLAGS) $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \ ++ $(PYLDFLAGS) $(LDLIBS) + + main-debug.o: main-debug.cc + $(CXX) $(CXXFLAGS) $(PYIFLAGS) -c $(SPARKY_SRC)/main-debug.cc diff --git a/sci-chemistry/sparky/files/3.115-makefile.patch b/sci-chemistry/sparky/files/3.115-makefile.patch new file mode 100644 index 000000000000..7c810dcbd8ae --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-makefile.patch @@ -0,0 +1,17 @@ +diff --git a/Makefile b/Makefile +index bb27034..30979bd 100644 +--- a/Makefile ++++ b/Makefile +@@ -48,6 +48,12 @@ TKINTER_PYMOD = _tkinter$(PYMOD_SUFFIX) + all nopython $(SPY_PYMOD) $(TKINTER_PYMOD) $(EXECUTABLES) debug-sparky clean: force + cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $@ + ++libraries: ++ cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(SPY_PYMOD) $(TKINTER_PYMOD) ++ ++binaries: ++ cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(EXECUTABLES) debug-sparky ++ + Makefile.dep TAGS: force + cd $(SPARKY_SRC) && $(MAKE) -f Makefile -e $@ + diff --git a/sci-chemistry/sparky/files/3.115-paths.patch b/sci-chemistry/sparky/files/3.115-paths.patch new file mode 100644 index 000000000000..20d9a801ecd6 --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-paths.patch @@ -0,0 +1,13 @@ +diff --git a/c++/paths.h b/c++/paths.h +index 2a21366..38aff52 100644 +--- a/c++/paths.h ++++ b/c++/paths.h +@@ -19,7 +19,7 @@ + // Installation subdirectories and files + // + #define SPARKY_MANUAL "manual" +-#define SPARKY_LIB "lib" ++#define SPARKY_LIB "." + #define SPARKY_PRINT "print-prolog.ps" // under lib directory + #define SPARKY_RESOURCE "Sparky" // under lib directory + #define SPARKY_SAMPLE_DATA "example" diff --git a/sci-chemistry/sparky/files/3.115-wrapper-r1.patch b/sci-chemistry/sparky/files/3.115-wrapper-r1.patch new file mode 100644 index 000000000000..d83b5b8510cc --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-wrapper-r1.patch @@ -0,0 +1,41 @@ +diff --git a/bin/sparky b/bin/sparky +index 8b51212..270723a 100644 +--- a/bin/sparky ++++ b/bin/sparky +@@ -4,18 +4,6 @@ + # + + # ----------------------------------------------------------------------------- +-# Figure out Sparky installation directory from $0. +-# +-set sparky_exe = "$0" +-while (-l "$sparky_exe") +- set ls_sparky_exe = `ls -l "$sparky_exe"` +- set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'` +-end +-set sparky_bin = `dirname "$sparky_exe"` +-set sparky_bin = `cd "$sparky_bin"; pwd` +-set sparky_inst = `dirname "$sparky_bin"` +- +-# ----------------------------------------------------------------------------- + # Sparky uses the SPARKY_INSTALL environment variable to find its + # application resource file and print prolog file. + # +@@ -25,7 +13,7 @@ setenv SPARKY_INSTALL "$sparky_inst" + # If Python is available start Sparky as a Python extension. + # Otherwise the standalone version of Sparky is started. + # +-set PYTHON = "$SPARKY_INSTALL/python2.5/bin/python2.5" ++set PYTHON = GENTOO_PYTHON + if (! -e "$PYTHON") then + set PYTHON = python2.5 + endif +@@ -79,7 +67,7 @@ if ($status == 0) then + # --------------------------------------------------------------------------- + # Add the Sparky package and Tkinter to the Python path + # +- set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/lib-tk" ++ set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/sparky" + if ($?PYTHONPATH) then + setenv PYTHONPATH "${SPARKY_PYTHONPATH}:$PYTHONPATH" + else diff --git a/sci-chemistry/sparky/files/3.115-wrapper.patch b/sci-chemistry/sparky/files/3.115-wrapper.patch new file mode 100644 index 000000000000..9498c0bec837 --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-wrapper.patch @@ -0,0 +1,41 @@ +diff --git a/bin/sparky b/bin/sparky +index 8b51212..270723a 100644 +--- a/bin/sparky ++++ b/bin/sparky +@@ -4,18 +4,6 @@ + # + + # ----------------------------------------------------------------------------- +-# Figure out Sparky installation directory from $0. +-# +-set sparky_exe = "$0" +-while (-l "$sparky_exe") +- set ls_sparky_exe = `ls -l "$sparky_exe"` +- set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'` +-end +-set sparky_bin = `dirname "$sparky_exe"` +-set sparky_bin = `cd "$sparky_bin"; pwd` +-set sparky_inst = `dirname "$sparky_bin"` +- +-# ----------------------------------------------------------------------------- + # Sparky uses the SPARKY_INSTALL environment variable to find its + # application resource file and print prolog file. + # +@@ -25,7 +13,7 @@ setenv SPARKY_INSTALL "$sparky_inst" + # If Python is available start Sparky as a Python extension. + # Otherwise the standalone version of Sparky is started. + # +-set PYTHON = "$SPARKY_INSTALL/python2.5/bin/python2.5" ++set PYTHON = "@GENTOO_PORTAGE_EPREFIX@/usr/bin/python" + if (! -e "$PYTHON") then + set PYTHON = python2.5 + endif +@@ -79,7 +67,7 @@ if ($status == 0) then + # --------------------------------------------------------------------------- + # Add the Sparky package and Tkinter to the Python path + # +- set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/lib-tk" ++ set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/sparky" + if ($?PYTHONPATH) then + setenv PYTHONPATH "${SPARKY_PYTHONPATH}:$PYTHONPATH" + else diff --git a/sci-chemistry/sparky/files/fix-install.patch b/sci-chemistry/sparky/files/fix-install.patch new file mode 100644 index 000000000000..4eefaa891f99 --- /dev/null +++ b/sci-chemistry/sparky/files/fix-install.patch @@ -0,0 +1,259 @@ +diff -ur -x make-sparky sparky.orig/bin/sparky sparky/bin/sparky +--- sparky.orig/bin/sparky 2004-03-05 11:32:10.000000000 -0800 ++++ sparky/bin/sparky 2005-12-17 17:36:51.000000000 -0800 +@@ -4,22 +4,10 @@ + # + + # ----------------------------------------------------------------------------- +-# Figure out Sparky installation directory from $0. +-# +-set sparky_exe = $0 +-while (-l $sparky_exe) +- set ls_sparky_exe = `ls -l "$sparky_exe"` +- set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'` +-end +-set sparky_bin = `dirname "$sparky_exe"` +-set sparky_bin = `cd "$sparky_bin"; pwd` +-set sparky_inst = `dirname "$sparky_bin"` +- +-# ----------------------------------------------------------------------------- + # Sparky uses the SPARKY_INSTALL environment variable to find its + # application resource file and print prolog file. + # +-setenv SPARKY_INSTALL $sparky_inst ++setenv SPARKY_INSTALL @GENTOO_PORTAGE_EPREFIX@/usr/lib/sparky + + # ----------------------------------------------------------------------------- + # If Python is available start Sparky as a Python extension. +diff -ur -x make-sparky sparky.orig/c++/Makefile sparky/c++/Makefile +--- sparky.orig/c++/Makefile 2004-02-03 15:56:24.000000000 -0800 ++++ sparky/c++/Makefile 2005-12-18 10:49:08.000000000 -0800 +@@ -22,6 +22,7 @@ + PYTHON_PREFIX = /usr/local + PYTHON_LIB = $(PYTHON_PREFIX)/lib/python$(PYTHON_VERSION) + PYTHON_INC = $(PYTHON_PREFIX)/include/python$(PYTHON_VERSION) ++PYDIR = $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages + TCLTK_VERSION = 8.4 + TCLTK_VER_WIN32 = 84 + TK_PREFIX = /usr/local +@@ -113,21 +114,20 @@ + + nopython: $(EXECUTABLES) + +-install-python: $(SPY_PYMOD) $(TKINTER_PYMOD) $(SPARKY_INSTALL)/python \ +- $(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk +- $(INSTALL) $(SPY_PYMOD) $(SPARKY_INSTALL)/python/sparky +- chmod 755 $(SPARKY_INSTALL)/python/sparky/$(SPY_PYMOD) +- $(INSTALL) $(TKINTER_PYMOD) $(SPARKY_INSTALL)/python/lib-tk +- chmod 755 $(SPARKY_INSTALL)/python/lib-tk/$(TKINTER_PYMOD) ++install-python: $(SPY_PYMOD) $(TKINTER_PYMOD) $(PYDIR) \ ++ $(PYDIR)/sparky $(PYDIR)/lib-tk ++ $(INSTALL) $(SPY_PYMOD) $(PYDIR)/sparky ++ chmod 755 $(PYDIR)/sparky/$(SPY_PYMOD) ++ $(INSTALL) $(TKINTER_PYMOD) $(PYDIR)/lib-tk ++ chmod 755 $(PYDIR)/lib-tk/$(TKINTER_PYMOD) + + install-nopython: $(EXECUTABLES) $(SPARKY_INSTALL)/bin + $(INSTALL) $(EXECUTABLES) $(SPARKY_INSTALL)/bin + cd $(SPARKY_INSTALL)/bin ; \ + chmod 755 $(EXECUTABLES) + +-$(SPARKY_INSTALL)/bin $(SPARKY_INSTALL)/python \ +-$(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk: +- mkdir $@ ++$(SPARKY_INSTALL)/bin $(PYDIR) $(PYDIR)/sparky $(PYDIR)/lib-tk: ++ mkdir -p $@ + chmod 755 $@ + + sparky-no-python$(EXE_SUFFIX): main.o $(SPARKY_OBJS) +diff -ur -x make-sparky sparky.orig/c++/paths.h sparky/c++/paths.h +--- sparky.orig/c++/paths.h 2002-01-17 19:15:06.000000000 -0800 ++++ sparky/c++/paths.h 2005-12-17 20:57:15.000000000 -0800 +@@ -19,7 +19,7 @@ + // Installation subdirectories and files + // + #define SPARKY_MANUAL "manual" +-#define SPARKY_LIB "lib" ++#define SPARKY_LIB "" + #define SPARKY_PRINT "print-prolog.ps" // under lib directory + #define SPARKY_RESOURCE "Sparky" // under lib directory + #define SPARKY_SAMPLE_DATA "example" +diff -ur -x make-sparky sparky.orig/c++/system-unix.cc sparky/c++/system-unix.cc +--- sparky.orig/c++/system-unix.cc 2004-02-26 10:57:54.000000000 -0800 ++++ sparky/c++/system-unix.cc 2005-12-17 20:56:58.000000000 -0800 +@@ -95,7 +95,7 @@ + // + Stringy default_sparky_install_path() + { +- return file_path(file_path(file_path("", "usr"), "local"), "sparky"); ++ return file_path(file_path(file_path("", "usr"), "lib"), "sparky"); + } + + // ---------------------------------------------------------------------------- +diff -ur -x make-sparky sparky.orig/lib/Makefile sparky/lib/Makefile +--- sparky.orig/lib/Makefile 2004-02-18 10:53:29.000000000 -0800 ++++ sparky/lib/Makefile 2005-12-17 16:03:21.000000000 -0800 +@@ -18,9 +18,9 @@ + TCL_SHLIB = lib$(TCL_VERSION)$(TCLTK_SHLIB_SUFFIX) + TK_SHLIB = lib$(TK_VERSION)$(TCLTK_SHLIB_SUFFIX) + +-install: $(SPARKY_INSTALL)/lib install-tcl-tk +- $(INSTALL) Sparky print-prolog.ps $(SPARKY_INSTALL)/lib +- cd $(SPARKY_INSTALL)/lib ; \ ++install: $(SPARKY_INSTALL)/lib ++ $(INSTALL) Sparky print-prolog.ps $(SPARKY_INSTALL)/lib/sparky ++ cd $(SPARKY_INSTALL)/lib/sparky ; \ + chmod 644 Sparky print-prolog.ps + + install-tcl-tk: $(SPARKY_INSTALL)/lib +diff -ur -x make-sparky sparky.orig/Makefile sparky/Makefile +--- sparky.orig/Makefile 2004-02-18 10:40:04.000000000 -0800 ++++ sparky/Makefile 2005-12-17 19:40:48.000000000 -0800 +@@ -40,18 +40,22 @@ + + PYTHON_VERSION = 2.3 + PYTHON_DIR = ++PYDIR = $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages + + PYMOD_SUFFIX = .so + SPY_PYMOD = spy$(PYMOD_SUFFIX) + TKINTER_PYMOD = _tkinter$(PYMOD_SUFFIX) + ++PYDIR = $(SPARKY_INSTALL)/lib/sparky/python ++DOCDIR = $(SPARKY_INSTALL)/share/doc/sparky ++ + all nopython $(SPY_PYMOD) $(TKINTER_PYMOD) $(EXECUTABLES) debug-sparky clean: force + cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $@ + + Makefile.dep TAGS: force + cd $(SPARKY_SRC) && $(MAKE) -f Makefile -e $@ + +-install: install-nopython $(SPARKY_INSTALL) install-python ++install: install-nopython $(SPARKY_INSTALL) + cd $(SPARKY_OBJ) && \ + $(MAKE) -f $(SPARKY_SRC)/Makefile -e install-python + cd $(SPARKY)/python && $(MAKE) -f Makefile -e install +@@ -67,7 +71,8 @@ + chmod 755 sparky$(SCRIPT_SUFFIX) + + install-example: $(SPARKY_INSTALL) +- cd $(SPARKY) ; $(INSTALLDIR) example $(SPARKY_INSTALL) ++ mkdir -p $(DOCDIR)/example ++ cd $(SPARKY) ; $(INSTALLDIR) example $(DOCDIR) + + install-lib: $(SPARKY_INSTALL) + cd $(SPARKY)/lib && $(MAKE) -f Makefile -e install +@@ -76,21 +81,14 @@ + cd $(SPARKY)/manual && $(MAKE) -f Makefile -e install + + install-misc: $(SPARKY_INSTALL) +- cd $(SPARKY) ; $(INSTALL) LICENSE README $(SPARKY_INSTALL) +- cd $(SPARKY_INSTALL) ; chmod 644 LICENSE README +- +-install-python: $(SPARKY_INSTALL) $(SPARKY_INSTALL)/python$(PYTHON_VERSION) +-ifdef PYTHON_DIR +- $(INSTALLDIR) $(PYTHON_DIR)/* $(SPARKY_INSTALL)/python$(PYTHON_VERSION) +-else +- echo "Not packaging Python with Sparky." +-endif ++ cd $(SPARKY) ; $(INSTALL) LICENSE README $(DOCDIR) ++ cd $(DOCDIR) ; chmod 644 LICENSE README + + install-mac: + cd $(SPARKY)/mac && $(MAKE) -f Makefile -e install + +-$(SPARKY_INSTALL) $(SPARKY_INSTALL)/bin $(SPARKY_INSTALL)/python$(PYTHON_VERSION): +- mkdir $@ ++$(SPARKY_INSTALL) $(SPARKY_INSTALL)/bin $(PYDIR): ++ mkdir -p $@ + chmod 755 $@ + + force: +diff -ur -x make-sparky sparky.orig/manual/Makefile sparky/manual/Makefile +--- sparky.orig/manual/Makefile 2004-03-08 15:40:06.000000000 -0800 ++++ sparky/manual/Makefile 2005-12-17 19:37:45.000000000 -0800 +@@ -13,6 +13,8 @@ + + SPARKY_INSTALL = /usr/local/sparky + MANUAL_WWW = /usr/local/html/cgl/sparky/manual ++DOCDIR = $(SPARKY_INSTALL)/share/doc/sparky ++MANUAL_LOC = $(DOCDIR)/manual + + MANUAL_SECTIONS = overview.html intro.html views.html peaks.html \ + extensions.html autoassign.html misc.html \ +@@ -45,17 +47,17 @@ + + all: $(MANUAL_FILES) + +-install: $(MANUAL_FILES) $(SPARKY_INSTALL)/manual \ +- $(SPARKY_INSTALL)/manual/images +- $(INSTALL) $(MANUAL_FILES) $(SPARKY_INSTALL)/manual +- cd $(SPARKY_INSTALL)/manual ; \ ++install: $(MANUAL_FILES) $(MANUAL_LOC) \ ++ $(MANUAL_LOC)/images ++ $(INSTALL) $(MANUAL_FILES) $(MANUAL_LOC) ++ cd $(MANUAL_LOC) ; \ + chmod 644 $(MANUAL_FILES) + cd images ; \ +- $(INSTALL) $(IMAGE_FILES) $(SPARKY_INSTALL)/manual/images +- cd $(SPARKY_INSTALL)/manual/images ; \ ++ $(INSTALL) $(IMAGE_FILES) $(MANUAL_LOC)/images ++ cd $(MANUAL_LOC)/images ; \ + chmod 644 $(IMAGE_FILES) + +-$(SPARKY_INSTALL)/manual $(SPARKY_INSTALL)/manual/images: ++$(MANUAL_LOC) $(MANUAL_LOC)/images: + mkdir $@ + chmod 755 $@ + +Only in sparky/manual: manual-postscript.gz +diff -ur -x make-sparky sparky.orig/python/Makefile sparky/python/Makefile +--- sparky.orig/python/Makefile 2004-02-18 10:51:06.000000000 -0800 ++++ sparky/python/Makefile 2005-12-17 19:43:06.000000000 -0800 +@@ -9,6 +9,8 @@ + PYTHON_VERSION = 2.3 + PYTHON = $(PYTHON_PREFIX)/bin/python$(PYTHON_VERSION) + PYTHON_LIB = $(PYTHON_PREFIX)/lib/python$(PYTHON_VERSION) ++PYDIR = $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages ++DOCDIR = $(SPARKY_INSTALL)/share/doc/sparky + + PYTHON_CODE = __init__.py align.py assigngraph.py atomnames.py \ + atoms.py autoassign.py axes.py \ +@@ -27,18 +29,13 @@ + sputil.py start_in_chimera.py strips.py subprocess.py \ + tkutil.py volumeerror.py xeasy.py xplor.py + +-install: $(SPARKY_INSTALL)/python $(SPARKY_INSTALL)/python/sparky \ +- $(SPARKY_INSTALL)/python/lib-tk +- $(INSTALL) README $(SPARKY_INSTALL)/python +- $(INSTALL) $(PYTHON_CODE) $(SPARKY_INSTALL)/python/sparky +- $(INSTALL) lib-tk/*.py $(SPARKY_INSTALL)/python/lib-tk +- chmod 644 $(SPARKY_INSTALL)/python/README +- cd $(SPARKY_INSTALL)/python/sparky ; chmod 644 $(PYTHON_CODE) +- chmod 644 $(SPARKY_INSTALL)/python/lib-tk/*.py +- $(PYTHON) $(PYTHON_LIB)/compileall.py $(SPARKY_INSTALL)/python/sparky +- $(PYTHON) $(PYTHON_LIB)/compileall.py $(SPARKY_INSTALL)/python/lib-tk ++install: $(PYDIR) $(PYDIR)/sparky $(DOCDIR)/python ++ $(INSTALL) README $(DOCDIR)/python ++ $(INSTALL) $(PYTHON_CODE) $(PYDIR)/sparky ++ chmod 644 $(DOCDIR)/python/README ++ cd $(PYDIR)/sparky ; chmod 644 $(PYTHON_CODE) + +-$(SPARKY_INSTALL)/python $(SPARKY_INSTALL)/python/sparky \ +- $(SPARKY_INSTALL)/python/lib-tk: ++$(PYDIR) $(PYDIR)/sparky \ ++ $(PYDIR)/lib-tk $(DOCDIR)/python: + mkdir $@ + chmod 755 $@ +diff -ur -x make-sparky sparky.orig/python/spingraph.py sparky/python/spingraph.py +--- sparky.orig/python/spingraph.py 2001-12-17 10:51:10.000000000 -0800 ++++ sparky/python/spingraph.py 2005-12-17 22:09:17.000000000 -0800 +@@ -831,7 +831,7 @@ + 'by creating a file specifying atom positions, colors,\n' + + 'sizes, and text label positions. Sparky provides a\n' + + 'default layout file\n' + +- '\n\t/usr/local/sparky/python/spinlayout.py\n\n' + ++ '\n\t/usr/lib/python*/site-packages/sparky/python/spinlayout.py\n\n' + + 'You override this file by making your own copy\n' + + '\n\t~/Sparky/Python/spinlayout.py\n\n' + + 'You can create the desired template on the screen\n' diff --git a/sci-chemistry/sparky/metadata.xml b/sci-chemistry/sparky/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/sparky/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/sparky/sparky-3.115-r1.ebuild b/sci-chemistry/sparky/sparky-3.115-r1.ebuild new file mode 100644 index 000000000000..b28e5351dc5b --- /dev/null +++ b/sci-chemistry/sparky/sparky-3.115-r1.ebuild @@ -0,0 +1,119 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs + +DESCRIPTION="Graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers" +HOMEPAGE="http://www.cgl.ucsf.edu/home/sparky/" +SRC_URI="http://www.cgl.ucsf.edu/home/sparky/distrib-${PV}/${PN}-source-${PV}.tar.gz" + +LICENSE="sparky" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + app-shells/tcsh + dev-lang/tcl:0= + dev-lang/tk:0=" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}/${PN}" + +PATCHES=( + "${FILESDIR}"/${PV}-ldflags.patch + "${FILESDIR}"/${PV}-wrapper-r1.patch + "${FILESDIR}"/${PV}-paths.patch + "${FILESDIR}"/${PV}-makefile.patch + ) + +pkg_setup() { + python-single-r1_pkg_setup + TKVER=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + PYVER=${EPYTHON#python} +} + +src_prepare() { + epatch ${PATCHES[@]} + + sed -i \ + -e "s:^\(set PYTHON =\).*:\1 ${EPREFIX}/usr/bin/${EPYTHON}:g" \ + -e "s:^\(setenv SPARKY_INSTALL[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir)/${PN}:g" \ + -e "s:tcl8.4:tcl${TKVER}:g" \ + -e "s:tk8.4:tk${TKVER}:g" \ + -e "s:^\(setenv TCLTK_LIB[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir):g" \ + "${S}"/bin/sparky || die + eprefixify "${S}"/bin/sparky +} + +src_compile() { + emake \ + SPARKY="${S}" \ + PYTHON_VERSION="${PYVER}" \ + PYTHON_PREFIX="${EPREFIX}/usr" \ + PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \ + PYTHON_INC="${EPREFIX}/usr/include/${EPYTHON}" \ + TK_PREFIX="${EPREFIX}/usr" \ + TCLTK_VERSION="${TKVER}" \ + TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \ + CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + LDSHARED="-shared" \ + binaries + + rm c++/*.o || die + + emake \ + SPARKY="${S}" \ + PYTHON_VERSION="${PYVER}" \ + PYTHON_PREFIX="${EPREFIX}/usr" \ + PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \ + PYTHON_INC="${EPREFIX}/usr/include/${EPYTHON}" \ + TK_PREFIX="${EPREFIX}/usr" \ + TCLTK_VERSION="${TKVER}" \ + TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \ + CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + CXXFLAGS="${CXXFLAGS} -fPIC" \ + CFLAGS="${CFLAGS} -fPIC" \ + LDSHARED="-shared -fPIC" \ + libraries +} + +src_install() { + # The symlinks are needed to avoid hacking the complete code to fix the locations + + dobin c++/{{bruk,matrix,peaks,pipe,vnmr}2ucsf,ucsfdata,sparky-no-python} bin/${PN} + + insinto /usr/share/${PN}/ + doins lib/{print-prolog.ps,Sparky} + dosym ../../share/${PN}/print-prolog.ps /usr/$(get_libdir)/${PN}/print-prolog.ps + dosym ../../share/${PN}/Sparky /usr/$(get_libdir)/${PN}/Sparky + + dohtml -r manual/* + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/manual + + python_moduleinto ${PN} + python_domodule python/*.py c++/{spy.so,_tkinter.so} + + python_optimize + + dosym ../${EPYTHON}/site-packages /usr/$(get_libdir)/${PN}/python + + if use examples; then + insinto /usr/share/doc/${PF}/ + doins -r example || die + dosym ../../share/doc/${PF}/example /usr/$(get_libdir)/${PN}/example + fi + + dodoc README + newdoc python/README README.python +} diff --git a/sci-chemistry/suitename/Manifest b/sci-chemistry/suitename/Manifest new file mode 100644 index 000000000000..eac0c677a2bb --- /dev/null +++ b/sci-chemistry/suitename/Manifest @@ -0,0 +1 @@ +DIST suitename.0.3.070628.src.tgz 29914 SHA256 5c2a709aa2d815b259475344aa2b982c157868eb9a7e5d6407b8f525f7e28c4c diff --git a/sci-chemistry/suitename/metadata.xml b/sci-chemistry/suitename/metadata.xml new file mode 100644 index 000000000000..06ac91e5fb9e --- /dev/null +++ b/sci-chemistry/suitename/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +Suitename is a new C program that supports the ROC RNA Ontology Consortium +consensus RNA backbone nomenclature and conformer-list development (see our RNA +backbone rotamer section. +From dihedral-angle input for a specific RNA structure (usually from Dangle), +Suitename categorizes the RNA backbone geometry of each suite (the +sugar-to-sugar version of a residue) either as an outlier ("!!") or as belonging +to one of the 53 defined conformer bins. The output is either a +one-line-per-suite report, or a linear conformer string (as shown below the +image here) in one of several variant formats. Suitename is built into +MolProbity, producing entries in the multi-criterion chart for an RNA model and +also a suitestring file. The Suitename code is made available here for bulk or +individual command-line use. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/suitename/suitename-0.3.070628.ebuild b/sci-chemistry/suitename/suitename-0.3.070628.ebuild new file mode 100644 index 000000000000..fb11e075c8d6 --- /dev/null +++ b/sci-chemistry/suitename/suitename-0.3.070628.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit toolchain-funcs + +MY_P="${PN}.${PV}" + +DESCRIPTION="The ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/suitename.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${MY_P}.src.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="richardson" +IUSE="" + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + tc-export CC + cp Makefile.linux Makefile || die + sed \ + -e 's:cc:${CC}:g' \ + -e "s:-o:${LDFLAGS} -o:g" \ + -i Makefile || die +} + +src_compile() { + emake CFLAGS="${CFLAGS}" +} + +src_install() { + dobin ${PN} +} diff --git a/sci-chemistry/surf/Manifest b/sci-chemistry/surf/Manifest new file mode 100644 index 000000000000..7e50ca58e561 --- /dev/null +++ b/sci-chemistry/surf/Manifest @@ -0,0 +1 @@ +DIST surf-1.0.tar.Z 74347 SHA256 6d032e4b749e5e1971b5d97b0fcf552029068a87bcaebd6ce92db27179f7cb0a diff --git a/sci-chemistry/surf/metadata.xml b/sci-chemistry/surf/metadata.xml new file mode 100644 index 000000000000..9ac9ffdb3a41 --- /dev/null +++ b/sci-chemistry/surf/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/surf/surf-1.0.ebuild b/sci-chemistry/surf/surf-1.0.ebuild new file mode 100644 index 000000000000..eadfa758a755 --- /dev/null +++ b/sci-chemistry/surf/surf-1.0.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="4" + +inherit toolchain-funcs + +DESCRIPTION="Solvent accesible Surface calculator" +HOMEPAGE="http://www.ks.uiuc.edu/" +SRC_URI="http://www.ks.uiuc.edu/Research/vmd/extsrcs/surf.tar.Z -> ${P}.tar.Z" + +LICENSE="SURF" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="" + +DEPEND=" + !www-client/surf + sys-apps/ed + x11-misc/makedepend" +RDEPEND="" + +S=${WORKDIR} + +src_prepare() { + sed \ + -e 's:$(CC) $(CFLAGS) $(OBJS):$(CC) $(CFLAGS) $(LDFLAGS) $(OBJS):g' \ + -i Makefile || die +} + +src_compile() { + emake depend \ + && emake \ + CC="$(tc-getCC)" \ + OPT_CFLAGS="${CFLAGS} \$(INCLUDE)" \ + CFLAGS="${CFLAGS} \$(INCLUDE)" \ + || die +} + +src_install() { + dobin ${PN} || die + dodoc README || die +} diff --git a/sci-chemistry/theseus/Manifest b/sci-chemistry/theseus/Manifest new file mode 100644 index 000000000000..9708bc4e5cf6 --- /dev/null +++ b/sci-chemistry/theseus/Manifest @@ -0,0 +1,3 @@ +DIST theseus_2.0.6.tar.gz 1257560 SHA256 f63f4d5fd9ce9d30048312e31807a1a413b433e2bbcfd0cefb3703f455551c23 SHA512 70604c468eb841b92e77a3e91cd57120b96c171512fb1cc31a407b7c4816150dfa31ec123fb9568a842e623f3252c60df0dc53d40fa2a4aece6e3c77039f4696 WHIRLPOOL 01c73e5bec0f4e9a98cd926a15f3213f30d20db10a500e88cfa54e31b92324d3fb741899c30c5c45e8d5a2d31eb68e742113b29a077f70430cf7acda9c02bc54 +DIST theseus_3.0.0.tar.gz 1213574 SHA256 4e474efabf1cfc9a48e96e86ac9e5b0f8035b57677017542e66478759bdc7866 SHA512 251e6273624126406609691e1205d9693c18dcbc8c81e10c77101ac4a1b6bdffcb56a47fd5fdc7ed6ed4fa107c2ed26b03a1780f951f9cc69a25c0722996e7b2 WHIRLPOOL 5a15c0f5270411114ebbca4fc9cad1e4db0449d1e6d8d1693f1e58d6a54f61b401cc6a2df2539d2ca34dd4dc52a09e1c45c0af8b80eb5c8916d8f168bf536ad3 +DIST theseus_3.3.0.tar.gz 22548124 SHA256 3cfd4f906717f9cb8e77f689fc97059b32df355c0696077034ea99a485e3f2fe SHA512 1fba3e8019a40214defdae13d4721d170ee698337d8efd4e872af22f8ab3cb1fdd52fa9f19a858ee51bc98150692af0c6016033feb0d76f29acaf7fffbb430e2 WHIRLPOOL c1baf4daea1e2a0c78b73d8d91ff735aa9bb82bd6edf533aab0f9d20a9e82b7f61fdf8c4b09c92b58447f686e954b6eaf7f02d7c9e5304c8d52b4c09b6d323af diff --git a/sci-chemistry/theseus/metadata.xml b/sci-chemistry/theseus/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/theseus/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/theseus/theseus-2.0.6.ebuild b/sci-chemistry/theseus/theseus-2.0.6.ebuild new file mode 100644 index 000000000000..56d58ae9fb9e --- /dev/null +++ b/sci-chemistry/theseus/theseus-2.0.6.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit multilib toolchain-funcs + +DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures" +HOMEPAGE="http://www.theseus3d.org/" +SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-libs/gsl + || ( + sci-biology/muscle + sci-biology/probcons + sci-biology/mafft + sci-biology/t-coffee + sci-biology/kalign + sci-biology/clustalw:2 + )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}"/${PN}_src/ + +src_prepare() { + cat >> make.inc <<- EOF + ARCH = $(tc-getAR) + ARCHFLAGS = -rvs + RANLIB = $(tc-getRANLIB) + LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir) + SYSLIBS = $(pkg-config --libs gsl) -lpthread + LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus + LIBDIR = -L./lib + INSTALLDIR = "${ED}"/usr/bin + OPT = + WARN = + CFLAGS = ${CFLAGS} \$(WARN) + CC = $(tc-getCC) + EOF + + sed \ + -e 's|theseus:|theseus: libs|g' \ + -e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \ + -i Makefile || die + + sed \ + -e 's:/usr/bin/sed:sed:g' \ + -e "s:/usr/local/bin/:/usr/bin/:g" \ + -e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \ + -i theseus_align || die +} + +src_install() { + dobin theseus theseus_align + dodoc theseus_man.pdf README AUTHORS + use examples && insinto /usr/share/${PN} && doins -r examples +} diff --git a/sci-chemistry/theseus/theseus-3.0.0.ebuild b/sci-chemistry/theseus/theseus-3.0.0.ebuild new file mode 100644 index 000000000000..ed80be95d26b --- /dev/null +++ b/sci-chemistry/theseus/theseus-3.0.0.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit multilib toolchain-funcs + +DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures" +HOMEPAGE="http://www.theseus3d.org/" +SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-libs/gsl + || ( + sci-biology/muscle + sci-biology/probcons + sci-biology/mafft + sci-biology/t-coffee + sci-biology/kalign + sci-biology/clustalw:2 + )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}"/${PN}_src/ + +src_prepare() { + cat >> make.inc <<- EOF + ARCH = $(tc-getAR) + ARCHFLAGS = -rvs + RANLIB = $(tc-getRANLIB) + LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir) + SYSLIBS = $(pkg-config --libs gsl) -lpthread + LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus + LIBDIR = -L./lib + INSTALLDIR = "${ED}"/usr/bin + OPT = + WARN = + CFLAGS = ${CFLAGS} -std=c11 \$(WARN) + CC = $(tc-getCC) + EOF + + sed \ + -e 's|theseus:|theseus: libs|g' \ + -e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \ + -i Makefile || die + + sed \ + -e 's:/usr/bin/sed:sed:g' \ + -e "s:/usr/local/bin/:/usr/bin/:g" \ + -e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \ + -i theseus_align || die +} + +src_compile () { + emake ltheseus + default +} + +src_install() { + dobin theseus theseus_align + dodoc theseus_man.pdf README AUTHORS + use examples && insinto /usr/share/${PN} && doins -r examples +} diff --git a/sci-chemistry/theseus/theseus-3.3.0.ebuild b/sci-chemistry/theseus/theseus-3.3.0.ebuild new file mode 100644 index 000000000000..ed80be95d26b --- /dev/null +++ b/sci-chemistry/theseus/theseus-3.3.0.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit multilib toolchain-funcs + +DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures" +HOMEPAGE="http://www.theseus3d.org/" +SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-libs/gsl + || ( + sci-biology/muscle + sci-biology/probcons + sci-biology/mafft + sci-biology/t-coffee + sci-biology/kalign + sci-biology/clustalw:2 + )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}"/${PN}_src/ + +src_prepare() { + cat >> make.inc <<- EOF + ARCH = $(tc-getAR) + ARCHFLAGS = -rvs + RANLIB = $(tc-getRANLIB) + LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir) + SYSLIBS = $(pkg-config --libs gsl) -lpthread + LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus + LIBDIR = -L./lib + INSTALLDIR = "${ED}"/usr/bin + OPT = + WARN = + CFLAGS = ${CFLAGS} -std=c11 \$(WARN) + CC = $(tc-getCC) + EOF + + sed \ + -e 's|theseus:|theseus: libs|g' \ + -e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \ + -i Makefile || die + + sed \ + -e 's:/usr/bin/sed:sed:g' \ + -e "s:/usr/local/bin/:/usr/bin/:g" \ + -e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \ + -i theseus_align || die +} + +src_compile () { + emake ltheseus + default +} + +src_install() { + dobin theseus theseus_align + dodoc theseus_man.pdf README AUTHORS + use examples && insinto /usr/share/${PN} && doins -r examples +} diff --git a/sci-chemistry/threeV/Manifest b/sci-chemistry/threeV/Manifest new file mode 100644 index 000000000000..87b89d3f552f --- /dev/null +++ b/sci-chemistry/threeV/Manifest @@ -0,0 +1 @@ +DIST 3v-1.2.tgz 599194 RMD160 133d770fd2c7c353b05db74594998954be92e9a0 SHA1 86895fb5c33360db2c30cec258dacbc01f39638a SHA256 ae11ce61e6b7cac6aa07d91914b59507a04a1dbfbe624ed8356154cbabc6e8af diff --git a/sci-chemistry/threeV/files/1.2-gentoo.patch b/sci-chemistry/threeV/files/1.2-gentoo.patch new file mode 100644 index 000000000000..0827551599ba --- /dev/null +++ b/sci-chemistry/threeV/files/1.2-gentoo.patch @@ -0,0 +1,107 @@ +diff --git a/src/Makefile b/src/Makefile +index a58462c..616f51a 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -1,7 +1,7 @@ +-CC = g++ +-EXT=$(shell ./cpuflags.pl --opt ) +-FLAGS = -Wall $(EXT) +-#FLAGS = -O3 -Wall -ffast-math ++CXX ?= g++ ++#EXT=$(shell ./cpuCXXFLAGS.pl --opt ) ++#CXXFLAGS = -Wall $(EXT) ++#CXXFLAGS = -O3 -Wall -ffast-math + OBJS = utils-main.o utils-output.o utils-mrc.o + + all: cav chan fsv sol tun vdw vol +@@ -17,54 +17,65 @@ volume: vol + objects: utils-main.o utils-output.o utils-mrc.o + + cav: objects cavities.cpp +- $(CC) $(FLAGS) -o Cavities.exe $(OBJS) cavities.cpp +- chmod 777 Cavities.exe +- mv Cavities.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o cavities.o cavities.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o Cavities $(OBJS) cavities.o ++ chmod 755 Cavities ++ mv Cavities ../bin + + chan: objects channel.cpp +- $(CC) $(FLAGS) -o Channel.exe $(OBJS) channel.cpp +- chmod 777 Channel.exe +- mv Channel.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o channel.o channel.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o Channel $(OBJS) channel.o ++ chmod 755 Channel ++ mv Channel ../bin + + fsv: objects fsv_calc.cpp +- $(CC) $(FLAGS) -o FsvCalc.exe $(OBJS) fsv_calc.cpp +- chmod 777 FsvCalc.exe +- mv FsvCalc.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o fsv_calc.o fsv_calc.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o FsvCalc $(OBJS) fsv_calc.o ++ chmod 755 FsvCalc ++ mv FsvCalc ../bin + + sol: objects solvent.cpp +- $(CC) $(FLAGS) -o Solvent.exe $(OBJS) solvent.cpp +- chmod 777 Solvent.exe +- mv Solvent.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o solvent.o solvent.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o Solvent $(OBJS) solvent.o ++ chmod 755 Solvent ++ mv Solvent ../bin + + tun: objects tunnel.cpp +- $(CC) $(FLAGS) -o Tunnel.exe $(OBJS) tunnel.cpp +- chmod 777 Tunnel.exe +- mv Tunnel.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o tunnel.o tunnel.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o Tunnel $(OBJS) tunnel.o ++ chmod 755 Tunnel ++ mv Tunnel ../bin + + vdw: objects vdw.cpp +- $(CC) $(FLAGS) -o VDW.exe $(OBJS) vdw.cpp +- chmod 777 VDW.exe +- mv VDW.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o vdw.o vdw.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o VDW $(OBJS) vdw.o ++ chmod 755 VDW ++ mv VDW ../bin + + vol: objects volume.cpp +- $(CC) $(FLAGS) -o Volume.exe $(OBJS) volume.cpp +- chmod 777 Volume.exe +- mv Volume.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o volume.o volume.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o Volume $(OBJS) volume.o ++ chmod 755 Volume ++ mv Volume ../bin + + utils-main.o: utils-main.cpp +- $(CC) $(FLAGS) -c -o utils-main.o utils-main.cpp ++ $(CXX) $(CXXFLAGS) -c -o utils-main.o utils-main.cpp + + utils-output.o: utils-main.o utils-output.cpp +- $(CC) $(FLAGS) -c -o utils-output.o utils-output.cpp ++ $(CXX) $(CXXFLAGS) -c -o utils-output.o utils-output.cpp + + utils-mrc.o: utils-mrc.cpp +- $(CC) $(FLAGS) -c -o utils-mrc.o utils-mrc.cpp ++ $(CXX) $(CXXFLAGS) -c -o utils-mrc.o utils-mrc.cpp ++ ++install: ++ install -d $(DESTDIR)/usr/bin ++ install ../bin/* $(DESTDIR)/usr/bin/ + + clean: + rm -fv *.o *~ + + distclean: +- rm -fv *.o ../bin/*.exe *~ ++ rm -fv *.o ../bin/* *~ + + none: + echo "Please type make xxx, where xxx = cav, cha, fsv, sol, tun, vdw, or vol" diff --git a/sci-chemistry/threeV/metadata.xml b/sci-chemistry/threeV/metadata.xml new file mode 100644 index 000000000000..043cc7527474 --- /dev/null +++ b/sci-chemistry/threeV/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +<maintainer> + <email>jlec@gentoo.org</email> +</maintainer> +</pkgmetadata> diff --git a/sci-chemistry/threeV/threeV-1.2.ebuild b/sci-chemistry/threeV/threeV-1.2.ebuild new file mode 100644 index 000000000000..7aaa18bba004 --- /dev/null +++ b/sci-chemistry/threeV/threeV-1.2.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit eutils toolchain-funcs + +DESCRIPTION="3V: Voss Volume Voxelator" +HOMEPAGE="http://geometry.molmovdb.org/3v/" +SRC_URI="http://geometry.molmovdb.org/3v/3v-${PV}.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +PDEPEND="sci-chemistry/msms-bin" +# sci-chemistry/usf-rave" + +S="${WORKDIR}/3v-${PV}/src" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + tc-export CXX + emake distclean || die +} + +src_install() { + emake DESTDIR="${ED}" install || die + + cd .. + dodoc AUTHORS ChangeLog QUICKSTART README TODO VERSION || die +} diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest new file mode 100644 index 000000000000..1628482e5af4 --- /dev/null +++ b/sci-chemistry/tinker/Manifest @@ -0,0 +1 @@ +DIST tinker-7.1.2.tar.gz 28468683 SHA256 fdee18915cff9044fd083bb2271083c221db6d05de2cb98fc111b136e23e6899 SHA512 4524259754b0f11d7e2e8997ebd85eae7d28f8dbb1edb2d9818aa0a96640de0049aa4937236694f1a11743dee187d612f775b233a73cc96c2708d620457a7dc2 WHIRLPOOL f3e29eaf67d25ae6d4f3c4e3546798e66bd626929fddd45b9d1ff9f2143cd57dcc5079226f3ceaa142f4c6a168c4a150a51be1336a5ca13384338795ef3a6d46 diff --git a/sci-chemistry/tinker/files/5.1.09-Makefile.patch b/sci-chemistry/tinker/files/5.1.09-Makefile.patch new file mode 100644 index 000000000000..68a095add706 --- /dev/null +++ b/sci-chemistry/tinker/files/5.1.09-Makefile.patch @@ -0,0 +1,13 @@ +diff --git a/make/Makefile b/make/Makefile +index 221ab45..7634474 100644 +--- a/make/Makefile ++++ b/make/Makefile +@@ -607,7 +607,7 @@ clean: + listing: + cat *.i *.f > tinker.txt + +-rename: ++rename: ${EXEFILES} + mv alchemy.x $(BINDIR)/alchemy + mv analyze.x $(BINDIR)/analyze + mv anneal.x $(BINDIR)/anneal diff --git a/sci-chemistry/tinker/files/6-openmp.patch b/sci-chemistry/tinker/files/6-openmp.patch new file mode 100644 index 000000000000..3666fbd0bfc4 --- /dev/null +++ b/sci-chemistry/tinker/files/6-openmp.patch @@ -0,0 +1,15 @@ +diff --git a/source/initial.f b/source/initial.f +index 835f228..4099c74 100644 +--- a/source/initial.f ++++ b/source/initial.f +@@ -73,8 +73,8 @@ c + c + c Intel compiler extensions to OpenMP standard + c +-!$ call kmp_set_stacksize (2**30) +-!$ call kmp_set_blocktime (0) ++! call kmp_set_stacksize (2**30) ++! call kmp_set_blocktime (0) + c + c values of machine precision constants + c diff --git a/sci-chemistry/tinker/files/7.1.2-openmp.patch b/sci-chemistry/tinker/files/7.1.2-openmp.patch new file mode 100644 index 000000000000..f3e8e2932b4a --- /dev/null +++ b/sci-chemistry/tinker/files/7.1.2-openmp.patch @@ -0,0 +1,15 @@ +diff --git a/source/initial.f b/source/initial.f +index 835f228..4099c74 100644 +--- a/source/initial.f ++++ b/source/initial.f +@@ -73,8 +73,8 @@ c + c + c Intel compiler extensions to OpenMP standard + c +-!$ call kmp_set_stacksize_s (2**28) +-!$ call kmp_set_blocktime (0) ++! call kmp_set_stacksize_s (2**28) ++! call kmp_set_blocktime (0) + c + c values of machine precision constants + c diff --git a/sci-chemistry/tinker/files/tinker-7.1.2-build.patch b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch new file mode 100644 index 000000000000..d6ef484b19a4 --- /dev/null +++ b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch @@ -0,0 +1,17 @@ + make/Makefile | 3 +-- + 1 file changed, 1 insertion(+), 2 deletions(-) + +diff --git a/make/Makefile b/make/Makefile +index 61d5037..9be384a 100644 +--- a/make/Makefile ++++ b/make/Makefile +@@ -719,8 +719,7 @@ EXEFILES = alchemy.x \ + %.x: %.o libtinker.a + ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@ + +-all: +- ${EXEFILES} ++all: ${EXEFILES} + + install: + rename diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml new file mode 100644 index 000000000000..e42d0af60f42 --- /dev/null +++ b/sci-chemistry/tinker/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/tinker/tinker-7.1.2.ebuild b/sci-chemistry/tinker/tinker-7.1.2.ebuild new file mode 100644 index 000000000000..e81b4a6b6a1d --- /dev/null +++ b/sci-chemistry/tinker/tinker-7.1.2.ebuild @@ -0,0 +1,104 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs + +DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM" +HOMEPAGE="http://dasher.wustl.edu/tinker/" +SRC_URI="http://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz" + +SLOT="0" +LICENSE="Tinker" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +DEPEND=" + >=virtual/jdk-1.6" +RDEPEND=" + >=sci-libs/fftw-3.2.2-r1[fortran,threads] + dev-libs/maloc + !dev-util/diffuse + >=virtual/jre-1.6" + +RESTRICT="mirror" + +S="${WORKDIR}"/${PN}/source + +pkg_setup() { + fortran-2_pkg_setup + java-pkg-opt-2_pkg_setup + tc-has-openmp || die "Please use an openmp capable compiler like gcc[openmp]" +} + +src_prepare() { + sed 's:strip:true:g' -i ../make/Makefile + [[ $(tc-getFC) =~ "ifort" ]] || epatch "${FILESDIR}"/${PV}-openmp.patch + cd .. && epatch "${FILESDIR}"/${P}-build.patch +} + +src_compile() { + local javalib= + for i in $(java-config -g LDPATH | sed 's|:| |g'); do + [[ -f ${i}/libjvm.so ]] && javalib=${i} + done + + # use dummy routines in pmpb.f instead of apbs calls + rm pmpb.c || die + + if [[ $(tc-getFC) =~ "gfortran" ]]; then + append-flags -fopenmp + _omplib="-lgomp" + else + append-flags -openmp + _omplib="-liomp5" + fi + + _fftwlib="$($(tc-getPKG_CONFIG) --libs fftw3 fftw3_threads)" + + emake \ + -f ../make/Makefile \ + F77="$(tc-getFC)" \ + CC="$(tc-getCC) -c" \ + F77FLAGS=-c \ + OPTFLAGS="${FFLAGS}" \ + LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \ + INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \ + LIBS="-lmaloc -L${javalib} -ljvm ${_omplib} ${_fftwlib}" \ + all + + mkdir "${S}"/../bin || die + + emake \ + -f ../make/Makefile \ + BINDIR="${S}"/../bin \ + rename +} + +src_test() { + cd "${WORKDIR}"/${PN}/test/ + for test in *.run; do + einfo "Testing ${test} ..." + bash ${test} || die + done +} + +src_install() { + dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/* + + insinto /usr/share/${PN}/ + doins -r "${WORKDIR}"/${PN}/params + + dodoc \ + "${WORKDIR}"/${PN}/doc/{*.txt,*.pdf,0README} + + if use examples; then + insinto /usr/share/${P} + doins -r "${WORKDIR}"/${PN}/example + + doins -r "${WORKDIR}"/${PN}/test + fi + +} diff --git a/sci-chemistry/tm-align/Manifest b/sci-chemistry/tm-align/Manifest new file mode 100644 index 000000000000..d9e8dc8632b3 --- /dev/null +++ b/sci-chemistry/tm-align/Manifest @@ -0,0 +1 @@ +DIST TMtools20140601.tar.gz 934391 SHA256 5032f7ab1824c8b2191b4a3667e1405feb6ccf7c900f57632aa506fff8ec1bf5 SHA512 99b90425ff051c836e19225601ddfb1576bec9c8f233aafeba96075f924a3c0892b5b1cfef36254ff5ef468a6dbf64f7fcc9a3ce24a0d869b3c1eb87c0149765 WHIRLPOOL 5ba7d9cb71e3055dff62851c68e127314b9ca70c4bbc39aeba35e5a4b02dc0cffeacb52c6369c90875d8062603c830acf604cfc339bdecfeb3dd6c10015e20de diff --git a/sci-chemistry/tm-align/files/CMakeLists.txt b/sci-chemistry/tm-align/files/CMakeLists.txt new file mode 100644 index 000000000000..506ef136309e --- /dev/null +++ b/sci-chemistry/tm-align/files/CMakeLists.txt @@ -0,0 +1,6 @@ +cmake_minimum_required (VERSION 2.6) +project (TMTools Fortran) +add_executable(TMalign TMalign.f) +add_executable(TMscore TMscore.f) + +install (TARGETS TMalign TMscore DESTINATION bin) diff --git a/sci-chemistry/tm-align/metadata.xml b/sci-chemistry/tm-align/metadata.xml new file mode 100644 index 000000000000..1e724495b8e2 --- /dev/null +++ b/sci-chemistry/tm-align/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +TM-align is a computer algorithm for protein structure alignment using dynamic +programming and TM-score rotation matrix. An optimal alignment between two +proteins, as well as the TM-score, will be reported for each comparison. The +value of TM-score lies in (0,1]. In general, a comparison of TM-score smaller +0.2 indicates that there is no similarity between two structures; a TM-score +greater 0.5 means the structures share the same fold. + +What is the difference between TM-score and TM-align? The TM-score program +is to compare two models based on their given and known residue equivalency. +It is usually NOT applied to compare two proteins of different sequences. The +TM-align is a structural alignment program for comparing two proteins whose +sequences can be different. The TM-align will first find the best equivalent +residues of two proteins based on the structure similarity and then output a +TM-score. The TM-score values in both programs have the same definition. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/tm-align/tm-align-20140601.ebuild b/sci-chemistry/tm-align/tm-align-20140601.ebuild new file mode 100644 index 000000000000..e7718e305db1 --- /dev/null +++ b/sci-chemistry/tm-align/tm-align-20140601.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils flag-o-matic fortran-2 + +DESCRIPTION="Quick & Accurate Structural Alignment" +HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/TM-align/" +SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz" + +LICENSE="tm-align" +SLOT="0" +KEYWORDS="amd64 ppc ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="static custom-cflags" + +S="${WORKDIR}" + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + use static && append-fflags -static && append-ldflags -static + # recommended by upstream + use custom-cflags || replace-flags -O* -O3 && append-fflags -ffast-math +} diff --git a/sci-chemistry/viewmol/Manifest b/sci-chemistry/viewmol/Manifest new file mode 100644 index 000000000000..42b77e70d864 --- /dev/null +++ b/sci-chemistry/viewmol/Manifest @@ -0,0 +1 @@ +DIST viewmol-2.4.1.src.tgz 2229379 SHA256 dfed3eed6441d89c4bf2be1c13cbe263341c8880edf1742d446fc0f8f4a99e19 diff --git a/sci-chemistry/viewmol/files/2.4.1-change-default-path-to-usr.patch b/sci-chemistry/viewmol/files/2.4.1-change-default-path-to-usr.patch new file mode 100644 index 000000000000..e5e22ffee893 --- /dev/null +++ b/sci-chemistry/viewmol/files/2.4.1-change-default-path-to-usr.patch @@ -0,0 +1,11 @@ +--- viewmol-2.4.1.orig/source/getrc.c 2004-10-20 05:54:35.000000000 -0700 ++++ viewmol-2.4.1/source/getrc.c 2005-12-02 11:38:32.000000000 -0800 +@@ -87,7 +87,7 @@ + + static char viewmolpath[MAXLENLINE]; + +-#define DEFAULTPATH "/usr/local/lib/viewmol" ++#define DEFAULTPATH "/usr/lib/viewmol" + + int getrc(void) + { diff --git a/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch b/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch new file mode 100644 index 000000000000..16a3d7ef7e38 --- /dev/null +++ b/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch @@ -0,0 +1,68 @@ +diff --git a/source/getrc.c b/source/getrc.c +index a39b436..c130096 100644 +--- a/source/getrc.c ++++ b/source/getrc.c +@@ -87,7 +87,7 @@ extern XtAppContext app; + + static char viewmolpath[MAXLENLINE]; + +-#define DEFAULTPATH "/usr/local/lib/viewmol" ++#define DEFAULTPATH "@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR/viewmol" + + int getrc(void) + { +diff --git a/source/install b/source/install +index 580865b..f136af3 100755 +--- a/source/install ++++ b/source/install +@@ -54,24 +54,27 @@ fi + cp $dirorig/viewmol $ROOT/bin + chmod 711 $ROOT/bin/viewmol + +-# install other files needed in $ROOT/lib/viewmol +-if [ ! -d $ROOT/lib/viewmol/$dir ] ++# install other files needed in $ROOT/GENTOOLIBDIR/viewmol ++if [ ! -d $ROOT/GENTOOLIBDIR/viewmol/$dir ] + then +- mkdir -p $ROOT/lib/viewmol/$dir +- chmod 755 $ROOT/lib/viewmol/$dir ++ mkdir -p $ROOT/GENTOOLIBDIR/viewmol/$dir ++ chmod 755 $ROOT/GENTOOLIBDIR/viewmol/$dir + fi + cd $dirorig +-cp tm bio readgamess readgauss readmopac readpdb $ROOT/lib/viewmol/$dir +-chmod 711 $ROOT/lib/viewmol/$dir/* ++cp tm bio readgamess readgauss readmopac readpdb $ROOT/GENTOOLIBDIR/viewmol/$dir ++chmod 711 $ROOT/GENTOOLIBDIR/viewmol/$dir/* + cd ../.. +-cp readdmol readdmol.awk readgulp readpqs writecar writegauss.py writemol writetm $ROOT/lib/viewmol +-chmod 755 $ROOT/lib/viewmol/* +-cp -r doc examples locale scripts tests $ROOT/lib/viewmol +-find $ROOT/lib/viewmol -type f -exec chmod a+r {} \; +-find $ROOT/lib/viewmol -type d -exec chmod a+rx {} \; +-sed 's/\/source//g' viewmolrc > $ROOT/lib/viewmol/viewmolrc +-chmod -R 644 $ROOT/lib/viewmol/viewmolrc +-if [ -d /usr/X11R6/lib/X11/app-defaults ] ++cp readdmol readdmol.awk readgulp readpqs writecar writegauss.py writemol writetm $ROOT/GENTOOLIBDIR/viewmol ++chmod 755 $ROOT/GENTOOLIBDIR/viewmol/* ++mkdir -p $ROOT/usr/share/viewmol $ROOT/usr/share/doc/GENTOODOCDIR/ $ROOT/GENTOOLIBDIR/viewmol/ ++cp -r examples scripts tests $ROOT/usr/share/viewmol ++cp -r locale $ROOT/GENTOOLIBDIR/viewmol/ ++cp -r doc/* examples scripts tests $ROOT/usr/share/doc/GENTOODOCDIR/ ++find $ROOT/GENTOOLIBDIR/viewmol -type f -exec chmod a+r {} \; ++find $ROOT/GENTOOLIBDIR/viewmol -type d -exec chmod a+rx {} \; ++sed 's/\/source//g' viewmolrc > $ROOT/GENTOOLIBDIR/viewmol/viewmolrc ++chmod -R 644 $ROOT/GENTOOLIBDIR/viewmol/viewmolrc ++if [ -d $ROOT/X11R6/GENTOOLIBDIR/X11/app-defaults ] + then + locale=`echo $LANG | cut -c1-2` + if [ "$locale" = "en" ] +@@ -82,6 +85,6 @@ then + # The C locale is defined by default for rpm builds, overwrite it + locale="en_US" + fi +- cp locale/${locale}/Viewmol /usr/X11R6/lib/X11/app-defaults +- chmod a+r /usr/X11R6/lib/X11/app-defaults/Viewmol ++ cp locale/${locale}/Viewmol ${ROOT}/X11R6/GENTOOLIBDIR/X11/app-defaults ++ chmod a+r ${ROOT}/X11R6/GENTOOLIBDIR/X11/app-defaults/Viewmol + fi diff --git a/sci-chemistry/viewmol/files/2.4.1-look-for-python-in-right-place.patch b/sci-chemistry/viewmol/files/2.4.1-look-for-python-in-right-place.patch new file mode 100644 index 000000000000..4f981a0fd1cb --- /dev/null +++ b/sci-chemistry/viewmol/files/2.4.1-look-for-python-in-right-place.patch @@ -0,0 +1,20 @@ +--- viewmol-2.4.1.orig/source/getmachine 2004-08-29 08:04:09.000000000 -0700 ++++ viewmol-2.4.1/source/getmachine 2005-12-02 11:19:36.000000000 -0800 +@@ -156,7 +158,7 @@ + echo "PNGINCLUDE = $pnginclude" >> .config.$os + + # Python +- list=`find /usr -name Python.h -print 2> /dev/null` ++ list=`find /usr/include -name Python.h -print 2> /dev/null` + version=`(for i in $list + do + dir=\`dirname $i\` +@@ -179,7 +181,7 @@ + echo "PYTHONINCLUDE = $pythoninclude" >> .config.$os + if [ "$version" != "" ] + then +- pythonlib=`dirname \`find /usr -name "lib${version}*.a" -print 2> /dev/null | grep "$version/"\`` ++ pythonlib=`dirname \`find /usr/lib -name "lib${version}*.a" -print 2> /dev/null | grep "$version/"\`` + else + givehint + echo -n "Please enter the name of the directory where the Python library can be found: " diff --git a/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch b/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch new file mode 100644 index 000000000000..c328e9cc79ab --- /dev/null +++ b/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch @@ -0,0 +1,23 @@ +diff -urN viewmol-2.4.1.orig/source/getmachine viewmol-2.4.1/source/getmachine +--- viewmol-2.4.1.orig/source/getmachine 2004-08-29 08:04:09.000000000 -0700 ++++ viewmol-2.4.1/source/getmachine 2005-12-02 09:30:49.000000000 -0800 +@@ -269,19 +269,11 @@ + makedir + cat ../.config.$os > makefile + use_icc=`type icc 2> /dev/null` +- if [ "$use_icc" = "" ] +- then + findProcessor + echo 'COMPILER=gcc' >> makefile + echo "OPT=-O6 -mcpu=$processor -fomit-frame-pointer -ffast-math -malign-double" >> makefile + echo 'CFLAGS=-Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing' >> makefile + echo "LDFLAGS=$LINKFORSHARED" >> makefile +- else +- echo 'COMPILER=icc' >> makefile +- echo 'OPT=-O2 -ipo' >> makefile +- echo 'CFLAGS=-I/opt/intel/compiler50/ia32/include -I/usr/X11R6/include -DLINUX' >> makefile +- echo "LDFLAGS=$LINKFORSHARED -ipo" >> makefile +- fi + echo 'SCANDIR=' >> makefile + echo 'INCLUDE=$(TIFFINCLUDE) -I$(PNGINCLUDE) -I$(PYTHONINCLUDE)' >> makefile + echo 'LIBRARY=$(LIBTIFF) $(LIBPNG) -L$(LIBPYTHON)' >> makefile diff --git a/sci-chemistry/viewmol/files/2.4.1-use-root-for-app-defaults.patch b/sci-chemistry/viewmol/files/2.4.1-use-root-for-app-defaults.patch new file mode 100644 index 000000000000..c04da305c144 --- /dev/null +++ b/sci-chemistry/viewmol/files/2.4.1-use-root-for-app-defaults.patch @@ -0,0 +1,20 @@ +--- viewmol-2.4.1.orig/source/install 2004-10-09 08:38:31.000000000 -0700 ++++ viewmol-2.4.1/source/install 2005-12-02 11:34:35.000000000 -0800 +@@ -71,7 +71,7 @@ + find $ROOT/lib/viewmol -type d -exec chmod a+rx {} \; + sed 's/\/source//g' viewmolrc > $ROOT/lib/viewmol/viewmolrc + chmod -R 644 $ROOT/lib/viewmol/viewmolrc +-if [ -d /usr/X11R6/lib/X11/app-defaults ] ++if [ -d $ROOT/X11R6/lib/X11/app-defaults ] + then + locale=`echo $LANG | cut -c1-2` + if [ "$locale" = "en" ] +@@ -82,6 +82,6 @@ + # The C locale is defined by default for rpm builds, overwrite it + locale="en_US" + fi +- cp locale/${locale}/Viewmol /usr/X11R6/lib/X11/app-defaults +- chmod a+r /usr/X11R6/lib/X11/app-defaults/Viewmol ++ cp locale/${locale}/Viewmol $ROOT/X11R6/lib/X11/app-defaults ++ chmod a+r $ROOT/X11R6/lib/X11/app-defaults/Viewmol + fi diff --git a/sci-chemistry/viewmol/metadata.xml b/sci-chemistry/viewmol/metadata.xml new file mode 100644 index 000000000000..c23d7012cd04 --- /dev/null +++ b/sci-chemistry/viewmol/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">viewmol</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/viewmol/viewmol-2.4.1-r2.ebuild b/sci-chemistry/viewmol/viewmol-2.4.1-r2.ebuild new file mode 100644 index 000000000000..33fcaab73c3a --- /dev/null +++ b/sci-chemistry/viewmol/viewmol-2.4.1-r2.ebuild @@ -0,0 +1,87 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="2" +PYTHON_USE_WITH="tk" + +inherit eutils multilib prefix python toolchain-funcs + +DESCRIPTION="Open-source graphical front end for computational chemistry programs" +HOMEPAGE="http://viewmol.sourceforge.net/" +SRC_URI="mirror://sourceforge/viewmol/${P}.src.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + media-libs/libpng + media-libs/tiff + virtual/glu + virtual/opengl + x11-libs/libX11 + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXt + >=x11-libs/motif-2.3:0" +DEPEND="${RDEPEND} + x11-proto/inputproto + x11-proto/xproto" + +S="${WORKDIR}/${P}/source" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-remove-icc-check.patch \ + "${FILESDIR}"/${PV}-change-default-paths.patch + + eprefixify getrc.c + sed "s:GENTOOLIBDIR:$(get_libdir):g" \ + -i install getrc.c || die + sed "s:GENTOODOCDIR:${PF}:g" -i install || die + + LINKFORSHARED=$($(PYTHON) -c "import distutils.sysconfig; print distutils.sysconfig.get_config_var('LINKFORSHARED')") + + mkdir $(uname -s) && cd $(uname -s) + + cat >> .config.$(uname -s) <<- EOF + LIBTIFF = -L"${EPREFIX}/usr/$(get_libdir)" + TIFFINCLUDE = "${EPREFIX}/usr/include" + LIBPNG = -L"${EPREFIX}/usr/$(get_libdir)" + PNGINCLUDE = "${EPREFIX}/usr/include" + PYTHONVERSION = $(PYTHON) + PYTHONINCLUDE = "${EPREFIX}/$(python_get_includedir)" + PYTHONLIB = "${EPREFIX}/usr/$(get_libdir)" + COMPILER = $(tc-getCC) + CFLAGS = ${CFLAGS} -DLINUX + LDFLAGS = ${LDFLAGS} ${LINKFORSHARED} + SCANDIR= + INCLUDE=\$(TIFFINCLUDE) -I\$(PNGINCLUDE) -I\$(PYTHONINCLUDE) + LIBRARY=\$(LIBTIFF) \$(LIBPNG) -L\$(LIBPYTHON) + LIBS=-L"${EPREFIX}/usr/$(get_libdir)" $(python_get_library -l) -ltiff -lpng -lz -lGLU -lGL -L"${EPREFIX}/usr/X11R6/lib" -lXm -lXmu -lXp -lXi -lXext -lXt -lX11 -lpthread -lutil -ldl -lm + EOF + + cp .config.$(uname -s) makefile + cat ../Makefile >> makefile +} + +src_compile() { + pushd $(uname -s) + emake viewmol_ tm_ bio_ readgamess_ readgauss_ readmopac_ readpdb_ || die + popd + "${EPREFIX}"/bin/bash makeTranslations || die +} + +src_install() { + ./install "${ED}"/usr || die + mv "${ED}"/usr/{usr/share,} || die + rm -rf "${ED}"/usr/usr +} diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest new file mode 100644 index 000000000000..8f003565998f --- /dev/null +++ b/sci-chemistry/vmd/Manifest @@ -0,0 +1,2 @@ +DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 SHA256 91508b384cb0a8aab8d8cfc31c1e7e0bc4225dbd7cdb36fbaefcfe8baca9442c SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51 WHIRLPOOL 3f87d24ad0ca7eb60e0ae3d561da7c61e0caa9fe8bb71cd3a06731228926d4c16ee03699d80adf02e2c9b263f96ea8d5b096e64e3e94b0208b1cb618c8a8a7ca +DIST vmd-1.9.2.src.tar.gz 34903084 SHA256 870ee1e483ad23eb7f3bb6ac816cb7be5df893879dddc0bda8423a011993ccdb SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef WHIRLPOOL e2489b4bd8f28359ee959d6ebec3a9e775fbaf7a25baa1324c99dd04c7768e002924c671c11830ec6e9589ecc9de4864f2bcf3dfaf9eb36f5a1d03d5e5841f17 diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch new file mode 100644 index 000000000000..ce842448decf --- /dev/null +++ b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch @@ -0,0 +1,28 @@ + vmd-1.9.1/src/CUDAMarchingCubes.cu | 1 + + vmd-1.9.1/src/CUDAQuickSurf.cu | 1 + + 2 files changed, 2 insertions(+) + +diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu +index 5bfe7bf..36faaf0 100755 +--- a/vmd-1.9.1/src/CUDAMarchingCubes.cu ++++ b/vmd-1.9.1/src/CUDAMarchingCubes.cu +@@ -45,6 +45,7 @@ + #include "CUDAMarchingCubes.h" + #include <thrust/scan.h> + #include <thrust/functional.h> ++#include <thrust/device_ptr.h> + + // The number of threads to use for triangle generation + // (limited by shared memory size) +diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu +index a21ebde..56a42c8 100755 +--- a/vmd-1.9.1/src/CUDAQuickSurf.cu ++++ b/vmd-1.9.1/src/CUDAQuickSurf.cu +@@ -22,6 +22,7 @@ + #include <stdlib.h> + #include <string.h> + #include <cuda.h> ++#include <thrust/device_ptr.h> + + #if CUDART_VERSION < 4000 + #error The VMD QuickSurf feature requires CUDA 4.0 or later diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch b/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch new file mode 100644 index 000000000000..0c3e45dd39c3 --- /dev/null +++ b/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch @@ -0,0 +1,25 @@ + plugins/molfile_plugin/src/webpdbplugin.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/plugins/molfile_plugin/src/webpdbplugin.c b/plugins/molfile_plugin/src/webpdbplugin.c +index 80b3bb9..78597f5 100644 +--- a/plugins/molfile_plugin/src/webpdbplugin.c ++++ b/plugins/molfile_plugin/src/webpdbplugin.c +@@ -202,7 +202,7 @@ static void *open_file_read(const char *filename, const char *filetype, + sprintf(url, "http://www.rcsb.org/pdb/downloadFile.do?fileFormat=pdb&compression=NO&structureId=%s",filename); + sprintf(cmd, "set token [::http::geturl \"%s\"]", url); + if (Tcl_Eval(interp, cmd) != TCL_OK) { +- fprintf(stderr, "Error loading PDB: %s\n",interp->result); ++ fprintf(stderr, "Error loading PDB: %s\n",Tcl_GetStringResult(interp)); + Tcl_DeleteInterp(interp); + return NULL; + } +@@ -211,7 +211,7 @@ static void *open_file_read(const char *filename, const char *filetype, + + result = Tcl_GetVar2(interp, (char *)"state", "body", TCL_GLOBAL_ONLY); + if (!result) { +- fprintf(stderr, "Error loading PDB: %s\n", interp->result); ++ fprintf(stderr, "Error loading PDB: %s\n", Tcl_GetStringResult(interp)); + Tcl_DeleteInterp(interp); + return NULL; + } diff --git a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch new file mode 100644 index 000000000000..3f9ea5c8c2ef --- /dev/null +++ b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch @@ -0,0 +1,16 @@ + plugins/molfile_plugin/src/maeffplugin.cxx | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/plugins/molfile_plugin/src/maeffplugin.cxx b/plugins/molfile_plugin/src/maeffplugin.cxx +index cfe1223..41d92bb 100644 +--- a/plugins/molfile_plugin/src/maeffplugin.cxx ++++ b/plugins/molfile_plugin/src/maeffplugin.cxx +@@ -1979,7 +1979,7 @@ namespace { + } + } + catch (std::exception &e) { +- fprintf(stderr, e.what()); ++ fprintf(stderr, "%s", e.what()); + return MOLFILE_ERROR; + } + return MOLFILE_SUCCESS; diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml new file mode 100644 index 000000000000..4b17d8d6b913 --- /dev/null +++ b/sci-chemistry/vmd/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <herd>sci-chemistry</herd> + <use> + <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag> + <flag name="gromacs">Add support for TNG file format</flag> + <flag name="msms">Add support for MSMS SAS calcualtion tool</flag> + <flag name="povray">Add support for povray raytracer for HQ images</flag> + <flag name="tachyon">Add support for tachyon raytracer for HQ images</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild new file mode 100644 index 000000000000..78e084df58ea --- /dev/null +++ b/sci-chemistry/vmd/vmd-1.9.2.ebuild @@ -0,0 +1,250 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs + +DESCRIPTION="Visual Molecular Dynamics" +HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" +SRC_URI=" + http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz + ${P}.src.tar.gz" + +SLOT="0" +LICENSE="vmd" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda gromacs msms povray sqlite tachyon xinerama" + +RESTRICT="fetch" + +# currently, tk-8.5* with USE=truetype breaks some +# tk apps such as Sequence Viewer or Timeline. +CDEPEND=" + >=dev-lang/tk-8.6.1 + dev-lang/perl + dev-libs/expat + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/netcdf + virtual/opengl + >=x11-libs/fltk-1.1.10-r2:1 + x11-libs/libXft + x11-libs/libXi + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) + gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] ) + sqlite? ( dev-db/sqlite:3= ) + tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) + xinerama? ( x11-libs/libXinerama )" +DEPEND="${CDEPEND} + virtual/pkgconfig + dev-lang/swig" +RDEPEND="${CDEPEND} + sci-biology/stride + sci-chemistry/surf + x11-terms/xterm + msms? ( sci-chemistry/msms-bin ) + povray? ( media-gfx/povray ) + " + +VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" +# Binary only plugin!! +QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" +QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" +QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" + +pkg_nofetch() { + elog "Please download ${P}.src.tar.gz from" + elog "${VMD_DOWNLOAD}" + elog "after agreeing to the license and get" + elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" + elog "Place both in ${DISTDIR}" +} + +src_prepare() { + use cuda && cuda_sanitize + + epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch + + cd "${WORKDIR}"/plugins || die + + epatch \ + "${WORKDIR}"/${P}-gentoo-plugins.patch \ + "${FILESDIR}"/${P}-format-security.patch + + [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) + + sed \ + -e "s:CC = gcc:CC = $(tc-getCC):" \ + -e "s:CXX = g++:CXX = $(tc-getCXX):" \ + -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ + -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ + -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ + -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ + -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ + -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ + -e "s:-ltcl8.5:-ltcl:" \ + -i Make-arch || die "Failed to set up plugins Makefile" + + sed \ + -e '/^AR /s:=:?=:g' \ + -e '/^RANLIB /s:=:?=:g' \ + -i ../plugins/*/Makefile || die + + tc-export AR RANLIB + + sed \ + -e "s:\$(CXXFLAGS)::g" \ + -i hesstrans/Makefile || die + + # prepare vmd itself + cd "${S}" || die + + epatch "${WORKDIR}"/${P}-gentoo-base.patch + + # PREFIX + sed \ + -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ + -i configure || die + + sed \ + -e "s:gentoo-bindir:${ED}/usr/bin:g" \ + -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ + -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ + -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:gentoo-gcc:$(tc-getCC):g" \ + -e "s:gentoo-g++:$(tc-getCXX):g" \ + -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ + -e "s:gentoo-cflags:${CFLAGS}:g" \ + -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ + -e "s:gentoo-nvflags::g" \ + -e "s:gentoo-ldflags:${LDFLAGS}:g" \ + -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ + -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ + -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ + -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ + -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -i configure || die + + if use cuda; then + sed \ + -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ + -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ + -i configure src/Makefile || die + sed \ + -e '/compute_/d' \ + -i configure || die + sed \ + -e 's:-gencode .*code=sm_..::' \ + -i src/Makefile || die + fi + + sed \ + -e "s:LINUXPPC:LINUX:g" \ + -e "s:LINUXALPHA:LINUX:g" \ + -e "s:LINUXAMD64:LINUX:g" \ + -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ + -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ + -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ + -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" + + EMAKEOPTS=( + TCLINC="-I${EPREFIX}/usr/include" + TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" + TCLLDFLAGS="-shared" + NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" + NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include" + NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" + NETCDFDYNAMIC=1 + EXPATINC="-I${EPREFIX}/usr/include" + EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" + EXPATLDFLAGS="-shared" + EXPATDYNAMIC=1 + ) + if use gromacs; then + EMAKEOPTS+=( + TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" + TNGINC="-I${EPREFIX}/usr/include" + TNGLDFLAGS="-shared" + TNGDYNAMIC=1 + ) + fi + if use sqlite; then + EMAKEOPTS+=( + SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" + SQLITEINC="-I${EPREFIX}/usr/include" + SQLITELDFLAGS="-shared" + SQLITEDYNAMIC=1 + ) + fi +} + +src_configure() { + local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" + rm -f configure.options && echo $myconf >> configure.options + + use cuda && myconf+=" CUDA" +# use mpi && myconf+=" MPI" + use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon" + use xinerama && myconf+=" XINERAMA" + + export \ + PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ + PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ + PYTHON_LIBRARY="$(python_get_LIBS)" \ + NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ + NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" + + perl ./configure LINUX \ + ${myconf} || die +} + +src_compile() { + # build plugins + cd "${WORKDIR}"/plugins || die + + emake \ + ${EMAKEOPTS[@]} \ + LINUX + + # build vmd + cd "${S}"/src || die + emake +} + +src_install() { + # install plugins + cd "${WORKDIR}"/plugins || die + emake \ + PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ + distrib + + # install vmd + cd "${S}"/src || die + emake install + + # install docs + cd "${S}" || die + dodoc Announcement README doc/ig.pdf doc/ug.pdf + + # remove some of the things we don't want and need in + # /usr/lib + cd "${ED}"/usr/$(get_libdir)/vmd || die + rm -fr doc README Announcement LICENSE || \ + die "failed to clean up /usr/lib/vmd directory" + + # adjust path in vmd wrapper + sed \ + -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ + -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ + || die "failed to set up vmd wrapper script" + + # install icon and generate desktop entry + insinto /usr/share/pixmaps + doins "${WORKDIR}"/vmd.png + eprefixify "${WORKDIR}"/vmd.desktop + sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die + domenu "${WORKDIR}"/vmd.desktop +} diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest new file mode 100644 index 000000000000..703d4fb187ad --- /dev/null +++ b/sci-chemistry/votca-csg/Manifest @@ -0,0 +1,6 @@ +DIST votca-csg-1.2.2.tar.gz 188405 SHA256 9974c30b8c3f2b9bbdfa56ca12e981cfd015fa7c557eec30cd11ee11cb167775 +DIST votca-csg-1.2.4.tar.gz 188345 SHA256 375b428c90247a3877f71c2d96200969bcaf2b081b8c7332ac770720df43646a SHA512 da814154be6700b56509d899ea16a2f974fd951792c78f2f8717b39b0165fe19121fefb2ef9531c63a8d4558d15776058d24b13e0e7ad0abb9d7b11fac0f5d1a WHIRLPOOL 64a86b09ae00435c68bf09e960c1d1738648811fe2a9ffb18f5529d30d6f94ebf1fc218b14e1ee0bfc911e5ca1e92c25404be045cf28e16ced98fd7ee4421418 +DIST votca-csg-manual-1.2.2.pdf 1009336 SHA256 c9760e3d46afbcd8e2bb44937a9680f68d53e86a36bba1513b4612c4c588d8b5 +DIST votca-csg-manual-1.2.4.pdf 1029132 SHA256 78a68955c96700d432249f712e0601376d5d61fef607860fe32d0ce0dcb70cff SHA512 66b7cf869b2b06d4133b341934fd013717b17c90426f4cdf637ef3bb6119e9f6b67cbde56b7f6b6c777dba9fb311df42dd34d8fe23331f1656439acb541d81bf WHIRLPOOL 629e0e6a8900bb7e4a96b7e1020f86ccacd5a7e7258a493d565c94986a0907371a37d45bf499517a74ad29cf2b606965746e0d90b6be91777f2b0a85f2781732 +DIST votca-csg-tutorials-1.2.2.tar.gz 3576523 SHA256 456a8317fff5770a5ebd6452673eefeaa455534b87a800cfbd4672248670f9bd +DIST votca-csg-tutorials-1.2.4.tar.gz 3721034 SHA256 94b10f23f6e49c1279cdeea87dfee9c19b44373c74212340acebc06eb11e0245 SHA512 8d78a6ff02aedf97c2b640714fd7acfb7c4b0d03ec0141fa89f0ba041e1d2ec07477653d92effd4c96a6497271ad58f5c3397e1fc183c1c856285f6f8b5ceaf5 WHIRLPOOL ea0df816d2f26f12271250137b51f42ecc4a16eea622d37833d4dcc299732c413ee9f71a67767957b13ce8b44a96e9b1389bbbbdb66015c4b5c6d577d4483cf1 diff --git a/sci-chemistry/votca-csg/metadata.xml b/sci-chemistry/votca-csg/metadata.xml new file mode 100644 index 000000000000..a7bc0762f8d6 --- /dev/null +++ b/sci-chemistry/votca-csg/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <use> + <flag name='gromacs'>Add support for gromacs file formats through <pkg>sci-chemistry/gromacs</pkg></flag> + <flag name='system-boost'>Use system boost (<pkg>dev-libs/boost</pkg>) instead of bundled one</flag> + <flag name='extras'>Pull in extra applications from <pkg>sci-chemistry/votca-csg-apps</pkg></flag> + </use> + <upstream> + <remote-id type="google-code">votca</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/votca-csg/votca-csg-1.2.2.ebuild b/sci-chemistry/votca-csg/votca-csg-1.2.2.ebuild new file mode 100644 index 000000000000..dc44ee04e33f --- /dev/null +++ b/sci-chemistry/votca-csg/votca-csg-1.2.2.ebuild @@ -0,0 +1,87 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc examples extras +gromacs +system-boost" +PDEPEND="extras? ( =sci-chemistry/votca-csgapps-${PV} )" +if [ "${PV}" != "9999" ]; then + SRC_URI="http://votca.googlecode.com/files/${PF}.tar.gz + doc? ( http://votca.googlecode.com/files/${PN}-manual-${PV}.pdf ) + examples? ( http://votca.googlecode.com/files/${PN}-tutorials-${PV}.tar.gz )" + RESTRICT="primaryuri" +else + SRC_URI="" + inherit mercurial + EHG_REPO_URI="https://csg.votca.googlecode.com/hg" + PDEPEND="${PDEPEND} doc? ( =app-doc/${PN}-manual-${PV} ) + examples? ( =sci-chemistry/${PN}-tutorials-${PV} )" +fi + +DESCRIPTION="Votca coarse-graining engine" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-macos" + +RDEPEND="=sci-libs/votca-tools-${PV}[system-boost=] + gromacs? ( sci-chemistry/gromacs ) + dev-lang/perl + app-shells/bash" + +DEPEND="${RDEPEND} + doc? ( || ( <app-doc/doxygen-1.7.6.1[-nodot] >=app-doc/doxygen-1.7.6.1[dot] ) ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +src_configure() { + local extra="-DWITH_GMX_DEVEL=OFF" + + use gromacs && has_version =sci-chemistry/gromacs-9999 && \ + extra="-DWITH_GMX_DEVEL=ON" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + mycmakeargs=( + $(cmake-utils_use system-boost EXTERNAL_BOOST) + $(cmake-utils_use_with gromacs GMX) + ${extra} + -DWITH_RC_FILES=OFF + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +src_install() { + DOCS=(README NOTICE ${CMAKE_BUILD_DIR}/CHANGELOG) + newbashcomp scripts/csg-completion.bash ${PN} + cmake-utils_src_install + if use doc; then + if [ -n "${PV##*9999}" ]; then + dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + fi + cd "${CMAKE_BUILD_DIR}" || die + cd share/doc || die + doxygen || die + dohtml -r html/* + fi + if use examples && [ -n "${PV##*9999}" ]; then + insinto "/usr/share/doc/${PF}/tutorials" + docompress -x "/usr/share/doc/${PF}/tutorials" + doins -r "${WORKDIR}/${PN}-tutorials-${PV}"/* + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " + einfo "http://dx.doi.org/10.1021/ct900369w" + einfo +} diff --git a/sci-chemistry/votca-csg/votca-csg-1.2.4-r1.ebuild b/sci-chemistry/votca-csg/votca-csg-1.2.4-r1.ebuild new file mode 100644 index 000000000000..fc2e6d6fe639 --- /dev/null +++ b/sci-chemistry/votca-csg/votca-csg-1.2.4-r1.ebuild @@ -0,0 +1,96 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc examples extras +gromacs" +PDEPEND="extras? ( =sci-chemistry/votca-csgapps-${PV} )" +if [ "${PV}" != "9999" ]; then + SRC_URI="http://downloads.votca.googlecode.com/hg/${P}.tar.gz + doc? ( http://downloads.votca.googlecode.com/hg/${PN}-manual-${PV}.pdf ) + examples? ( http://downloads.votca.googlecode.com/hg/${PN}-tutorials-${PV}.tar.gz )" +else + SRC_URI="" + inherit mercurial + EHG_REPO_URI="https://csg.votca.googlecode.com/hg" + PDEPEND="${PDEPEND} doc? ( =app-doc/${PN}-manual-${PV} ) + examples? ( =sci-chemistry/${PN}-tutorials-${PV} )" +fi + +DESCRIPTION="Votca coarse-graining engine" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-macos" + +#perl is only used for scripts +RDEPEND="~sci-libs/votca-tools-${PV} + gromacs? ( sci-chemistry/gromacs:= ) + dev-lang/perl + app-shells/bash" + +DEPEND="${RDEPEND} + doc? ( || ( <app-doc/doxygen-1.7.6.1[-nodot] >=app-doc/doxygen-1.7.6.1[dot] ) ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=(README NOTICE ChangeLog) + +src_configure() { + local GMX_DEV="OFF" GMX_DOUBLE="OFF" extra + + if use gromacs; then + has_version ">=sci-chemistry/gromacs-5" && GMX_DEV="ON" + has_version sci-chemistry/gromacs[double-precision] && GMX_DOUBLE="ON" + fi + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + mycmakeargs=( + $(cmake-utils_use_with gromacs GMX) + -DWITH_GMX_DEVEL="${GMX_DEV}" + -DGMX_DOUBLE="${GMX_DOUBLE}" + ${extra} + -DWITH_RC_FILES=OFF + -DEXTERNAL_BOOST=ON + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + newbashcomp scripts/csg-completion.bash csg_call + for i in "${ED}"/usr/bin/csg_*; do + [[ ${i} = *csg_call ]] && continue + bashcomp_alias csg_call "${i##*/}" + done + if use doc; then + if [ -n "${PV##*9999}" ]; then + dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + fi + cd "${CMAKE_BUILD_DIR}" || die + cd share/doc || die + doxygen || die + dohtml -r html/* + fi + if use examples && [ -n "${PV##*9999}" ]; then + insinto "/usr/share/doc/${PF}/tutorials" + docompress -x "/usr/share/doc/${PF}/tutorials" + doins -r "${WORKDIR}/${PN}-tutorials-${PV}"/* + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " + einfo "http://dx.doi.org/10.1021/ct900369w" + einfo +} diff --git a/sci-chemistry/votca-csgapps/Manifest b/sci-chemistry/votca-csgapps/Manifest new file mode 100644 index 000000000000..86c4abee696e --- /dev/null +++ b/sci-chemistry/votca-csgapps/Manifest @@ -0,0 +1,2 @@ +DIST votca-csgapps-1.2.2.tar.gz 8196 SHA256 09f0669627360dc0a0837899d980d877d8a58231b76919a6273c31fe0f7c341b +DIST votca-csgapps-1.2.4.tar.gz 10231 SHA256 f0b0e5ad059bd93df514656b6ba65943a7cb35fcf344f75ca4d2ef4e713f4708 SHA512 e52b1e5b8cd552a6a73e16e0a657c16611bc80de9e12ab4e696aa3c30f31c6f52311320862b71d4d082b3f6c0a816001f4c2fd78915ada3a440235feb3ded3ef WHIRLPOOL 43284ddd65f98727374f5eaa2e1a5c9742cc26bed3b68534084623a3afec09a03f982d07615ca0fcd532302b09c90611a7f6859aa89bc009e81e732b85fcb35c diff --git a/sci-chemistry/votca-csgapps/files/votca-csgapps-1.2.2-dso.patch b/sci-chemistry/votca-csgapps/files/votca-csgapps-1.2.2-dso.patch new file mode 100644 index 000000000000..eeec55d4e8e6 --- /dev/null +++ b/sci-chemistry/votca-csgapps/files/votca-csgapps-1.2.2-dso.patch @@ -0,0 +1,266 @@ +# HG changeset patch +# User Christoph Junghans <junghans@votca.org> +# Date 1326307444 25200 +# Branch stable +# Node ID 475999c2cd0d19f739e83c88b2df823c32730bc1 +# Parent 7e8f291a6d79da1ebbc512c370b8620714be0cb6 +cmake: make it DSO conform + +diff -r 7e8f291a6d79 -r 475999c2cd0d CMakeLists.txt +--- a/CMakeLists.txt Tue Jan 10 20:16:55 2012 -0700 ++++ b/CMakeLists.txt Wed Jan 11 11:44:04 2012 -0700 +@@ -4,9 +4,42 @@ + + project(csgapps) + +-file(GLOB_RECURSE DIRS */CMakeLists.txt) ++set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules) ++ ++if(NOT CMAKE_BUILD_TYPE) ++ #Release comes with -O3 by default ++ set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) ++endif(NOT CMAKE_BUILD_TYPE) ++ ++enable_language(CXX) ++include(CheckCXXCompilerFlag) ++ ++option(EXTERNAL_BOOST "Use external boost" ON) ++if (EXTERNAL_BOOST) ++ find_package(Boost 1.39.0 COMPONENTS program_options ) ++ if(NOT Boost_FOUND) ++ message(FATAL_ERROR "Boost not found, make sure you have also installed boost and it's dev package or use our internal replacement, if you have built tools with -DEXTERNAL_BOOST=OFF and set it here as well") ++ endif(NOT Boost_FOUND) ++ include_directories(${Boost_INCLUDE_DIRS}) ++ set (BOOST_LIBRARIES ${Boost_PROGRAM_OPTIONS_LIBRARY}) ++else(EXTERNAL_BOOST) ++ find_package(VOTCA_BOOST REQUIRED) ++ include_directories(${VOTCA_BOOST_INCLUDE_DIRS}) ++ set (BOOST_LIBRARIES ${VOTCA_BOOST_LIBRARIES}) ++endif(EXTERNAL_BOOST) ++ ++find_package(VOTCA_TOOLS REQUIRED) ++include_directories(${VOTCA_TOOLS_INCLUDE_DIRS}) ++find_package(VOTCA_CSG REQUIRED) ++include_directories(${VOTCA_CSG_INCLUDE_DIRS}) ++ ++file(GLOB_RECURSE DIRS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} */CMakeLists.txt) + foreach(DIR ${DIRS}) +- string(REGEX MATCH ^.*/ DIR ${DIR}) +- add_subdirectory(${DIR}) +- unset(NAME CACHE) ++ string(REGEX MATCH ^[^/]* DIR ${DIR}) ++ file(GLOB SRC ${DIR}/*.cc) ++ add_executable(${DIR} ${SRC}) ++ target_link_libraries(${DIR} ${VOTCA_CSG_LIBRARIES} ${VOTCA_TOOLS_LIBRARIES} ${BOOST_LIBRARIES}) ++ install(TARGETS ${DIR} RUNTIME DESTINATION bin) ++ file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${DIR}) ++ set_target_properties(${DIR} PROPERTIES OUTPUT_NAME ${DIR}/csg_${DIR}) + endforeach(DIR) +diff -r 7e8f291a6d79 -r 475999c2cd0d CMakeModules/FindSQLITE3.cmake +--- /dev/null Thu Jan 01 00:00:00 1970 +0000 ++++ b/CMakeModules/FindSQLITE3.cmake Wed Jan 11 11:44:04 2012 -0700 +@@ -0,0 +1,36 @@ ++# - Find libgmx ++# Find the native libgmx headers and libraries. ++# ++# SQLITE3_INCLUDE_DIRS - where to find sqlite3.h, etc ++# SQLITE3_LIBRARIES - List of libraries when using sqlite3. ++# SQLITE3_FOUND - True if sqlite3 found. ++# ++# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org) ++# ++# Licensed under the Apache License, Version 2.0 (the "License"); ++# you may not use this file except in compliance with the License. ++# You may obtain a copy of the License at ++# ++# http://www.apache.org/licenses/LICENSE-2.0 ++# ++# Unless required by applicable law or agreed to in writing, software ++# distributed under the License is distributed on an "AS IS" BASIS, ++# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. ++# See the License for the specific language governing permissions and ++# limitations under the License. ++# ++ ++find_package(PkgConfig) ++ ++pkg_check_modules(PC_SQLITE3 sqlite3) ++ ++find_path(SQLITE3_INCLUDE_DIR sqlite3.h HINTS ${PC_SQLITE3_INCLUDE_DIRS}) ++find_library(SQLITE3_LIBRARY NAMES sqlite3 HINTS ${PC_SQLITE3_LIBRARY_DIRS} ) ++ ++set(SQLITE3_LIBRARIES "${SQLITE3_LIBRARY}" ) ++set(SQLITE3_INCLUDE_DIRS "${SQLITE3_INCLUDE_DIR}" ) ++ ++include(FindPackageHandleStandardArgs) ++find_package_handle_standard_args(SQLITE3 DEFAULT_MSG SQLITE3_LIBRARY SQLITE3_INCLUDE_DIR ) ++ ++mark_as_advanced(SQLITE3_INCLUDE_DIR SQLITE3_LIBRARY ) +diff -r 7e8f291a6d79 -r 475999c2cd0d CMakeModules/FindVOTCA_BOOST.cmake +--- /dev/null Thu Jan 01 00:00:00 1970 +0000 ++++ b/CMakeModules/FindVOTCA_BOOST.cmake Wed Jan 11 11:44:04 2012 -0700 +@@ -0,0 +1,37 @@ ++# - Find libvotca_boost ++# Find the native libvotca_boost headers and libraries. ++# ++# VOTCA_BOOST_INCLUDE_DIRS - where to find headers etc. ++# VOTCA_BOOST_LIBRARIES - List of libraries when using expat. ++# VOTCA_BOOST_FOUND - True if expat found. ++# ++# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org) ++# ++# Licensed under the Apache License, Version 2.0 (the "License"); ++# you may not use this file except in compliance with the License. ++# You may obtain a copy of the License at ++# ++# http://www.apache.org/licenses/LICENSE-2.0 ++# ++# Unless required by applicable law or agreed to in writing, software ++# distributed under the License is distributed on an "AS IS" BASIS, ++# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. ++# See the License for the specific language governing permissions and ++# limitations under the License. ++# ++ ++find_package(PkgConfig) ++ ++pkg_check_modules(PC_VOTCA_BOOST libvotca_boost) ++find_path(VOTCA_BOOST_INCLUDE_DIR boost/algorithm/string/trim.hpp HINTS ${PC_VOTCA_BOOST_INCLUDE_DIRS} ) ++find_library(VOTCA_BOOST_LIBRARY NAMES votca_boost HINTS ${PC_VOTCA_BOOST_LIBRARY_DIRS} ) ++ ++set(VOTCA_BOOST_LIBRARIES "${VOTCA_BOOST_LIBRARY}" ) ++set(VOTCA_BOOST_INCLUDE_DIRS "${VOTCA_BOOST_INCLUDE_DIR}" ) ++ ++include(FindPackageHandleStandardArgs) ++# handle the QUIETLY and REQUIRED arguments and set VOTCA_BOOST_FOUND to TRUE ++# if all listed variables are TRUE ++find_package_handle_standard_args(VOTCA_BOOST DEFAULT_MSG VOTCA_BOOST_LIBRARY VOTCA_BOOST_INCLUDE_DIR) ++ ++mark_as_advanced(VOTCA_BOOST_INCLUDE_DIR VOTCA_BOOST_LIBRARY ) +diff -r 7e8f291a6d79 -r 475999c2cd0d CMakeModules/FindVOTCA_CSG.cmake +--- /dev/null Thu Jan 01 00:00:00 1970 +0000 ++++ b/CMakeModules/FindVOTCA_CSG.cmake Wed Jan 11 11:44:04 2012 -0700 +@@ -0,0 +1,51 @@ ++# - Find libvotca_csg ++# Find the native libvotca_csg headers and libraries. ++# ++# VOTCA_CSG_INCLUDE_DIRS - where to find votca/csg/version.h, etc. ++# VOTCA_CSG_LIBRARIES - List of libraries when using expat. ++# VOTCA_CSG_FOUND - True if expat found. ++# VOTCA_CSG_HAS_SQLITE3 - True if votca csg was build with sqlite3 support ++# ++# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org) ++# ++# Licensed under the Apache License, Version 2.0 (the "License"); ++# you may not use this file except in compliance with the License. ++# You may obtain a copy of the License at ++# ++# http://www.apache.org/licenses/LICENSE-2.0 ++# ++# Unless required by applicable law or agreed to in writing, software ++# distributed under the License is distributed on an "AS IS" BASIS, ++# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. ++# See the License for the specific language governing permissions and ++# limitations under the License. ++# ++ ++find_package(PkgConfig) ++ ++pkg_check_modules(PC_VOTCA_CSG libvotca_csg) ++find_path(VOTCA_CSG_INCLUDE_DIR votca/csg/version.h HINTS ${PC_VOTCA_CSG_INCLUDE_DIRS}) ++ ++find_library(VOTCA_CSG_LIBRARY NAMES votca_csg HINTS ${PC_VOTCA_CSG_LIBRARY_DIRS} ) ++ ++if("${VOTCA_CSG_LIBRARY}" MATCHES "libvotca_csg[^;]*\\.a") ++ if(PC_VOTCA_CSG_LIBRARIES) ++ list(REMOVE_ITEM PC_VOTCA_CSG_LIBRARIES votca_csg) ++ foreach (LIB ${PC_VOTCA_CSG_LIBRARIES}) ++ find_library(VOTCA_CSG_${LIB} NAMES ${LIB} HINTS ${PC_VOTCA_CSG_LIBRARY_DIRS} ) ++ list(APPEND VT_DEP_LIBRARIES ${VOTCA_CSG_${LIB}}) ++ unset(VOTCA_CSG_${LIB} CACHE) ++ endforeach(LIB) ++ endif(PC_VOTCA_CSG_LIBRARIES) ++ set(VOTCA_CSG_DEP_LIBRARIES "${VT_DEP_LIBRARIES}" CACHE FILEPATH "votca csg depency libs (only needed for static (.a) libvotca_csg") ++endif("${VOTCA_CSG_LIBRARY}" MATCHES "libvotca_csg[^;]*\\.a") ++ ++set(VOTCA_CSG_LIBRARIES "${VOTCA_CSG_LIBRARY};${VOTCA_CSG_DEP_LIBRARIES}" ) ++set(VOTCA_CSG_INCLUDE_DIRS "${VOTCA_CSG_INCLUDE_DIR}" ) ++ ++include(FindPackageHandleStandardArgs) ++# handle the QUIETLY and REQUIRED arguments and set VOTCA_CSG_FOUND to TRUE ++# if all listed variables are TRUE ++find_package_handle_standard_args(VOTCA_CSG DEFAULT_MSG VOTCA_CSG_LIBRARY VOTCA_CSG_INCLUDE_DIR ) ++ ++mark_as_advanced(VOTCA_CSG_INCLUDE_DIR VOTCA_CSG_LIBRARY ) +diff -r 7e8f291a6d79 -r 475999c2cd0d CMakeModules/FindVOTCA_TOOLS.cmake +--- /dev/null Thu Jan 01 00:00:00 1970 +0000 ++++ b/CMakeModules/FindVOTCA_TOOLS.cmake Wed Jan 11 11:44:04 2012 -0700 +@@ -0,0 +1,68 @@ ++# - Find libvotca_tools ++# Find the native libvotca_tools headers and libraries. ++# ++# VOTCA_TOOLS_INCLUDE_DIRS - where to find votca/tools/version.h, etc. ++# VOTCA_TOOLS_LIBRARIES - List of libraries when using expat. ++# VOTCA_TOOLS_FOUND - True if expat found. ++# VOTCA_TOOLS_HAS_SQLITE3 - True if votca tools was build with sqlite3 support ++# ++# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org) ++# ++# Licensed under the Apache License, Version 2.0 (the "License"); ++# you may not use this file except in compliance with the License. ++# You may obtain a copy of the License at ++# ++# http://www.apache.org/licenses/LICENSE-2.0 ++# ++# Unless required by applicable law or agreed to in writing, software ++# distributed under the License is distributed on an "AS IS" BASIS, ++# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. ++# See the License for the specific language governing permissions and ++# limitations under the License. ++# ++ ++find_package(PkgConfig) ++ ++pkg_check_modules(PC_VOTCA_TOOLS libvotca_tools) ++find_path(VOTCA_TOOLS_INCLUDE_DIR votca/tools/version.h HINTS ${PC_VOTCA_TOOLS_INCLUDE_DIRS}) ++ ++find_path(VOTCA_TOOLS_HAS_SQLITE3 votca/tools/database.h HINTS ${PC_VOTCA_TOOLS_INCLUDE_DIRS}) ++if (VOTCA_TOOLS_HAS_SQLITE3) ++ #due to include <sqlite3.h> in database.h ++ find_package(SQLITE3 REQUIRED) ++ set(VOTCA_TOOLS_INCLUDE_DIRS "${VOTCA_TOOLS_INCLUDE_DIR};${SQLITE3_INCLUDE_DIR}" ) ++else(VOTCA_TOOLS_HAS_SQLITE3) ++ set(VOTCA_TOOLS_INCLUDE_DIRS "${VOTCA_TOOLS_INCLUDE_DIR}" ) ++endif (VOTCA_TOOLS_HAS_SQLITE3) ++ ++ ++find_library(VOTCA_TOOLS_LIBRARY NAMES votca_tools HINTS ${PC_VOTCA_TOOLS_LIBRARY_DIRS} ) ++ ++if("${VOTCA_TOOLS_LIBRARY}" MATCHES "libvotca_tools[^;]*\\.a") ++ if(PC_VOTCA_TOOLS_LIBRARIES) ++ list(REMOVE_ITEM PC_VOTCA_TOOLS_LIBRARIES votca_tools) ++ foreach (LIB ${PC_VOTCA_TOOLS_LIBRARIES}) ++ find_library(VOTCA_TOOLS_${LIB} NAMES ${LIB} HINTS ${PC_VOTCA_TOOLS_LIBRARY_DIRS} ) ++ list(APPEND VT_DEP_LIBRARIES ${VOTCA_TOOLS_${LIB}}) ++ unset(VOTCA_TOOLS_${LIB} CACHE) ++ endforeach(LIB) ++ endif(PC_VOTCA_TOOLS_LIBRARIES) ++ set(VOTCA_TOOLS_DEP_LIBRARIES "${VT_DEP_LIBRARIES}" CACHE FILEPATH "votca tools depency libs (only needed for static (.a) libvotca_tools") ++endif("${VOTCA_TOOLS_LIBRARY}" MATCHES "libvotca_tools[^;]*\\.a") ++ ++set(VOTCA_TOOLS_LIBRARIES "${VOTCA_TOOLS_LIBRARY};${VOTCA_TOOLS_DEP_LIBRARIES}" ) ++ ++include(FindPackageHandleStandardArgs) ++# handle the QUIETLY and REQUIRED arguments and set VOTCA_TOOLS_FOUND to TRUE ++# if all listed variables are TRUE ++find_package_handle_standard_args(VOTCA_TOOLS DEFAULT_MSG VOTCA_TOOLS_LIBRARY VOTCA_TOOLS_INCLUDE_DIR ) ++ ++if (VOTCA_TOOLS_FOUND) ++ include(CheckLibraryExists) ++ check_library_exists("${VOTCA_TOOLS_LIBRARY};${VOTCA_TOOLS_DEP_LIBRARIES}" VotcaToolsFromC "" FOUND_VOTCA_TOOLS_VERSION) ++ if(NOT FOUND_VOTCA_TOOLS_VERSION) ++ message(FATAL_ERROR "Could not find VotcaToolsFromC in ${VOTCA_TOOLS_LIBRARY};${VOTCA_TOOLS_DEP_LIBRARIES}, take look at the error message in ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log to find out what was going wrong. If you don't have pkg-config installed you will most likely have to set VOTCA_TOOLS_LIBRARY and VOTCA_TOOLS_DEP_LIBRARIES by hand, which set votca_tools lib it's depencies (i.e. -DVOTCA_TOOLS_LIBRARY='/path/to/libvotca_tools.so" -VOTCA_TOOLS_DEP_LIBRARIES="/path/to/libgsl.so;/path/to/libm.so') !") ++ endif(NOT FOUND_VOTCA_TOOLS_VERSION) ++endif (VOTCA_TOOLS_FOUND) ++ ++mark_as_advanced(VOTCA_TOOLS_INCLUDE_DIR VOTCA_TOOLS_LIBRARY ) diff --git a/sci-chemistry/votca-csgapps/metadata.xml b/sci-chemistry/votca-csgapps/metadata.xml new file mode 100644 index 000000000000..40959c87ed5b --- /dev/null +++ b/sci-chemistry/votca-csgapps/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <upstream> + <remote-id type="google-code">votca</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.2.2.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.2.2.ebuild new file mode 100644 index 000000000000..0023ec511603 --- /dev/null +++ b/sci-chemistry/votca-csgapps/votca-csgapps-1.2.2.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils + +if [ "${PV}" != "9999" ]; then + SRC_URI="http://votca.googlecode.com/files/${PF}.tar.gz" + RESTRICT="primaryuri" +else + inherit mercurial + EHG_REPO_URI="https://csgapps.votca.googlecode.com/hg" +fi + +DESCRIPTION="Extra applications for votca-csg" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-macos" +IUSE="" + +RDEPEND="=sci-chemistry/${PN%apps}-${PV}" + +DEPEND="${RDEPEND}" + +DOCS=( README ) + +PATCHES=( "${FILESDIR}/${P}-dso.patch" ) diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.2.4.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.2.4.ebuild new file mode 100644 index 000000000000..1f209d21f52f --- /dev/null +++ b/sci-chemistry/votca-csgapps/votca-csgapps-1.2.4.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils + +if [ "${PV}" != "9999" ]; then + SRC_URI="http://downloads.votca.googlecode.com/hg/${PF}.tar.gz" +else + inherit mercurial + EHG_REPO_URI="https://csgapps.votca.googlecode.com/hg" +fi + +DESCRIPTION="Extra applications for votca-csg" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-macos" +IUSE="" + +RDEPEND="~sci-chemistry/${PN%apps}-${PV}" + +DEPEND="${RDEPEND}" + +DOCS=( README ) diff --git a/sci-chemistry/wxmacmolplt/Manifest b/sci-chemistry/wxmacmolplt/Manifest new file mode 100644 index 000000000000..0f1042d51294 --- /dev/null +++ b/sci-chemistry/wxmacmolplt/Manifest @@ -0,0 +1,2 @@ +DIST wxmacmolplt-7.4.2.tar.gz 1860528 SHA256 0e17295c8082af353311d3d13600bdda20d337d82f5ff8da1be8c2223bb54f76 +DIST wxmacmolplt-7.5.tar.gz 1965376 SHA256 df74762d106e4b44bba8ced84d2df78848052fea543937c51297479fa98fc787 SHA512 a1064d5068136b2a91328c7f912ff57d4741081d6d61437e7b4567fbf732917485b391493d637b8892bdad50b539363cfa9c778bb35407a9c0a2bfed20e42bc0 WHIRLPOOL 9cda289232f7323819b7426dc17532396e633514e292e11f71404f380f174c1439b788bffff594f8d9a72cc0ddca48d799a173ff14a9b783edb8bc64f0b4e04c diff --git a/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.4.2-glew.patch b/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.4.2-glew.patch new file mode 100644 index 000000000000..08986db5bff2 --- /dev/null +++ b/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.4.2-glew.patch @@ -0,0 +1,12 @@ +diff -urN wxmacmolplt-7.4.2.orig/configure.ac wxmacmolplt-7.4.2/configure.ac +--- wxmacmolplt-7.4.2.orig/configure.ac 2010-12-05 02:48:29.000000000 +0300 ++++ wxmacmolplt-7.4.2/configure.ac 2010-12-06 19:30:24.000000000 +0300 +@@ -20,7 +20,7 @@ + ;; + *) + HOST=LINUX +- LIBGL="-lGL -lGLU" ++ LIBGL=`pkg-config --libs glu glew` + ;; + esac + AM_CONDITIONAL(HOST_IS_MSW, [test "x$HOST" == xMSW]) diff --git a/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch b/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch new file mode 100644 index 000000000000..08986db5bff2 --- /dev/null +++ b/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch @@ -0,0 +1,12 @@ +diff -urN wxmacmolplt-7.4.2.orig/configure.ac wxmacmolplt-7.4.2/configure.ac +--- wxmacmolplt-7.4.2.orig/configure.ac 2010-12-05 02:48:29.000000000 +0300 ++++ wxmacmolplt-7.4.2/configure.ac 2010-12-06 19:30:24.000000000 +0300 +@@ -20,7 +20,7 @@ + ;; + *) + HOST=LINUX +- LIBGL="-lGL -lGLU" ++ LIBGL=`pkg-config --libs glu glew` + ;; + esac + AM_CONDITIONAL(HOST_IS_MSW, [test "x$HOST" == xMSW]) diff --git a/sci-chemistry/wxmacmolplt/metadata.xml b/sci-chemistry/wxmacmolplt/metadata.xml new file mode 100644 index 000000000000..cd9831eb3c5f --- /dev/null +++ b/sci-chemistry/wxmacmolplt/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> +wxMacMolPlt is a program for plotting 3D molecular structures and normal modes (vibrations), various orbitals and electron density maps. It reads a variety of file formats including any GAMESS input, log or IRC file directly to create animations. It has a simple GAMESS input (.inp) builder and a primitive molecule builder. +</longdescription> + <use> + <flag name="flash">Add support for flash movie generation using <pkg>media-libs/ming</pkg></flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.4.2.ebuild b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.4.2.ebuild new file mode 100644 index 000000000000..c53a1940546f --- /dev/null +++ b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.4.2.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +WX_GTK_VER=2.8 + +inherit autotools eutils wxwidgets + +DESCRIPTION="Chemical 3D graphics program with GAMESS input builder" +HOMEPAGE="http://www.scl.ameslab.gov/MacMolPlt/" +SRC_URI="http://www.scl.ameslab.gov/MacMolPlt/download/${P}.tar.gz" + +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86" +SLOT="0" +IUSE="flash" + +RDEPEND=" + >=media-libs/glew-1.5.3 + media-libs/mesa + x11-libs/wxGTK:${WX_GTK_VER}[X,opengl] + flash? ( media-libs/ming )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/${P}-glew.patch + sed \ + -e "/^dist_doc_DATA/d" \ + -i Makefile.am || die "Failed to disable installation of LICENSE file" + eautoreconf +} + +src_configure() { + econf \ + --with-glew \ + $(use_with flash ming) +} + +src_install() { + default + doicon resources/${PN}.png + make_desktop_entry ${PN} wxMacMolPlt ${PN} "Science;Education" +} diff --git a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5.ebuild b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5.ebuild new file mode 100644 index 000000000000..a578ee31c9b5 --- /dev/null +++ b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +WX_GTK_VER=2.9 + +inherit autotools eutils wxwidgets + +DESCRIPTION="Chemical 3D graphics program with GAMESS input builder" +HOMEPAGE="http://www.scl.ameslab.gov/MacMolPlt/" +SRC_URI="http://wxmacmolplt.googlecode.com/files/${P}.tar.gz" + +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86" +SLOT="0" +IUSE="flash" + +RDEPEND=" + media-libs/glew + media-libs/mesa + x11-libs/wxGTK:${WX_GTK_VER}[X,opengl] + flash? ( media-libs/ming )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/${P}-glew.patch + sed \ + -e "/^dist_doc_DATA/d" \ + -i Makefile.am || die "Failed to disable installation of LICENSE file" + eautoreconf +} + +src_configure() { + econf \ + --with-glew \ + $(use_with flash ming) +} + +src_install() { + default + doicon resources/${PN}.png + make_desktop_entry ${PN} wxMacMolPlt ${PN} "Science;DataVisualization;" +} diff --git a/sci-chemistry/xds-bin/Manifest b/sci-chemistry/xds-bin/Manifest new file mode 100644 index 000000000000..60095d8dd80b --- /dev/null +++ b/sci-chemistry/xds-bin/Manifest @@ -0,0 +1,3 @@ +DIST XDS-IA32_Linux_x86-20150301.tar.gz 7926947 SHA256 a88c83612f51ee4ee2c8c350a4a043ed63d4de81abbe38b66a5c7ce0729de7ec SHA512 d5ca9e2c48785e6f5409985a24df34361f913800f6a98b4fbc5cc5a16b58126e4577a7da45dc134cd12c44a0f96482e4cfb2ad2e7971ed7b70c1d062bf9ad436 WHIRLPOOL 73dec5eb595ffb1a7c4b30a9546bb82120d212ce73e7d9c004475fbdbe39bcabb7d3e6010ae492100a5fefd8b5abbc6303101091f0feff62e082bb7a0e7c5ce1 +DIST XDS-INTEL64_Linux_x86_64-20150301.tar.gz 9332728 SHA256 6b416b5c91829a2bbe3b9ed7b991edb38db7de7aad7a3ac00611ba12fc32f55a SHA512 361deea644e4f960ce73a0d42d6a3455e5895c288708cb007dd5e392828ab7f031da11c370f7b289a342b9f544e96b77bebde0e383d7b4e6a4ef6a33c930e0ed WHIRLPOOL e52ba19f48feff54af3634b50c8834352f32261bdd2216d6fd77ce9cc34ca49464f63b4685a2516b3eca4e27174c2d2be8406e00ec8fc935b04ce1dc643a7b29 +DIST XDS_html_doc-20150301.tar.gz 112862 SHA256 5ed1076bfc5086c6fb393ff8b19fcb4b4ff538977f74e2aea55b7f7b647fd37b SHA512 3492538de050e1e172a3e49b19a3616b496cd96ae78e726ab82567ebe3a5ecb91e0ea9f88d1fba9678d84ba54067494e1277b8be1a9fead57f8e0c85691d7d70 WHIRLPOOL 57bd75351cc64a7a24b7e78d3162842187d35ee33bce629d515b17306b49186dfda7ef06f9c53417c7b422db3b4636533cb0c753c358c8123903db61db33389d diff --git a/sci-chemistry/xds-bin/metadata.xml b/sci-chemistry/xds-bin/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/xds-bin/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/xds-bin/xds-bin-20150301.ebuild b/sci-chemistry/xds-bin/xds-bin-20150301.ebuild new file mode 100644 index 000000000000..3ddc187ce4d8 --- /dev/null +++ b/sci-chemistry/xds-bin/xds-bin-20150301.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="X-ray Detector Software for processing single-crystal monochromatic diffraction data" +HOMEPAGE="http://xds.mpimf-heidelberg.mpg.de/" +SRC_URI=" + x86? ( ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-IA32_Linux_x86.tar.gz -> XDS-IA32_Linux_x86-${PV}.tar.gz ) + amd64? ( ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz -> XDS-INTEL64_Linux_x86_64-${PV}.tar.gz ) + ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS_html_doc.tar.gz -> XDS_html_doc-${PV}.tar.gz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="-* ~amd64 ~x86" +IUSE="smp X" + +RDEPEND="X? ( sci-visualization/xds-viewer )" +DEPEND="" + +QA_PREBUILT="opt/xds-bin/*" + +src_unpack() { + unpack ${A} + mv XDS-* "${S}" +} + +src_install() { + local suffix bin + exeinto /opt/${PN} + doexe * + + use smp && suffix="_par" + + for bin in xds mintegrate mcolspot xscale; do + dosym ../${PN}/${bin}${suffix} /opt/bin/${bin} + done + + for bin in 2cbf cellparm forkcolspot forkintegrate merge2cbf pixlab xdsconv; do + dosym ../${PN}/${bin} /opt/bin/${bin} + done + + dohtml -r "${WORKDIR}"/XDS_html_doc/* + insinto /usr/share/${PN}/INPUT_templates + doins "${WORKDIR}"/XDS_html_doc/html_doc/INPUT_templates/* +} + +pkg_postinst() { + elog "This package will expire on March 31, 2016" +} diff --git a/sci-chemistry/xdsgui/Manifest b/sci-chemistry/xdsgui/Manifest new file mode 100644 index 000000000000..1156cfea39a4 --- /dev/null +++ b/sci-chemistry/xdsgui/Manifest @@ -0,0 +1,2 @@ +DIST xdsgui-0_p130530.32 10372936 SHA256 f9af76a1e4ef96ac5930a0f51f0052ecf02b0a2496ce832403c31b216a033ebd SHA512 f9ef5d914afb8e6a64f936508fee2e84f4e579898726774dc995e920e5a953341c48022e8078eb60f9a2a288190765949da03f394f221a48916d12dc26a898b1 WHIRLPOOL d7792edfcd273c37569c303e6c4f5acf9d832d4bc4f67048a063a25894e375f1dc1b612f879edc14e3c7fdc6ddda84f25990cb8a3d3fbea35f1784835a3febc5 +DIST xdsgui-0_p130530.64 12220790 SHA256 333de2bc7dd88051a43a912dc6e0903bdc17d0d32c16f8c175fa9ec27289f76a SHA512 bd54ddacf44a9156306354249c5b1b61deb9b1f9ebdad879b98d01354ccb51ab60c183e3c58c2be2bb1a42b55b96cea470ee70538110f0fc1b9e3b46ffce3d40 WHIRLPOOL 1002646b1e22cfad35f81287602c496d8d5c323cf9285604ceb9f3717e2a2b1416e9d1f9ef730e0284d972e4f090752a0d41b9bfcefa403a8d746bbc84b3feb2 diff --git a/sci-chemistry/xdsgui/metadata.xml b/sci-chemistry/xdsgui/metadata.xml new file mode 100644 index 000000000000..f80752c40789 --- /dev/null +++ b/sci-chemistry/xdsgui/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +XDSgui is a GUI (graphical user interface) for XDS that is supposed to help both +novice and experienced users. It graphically displays the ASCII and cbf files +that XDS writes, and can run useful shell commands with a simple mouse click. +The design goal of the program is to enable XDS data processing without the +commandline, and to supply additional graphical information. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/xdsgui/xdsgui-0_p130530.ebuild b/sci-chemistry/xdsgui/xdsgui-0_p130530.ebuild new file mode 100644 index 000000000000..0922da53b023 --- /dev/null +++ b/sci-chemistry/xdsgui/xdsgui-0_p130530.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="GUI for XDS that is supposed to help both novice and experienced users" +HOMEPAGE="http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XdsGUI" +SRC_URI=" + amd64? ( ftp://turn5.biologie.uni-konstanz.de/pub/xdsGUI.rhel6.64 -> ${P}.64 ) + x86? ( ftp://turn5.biologie.uni-konstanz.de/pub/xdsGUI.rhel6.32 -> ${P}.32 )" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-qt/qtcore:4 + dev-qt/qtgui:4 + dev-util/xxdiff + sci-chemistry/xds-bin + sci-chemistry/xdsstat-bin + sci-visualization/xds-viewer" +DEPEND="" + +S="${WORKDIR}" + +QA_PREBUILT="opt/bin/*" + +src_unpack() { + if use amd64; then + cp -rf "${DISTDIR}"/${P}.64 ${PN} || die + elif use x86; then + cp -rf "${DISTDIR}"/${P}.32 ${PN} || die + fi +} + +src_install() { + exeinto /opt/bin + doexe ${PN} +} diff --git a/sci-chemistry/xdsi/Manifest b/sci-chemistry/xdsi/Manifest new file mode 100644 index 000000000000..e33598d79364 --- /dev/null +++ b/sci-chemistry/xdsi/Manifest @@ -0,0 +1 @@ +DIST xdsi_0.92.tar.gz 886028 SHA256 416403f167d26b56965283b407783ea80927ace533df76e330b51ca37c9bb9e4 diff --git a/sci-chemistry/xdsi/files/0.92-gentoo.patch b/sci-chemistry/xdsi/files/0.92-gentoo.patch new file mode 100644 index 000000000000..f4a37ff1838d --- /dev/null +++ b/sci-chemistry/xdsi/files/0.92-gentoo.patch @@ -0,0 +1,27 @@ + xdsi | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/xdsi b/xdsi +index cbedee8..1037913 100755 +--- a/xdsi ++++ b/xdsi +@@ -20,8 +20,8 @@ + #################################################################### + # These are the only two things you should change# + +-set Templates "/mydir/templates" +-set initial "/mydir/SLS-2009" ++set Templates "GENTOOTEMPLATE" ++set initial "./" + + + #################################################################### +@@ -121,7 +121,7 @@ your system administrator." + } + + +-CheckExecutables "kpdf gnuplot xds_par xdsstat xds-viewer-0.6 convert pointless ipmosflm VIEW" ++CheckExecutables "kpdf gnuplot xds_par xds-viewer convert pointless ipmosflm" + + #wm resizable . 0 0 + diff --git a/sci-chemistry/xdsi/metadata.xml b/sci-chemistry/xdsi/metadata.xml new file mode 100644 index 000000000000..431fb2be13b4 --- /dev/null +++ b/sci-chemistry/xdsi/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <longdescription> +XDSi offers you the possibility to process all your datasets in a given directory with minimum effort. +* You just have to provide it with a resultdirectory and the directory where your frames are stored. +* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed. +* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package +* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset +* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated +* You can also generate plots for datasets that have been processed using XDS without XDSi +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild b/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild new file mode 100644 index 000000000000..6a6c9bb7ec8b --- /dev/null +++ b/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="A crude interface for running the XDS" +HOMEPAGE="http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsi" +SRC_URI="ftp://turn5.biologie.uni-konstanz.de/pub/${PN}_${PV}.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + app-text/mupdf + dev-lang/tk + || ( media-gfx/imagemagick media-gfx/graphicsmagick[imagemagick] ) + sci-chemistry/mosflm + sci-chemistry/pointless + sci-chemistry/xds-bin[smp] + sci-visualization/gnuplot + sci-visualization/xds-viewer" +# Need to clarified for licensing +# sci-chemistry/xdsstat-bin +DEPEND="" + +RESTRICT="mirror bindist" + +S="${WORKDIR}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + sed \ + -e "s:GENTOOTEMPLATE:${EPREFIX}/usr/share/${PN}/templates:g" \ + -e "s:kpdf:mupdf:g" \ + -e "s:xds-viewer-0.6:xds-viewer:g" \ + -i ${PN} || die +} + +src_install() { + dobin ${PN} + insinto /usr/share/${PN}/templates + doins templates/{*.INP,bohr*,fortran,pauli,info.png,*.pck,tablesf_xdsi} + dodoc templates/*.pdf +} + +pkg_postinst() { + elog "Documentation can be found here:" + elog "ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/xdsi_doc_print.pdf" +} diff --git a/sci-chemistry/xdsstat-bin/Manifest b/sci-chemistry/xdsstat-bin/Manifest new file mode 100644 index 000000000000..4ce0a18a1d13 --- /dev/null +++ b/sci-chemistry/xdsstat-bin/Manifest @@ -0,0 +1,2 @@ +DIST xdsstat-linux32.bz2 235255 SHA256 366b9565a172b9ab756e1669a353003c74b9e0341bba5b1822fef775a35e1290 SHA512 233c25b60501f794887a09960e2e8377c0443bce661c769624d8afcde288b58968b3406cc7e1bb02f0de010f4e6555ef0641fd5ebcfdd5f6396ec21a22c32985 WHIRLPOOL a304fd23eaf3d8292f3bc414e6bc1c1b5895590b4235e637d357a4a462c91939195fd99764b4233775f1dd6d65601391d4c6328fe578734dae498e6f382e96f7 +DIST xdsstat-linux64.bz2 256555 SHA256 45408d09cb13ec664e863863ec66a1cece204308e074f29f54f922d804f042f9 SHA512 d5b3043bec30a17f6960308d642a3721f7a73bc851a71ec28a813b5a98f2de4f215d3603e8da4a9bcb949cfa15030c3eac108bc5549ebdef6737885e60dbd626 WHIRLPOOL 5d81ba5998e6c527978f10e0aa2ded7c8ada53beb6340ba592d74b34a64a81e17c0184d101dc7698d4771458d0e27559fb857fd329be8eb95a4f75136f549790 diff --git a/sci-chemistry/xdsstat-bin/metadata.xml b/sci-chemistry/xdsstat-bin/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/xdsstat-bin/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/xdsstat-bin/xdsstat-bin-140225.ebuild b/sci-chemistry/xdsstat-bin/xdsstat-bin-140225.ebuild new file mode 100644 index 000000000000..7bed425330c3 --- /dev/null +++ b/sci-chemistry/xdsstat-bin/xdsstat-bin-140225.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MY_PN="${PN/-bin}" + +DESCRIPTION="Prints various statistics (that are not available from XDS itself)" +HOMEPAGE="http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSSTAT" +SRC_URI=" + amd64? ( ftp://turn5.biologie.uni-konstanz.de/pub/${MY_PN}-linux64.bz2 ) + x86? ( ftp://turn5.biologie.uni-konstanz.de/pub/${MY_PN}-linux32.bz2 ) +" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="sci-chemistry/xds-bin" +DEPEND="" + +RESTRICT="mirror" + +QA_PREBUILT="opt/bin/*" + +S="${WORKDIR}" + +src_install() { + exeinto /opt/bin + newexe ${MY_PN}* ${MY_PN} +} diff --git a/sci-chemistry/xia2/Manifest b/sci-chemistry/xia2/Manifest new file mode 100644 index 000000000000..e7fa594c3ec9 --- /dev/null +++ b/sci-chemistry/xia2/Manifest @@ -0,0 +1,6 @@ +DIST xia2-0.3.1.0.tar.bz2 3389906 SHA256 32f1866bc17b093cbf157ec7bc217e47d059957104b20c88ed1b5c3706fc7e28 +DIST xia2-0.3.1.6.tar.bz2 3464982 SHA256 fde814a763e6666a1618d01569c19d574f1bf71d754dc3960beeb13c35dd201f +DIST xia2-0.3.1.7.tar.bz2 3650285 SHA256 54beb26396c4b6ecb343544c777c2505238385f2127482d035d2c47b24a7fcf1 +DIST xia2-0.3.3.1.tar.bz2 3074989 SHA256 f1bf94cd9305f768fea1b541ac53d66917126e92620263a96f9c23923ec829c4 +DIST xia2-0.3.3.3.tar.bz2 2919316 SHA256 3cf09fcf9d2c0ea6d6cb8cf66a3c5af752b4345af6a882e2d398424cf3b4b0d3 +DIST xia2-0.3.4.0.tar.bz2 21404771 SHA256 20afe3d24c35446ef8c8944974d684229f053d3916e96e46766d8eefa4c5fabf diff --git a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch new file mode 100644 index 000000000000..9d92af7e33ce --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch @@ -0,0 +1,61 @@ +diff --git a/xia2-0.3.1.0/Applications/xia2find.py b/xia2-0.3.1.0/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.1.0/Applications/xia2find.py ++++ b/xia2-0.3.1.0/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2-0.3.1.0/Experts/DRStrategyExpert.py b/xia2-0.3.1.0/Experts/DRStrategyExpert.py +index 28b1dc3..dba3ef7 100644 +--- a/xia2-0.3.1.0/Experts/DRStrategyExpert.py ++++ b/xia2-0.3.1.0/Experts/DRStrategyExpert.py +@@ -48,24 +48,24 @@ strategy_dict = { + 'default':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'default':{ + 'score':2, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} ++ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, + 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':2, + 'pipeline':{ +- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} ++ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, + 'depends-on':['xds', 'xscale']} + } +diff --git a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch new file mode 100644 index 000000000000..7770a53c4451 --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch @@ -0,0 +1,61 @@ +diff --git a/xia2-0.3.1.6/Applications/xia2find.py b/xia2-0.3.1.6/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.1.6/Applications/xia2find.py ++++ b/xia2-0.3.1.6/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2-0.3.1.6/Experts/DRStrategyExpert.py b/xia2-0.3.1.6/Experts/DRStrategyExpert.py +index 28b1dc3..dba3ef7 100644 +--- a/xia2-0.3.1.6/Experts/DRStrategyExpert.py ++++ b/xia2-0.3.1.6/Experts/DRStrategyExpert.py +@@ -48,24 +48,24 @@ strategy_dict = { + 'default':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'default':{ + 'score':2, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} ++ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, + 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':2, + 'pipeline':{ +- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} ++ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, + 'depends-on':['xds', 'xscale']} + } +diff --git a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch new file mode 100644 index 000000000000..ec8ada48aad1 --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch @@ -0,0 +1,61 @@ +diff --git a/xia2-0.3.1.7/Applications/xia2find.py b/xia2-0.3.1.7/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.1.7/Applications/xia2find.py ++++ b/xia2-0.3.1.7/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2-0.3.1.7/Experts/DRStrategyExpert.py b/xia2-0.3.1.7/Experts/DRStrategyExpert.py +index 28b1dc3..dba3ef7 100644 +--- a/xia2-0.3.1.7/Experts/DRStrategyExpert.py ++++ b/xia2-0.3.1.7/Experts/DRStrategyExpert.py +@@ -48,24 +48,24 @@ strategy_dict = { + 'default':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'default':{ + 'score':2, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} ++ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, + 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':2, + 'pipeline':{ +- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} ++ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, + 'depends-on':['xds', 'xscale']} + } +diff --git a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch new file mode 100644 index 000000000000..36cf6bb60d1d --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch @@ -0,0 +1,61 @@ +diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.3.1/Applications/xia2find.py ++++ b/xia2-0.3.3.1/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2-0.3.3.0/Experts/DRStrategyExpert.py b/xia2-0.3.3.0/Experts/DRStrategyExpert.py +index 28b1dc3..dba3ef7 100644 +--- a/xia2-0.3.3.1/Experts/DRStrategyExpert.py ++++ b/xia2-0.3.3.1/Experts/DRStrategyExpert.py +@@ -48,24 +48,24 @@ strategy_dict = { + 'default':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'default':{ + 'score':2, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} ++ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, + 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':2, + 'pipeline':{ +- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} ++ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, + 'depends-on':['xds', 'xscale']} + } +diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch new file mode 100644 index 000000000000..53cacbb5c681 --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch @@ -0,0 +1,28 @@ +diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.3.3/Applications/xia2find.py ++++ b/xia2-0.3.3.3/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch new file mode 100644 index 000000000000..9ba4c94495ea --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch @@ -0,0 +1,28 @@ +diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.4.0/Applications/xia2find.py ++++ b/xia2-0.3.4.0/Applications/xia2find.py +@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory + from Experts.FindImages import image2template_directory + + known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', +- 'osc', 'cbf', 'mar2000']] ++ 'osc', 'cbf', 'mar2000'] + known_sweeps = { } + + def is_image_name(file): +diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py +@@ -49,8 +49,8 @@ def Cad(DriverType = None): + self.add_command_line(hklin) + + self.set_task('Rewriting reflections %s => %s' % +- ` (os.path.split(hklin)[-1], +- ` os.path.split(self.getHklout())[-1])) ++ (os.path.split(hklin)[-1], ++ os.path.split(self.getHklout())[-1])) + + self.start() + diff --git a/sci-chemistry/xia2/metadata.xml b/sci-chemistry/xia2/metadata.xml new file mode 100644 index 000000000000..9ac9ffdb3a41 --- /dev/null +++ b/sci-chemistry/xia2/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild new file mode 100644 index 000000000000..33b3d841acfa --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +src_prepare() { + find . -name '*.bat' | xargs rm || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT + XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} + XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} + PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild new file mode 100644 index 000000000000..537735e1351f --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + find . -name '*.bat' -delete || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch + python_convert_shebangs -r $(python_get_version) . +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT + XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} + XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} + PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild new file mode 100644 index 000000000000..16fbf797d1b4 --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + find . -name '*.bat' -delete || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch + python_convert_shebangs -r $(python_get_version) . +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT + XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} + XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} + PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild b/sci-chemistry/xia2/xia2-0.3.3.1.ebuild new file mode 100644 index 000000000000..26fb7d0d4c83 --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.3.1.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + find . -name '*.bat' -delete || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch + python_convert_shebangs -r $(python_get_version) . +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" + XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" + XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" + PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT + echo "" + elog "In order to use the package, you need to" + elog "\t source ${EPREFIX}/etc/profile" + echo "" +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xia2/xia2-0.3.3.3.ebuild b/sci-chemistry/xia2/xia2-0.3.3.3.ebuild new file mode 100644 index 000000000000..60778aa75fb9 --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.3.3.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + find . -name '*.bat' -delete || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch + python_convert_shebangs -r $(python_get_version) . +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" + XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" + XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" + PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT + echo "" + elog "In order to use the package, you need to" + elog "\t source ${EPREFIX}/etc/profile" + echo "" +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild b/sci-chemistry/xia2/xia2-0.3.4.0.ebuild new file mode 100644 index 000000000000..1d27abd355dc --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.4.0.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.ccp4.ac.uk/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/ccp4-apps-6.1.2 + sci-chemistry/mosflm + sci-chemistry/pointless + >=sci-libs/ccp4-libs-6.1.2 + sci-libs/cctbx" +DEPEND="${RDEPEND}" + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + find . -name '*.bat' -delete || die + + epatch "${FILESDIR}"/${PV}-fix-syntax.patch + python_convert_shebangs -r $(python_get_version) . +} + +src_install() { + rm -rf ${P}/binaries ${PN}core-${PV}/Test || die + + insinto /usr/share/ccp4/XIAROOT/ + doins -r * || die + + # Set programs executable +# fperms cannot handle wildcards + chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die + chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die + + cat >> "${T}"/23XIA <<- EOF + XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" + XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" + XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" + PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" + EOF + + doenvd "${T}"/23XIA +} + +pkg_postinst() { + python_mod_optimize /usr/share/ccp4/XIAROOT + echo "" + elog "In order to use the package, you need to" + elog "\t source ${EPREFIX}/etc/profile" + echo "" +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} diff --git a/sci-chemistry/xyza2pipe/Manifest b/sci-chemistry/xyza2pipe/Manifest new file mode 100644 index 000000000000..e724f9fb0d3c --- /dev/null +++ b/sci-chemistry/xyza2pipe/Manifest @@ -0,0 +1,2 @@ +DIST xyza2pipe-20101129.tgz 67301 SHA256 3ef853ee6df8eac521a6670d12278b4b5854919aba5d6519d65c73dadc776695 SHA512 19744d88be04afc8049b38179e96aab9ecd72daf8c6aa99cb21ab6a63d1da440f301bba274cff6ae3f9f4c2eec311294e1fe212bec63c81b22349c698609c1c3 WHIRLPOOL dfacea33e37d09d09d073bdab5e363f403ad1aaa81e9a0311769de57e7b06d12b5edce7362a6bd9bd3c667f089b8138ab699e75a8c8093df81b4fa1de270c72f +DIST xyza2pipe-20121001.tgz 61002 SHA256 c2e2d83dc6f0424afe519aa0ba83922f1c6d1b90933edf5d62722ac56af3b1de SHA512 b64abf46a8d7f3530eecaeec3bc8b143600c6823174a22727868087c2f7f17af0b538a0521e3a29806dc608b003948a1e31296ab395bc3c0089c5dc7a391d855 WHIRLPOOL fec47032811c81709d996712b938ed315e67435d72ae91c1ce2a01546c62eae4868d7e430585cd4f1830e158a8a994e23af02e6f23a897d44f98a81b2889baac diff --git a/sci-chemistry/xyza2pipe/files/20101129-gentoo.patch b/sci-chemistry/xyza2pipe/files/20101129-gentoo.patch new file mode 100644 index 000000000000..11586ee4f81c --- /dev/null +++ b/sci-chemistry/xyza2pipe/files/20101129-gentoo.patch @@ -0,0 +1,152 @@ +diff --git a/Makefile b/Makefile +index 7e00197..b078f06 100644 +--- a/Makefile ++++ b/Makefile +@@ -4,10 +4,11 @@ + # Last modified: Jun/30/2010 + # + +-CFLAGS = -O3 -lm ++CFLAGS ?= -O3 ++LIBS =-lm + + TARGETS = xyza2pipe ucsf2pipe nv2pipe xeasy2pipe azara2pipe vnmr2pipe xwnmr2pipe\ +- pipe2xyza pipe2ucsf pipe2nv pipe2xeasy pipe2azara\ ++ pipe2xyza pipe2ucsf-olivia pipe2nv pipe2xeasy pipe2azara-olivia \ + pipe2proj add2pipe adducsf2pipe addnv2pipe addxeasy2pipe addazara2pipe addvnmr2pipe addxwnmr2pipe + + OBJECTS_C = checklabel.o checkxyza.o cnvhdr.o\ +@@ -60,86 +61,90 @@ clean: + rm -f $(TARGETS) addxyza2pipe + + .o: +- $(CC) $< -c -o $@ $(CFLAGS) ++ $(CC) $(CFLAGS) $< -c -o $@ + + xyza2pipe: $(OBJECTS_C) $(OBJECTS_XP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + pipe2xyza: $(OBJECTS_C) $(OBJECTS_PX) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + ucsf2pipe: $(OBJECTS_C) $(OBJECTS_UP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + +-pipe2ucsf: $(OBJECTS_C) $(OBJECTS_PU) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++pipe2ucsf-olivia: $(OBJECTS_C) $(OBJECTS_PU) ++ $(CC) $(CFLAGS) $(LDFLAGS) pipe2ucsf.c $^ -o $@ \ ++ $(LIBS) + + nv2pipe: $(OBJECTS_C) $(OBJECTS_NP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + pipe2nv: $(OBJECTS_C) $(OBJECTS_PN) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + xeasy2pipe: $(OBJECTS_C) $(OBJECTS_EP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + pipe2xeasy: $(OBJECTS_C) $(OBJECTS_PE) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + azara2pipe: $(OBJECTS_C) $(OBJECTS_AP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + +-pipe2azara: $(OBJECTS_C) $(OBJECTS_PA) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++pipe2azara-olivia: $(OBJECTS_C) $(OBJECTS_PA) ++ $(CC) $(CFLAGS) $(LDFLAGS) pipe2azara.c $^ -o $@ \ ++ $(LIBS) + + vnmr2pipe: $(OBJECTS_C) $(OBJECTS_VP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + xwnmr2pipe: $(OBJECTS_C) $(OBJECTS_BP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + pipe2proj: $(OBJECTS_C) $(OBJECTS_PJ) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + add2pipe: $(OBJECTS_C) $(OBJECTS_DXP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + rm -f addxyza2pipe + ln -s add2pipe addxyza2pipe + + adducsf2pipe: $(OBJECTS_C) $(OBJECTS_DUP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + addnv2pipe: $(OBJECTS_C) $(OBJECTS_DNP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + addxeasy2pipe: $(OBJECTS_C) $(OBJECTS_DEP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + addazara2pipe: $(OBJECTS_C) $(OBJECTS_DAP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + addvnmr2pipe: $(OBJECTS_C) $(OBJECTS_DVP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) + + addxwnmr2pipe: $(OBJECTS_C) $(OBJECTS_DBP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(LIBS) ++ ++install: $(TARGETS) ++ install -d $(DESTDIR)/usr/bin ++ install $(TARGETS) $(DESTDIR)/usr/bin/ diff --git a/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch b/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch new file mode 100644 index 000000000000..ec4220dd0695 --- /dev/null +++ b/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch @@ -0,0 +1,168 @@ + Makefile | 106 +++++++++++++++++++++++++++++++++++++-------------------------- + 1 file changed, 63 insertions(+), 43 deletions(-) + +diff --git a/Makefile b/Makefile +index 15d4bd3..e738ec2 100644 +--- a/Makefile ++++ b/Makefile +@@ -4,7 +4,7 @@ + # Last modified: Feb/22/2012 + # + +-CFLAGS = -O3 ++CFLAGS ?= -O3 + MFLAGS = -lm + + TARGETS = xyza2pipe ucsf2pipe nv2pipe xeasy2pipe azara2pipe vnmr2pipe xwnmr2pipe\ +@@ -62,89 +62,109 @@ clean: + rm -f $(TARGETS) addxyza2pipe + + $(OBJECTS_MATH): +- $(CC) $*.c -c -o $@ $(CFLAGS) -D__XYZA2PIPE__ ++ $(CC) $(CPPFLAGS) -D__XYZA2PIPE__ $(CFLAGS) $*.c -c -o $@ + + .o: +- $(CC) $< -c -o $@ $(CFLAGS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $< -c -o $@ + + xyza2pipe: $(OBJECTS_C) $(OBJECTS_XP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2xyza: $(OBJECTS_C) $(OBJECTS_PX) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + ucsf2pipe: $(OBJECTS_C) $(OBJECTS_UP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2ucsf: $(OBJECTS_C) $(OBJECTS_PU) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + nv2pipe: $(OBJECTS_C) $(OBJECTS_NP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2nv: $(OBJECTS_C) $(OBJECTS_PN) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + xeasy2pipe: $(OBJECTS_C) $(OBJECTS_EP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2xeasy: $(OBJECTS_C) $(OBJECTS_PE) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + azara2pipe: $(OBJECTS_C) $(OBJECTS_AP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2azara: $(OBJECTS_C) $(OBJECTS_PA) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + vnmr2pipe: $(OBJECTS_C) $(OBJECTS_VP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + xwnmr2pipe: $(OBJECTS_C) $(OBJECTS_BP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2proj: $(OBJECTS_C) $(OBJECTS_PJ) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + add2pipe: $(OBJECTS_C) $(OBJECTS_DXP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + rm -f addxyza2pipe + ln -s add2pipe addxyza2pipe + + adducsf2pipe: $(OBJECTS_C) $(OBJECTS_DUP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + addnv2pipe: $(OBJECTS_C) $(OBJECTS_DNP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + addxeasy2pipe: $(OBJECTS_C) $(OBJECTS_DEP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + addazara2pipe: $(OBJECTS_C) $(OBJECTS_DAP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + addvnmr2pipe: $(OBJECTS_C) $(OBJECTS_DVP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + addxwnmr2pipe: $(OBJECTS_C) $(OBJECTS_DBP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ diff --git a/sci-chemistry/xyza2pipe/metadata.xml b/sci-chemistry/xyza2pipe/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/xyza2pipe/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/xyza2pipe/xyza2pipe-20101129.ebuild b/sci-chemistry/xyza2pipe/xyza2pipe-20101129.ebuild new file mode 100644 index 000000000000..51428079a77e --- /dev/null +++ b/sci-chemistry/xyza2pipe/xyza2pipe-20101129.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit eutils toolchain-funcs + +DESCRIPTION="Cross conversion environment of NMR spectra" +HOMEPAGE="http://fermi.pharm.hokudai.ac.jp/olivia/api/index.php/Xyza2pipe_src" +SRC_URI="mirror://gentoo/${P}.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="olivia" +IUSE="" + +S="${WORKDIR}"/${PN} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + tc-export CC +} + +src_install() { + emake DESTDIR="${ED}" install || die + dodoc README FEEDBACK || die +} diff --git a/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild b/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild new file mode 100644 index 000000000000..6e7af4ff9b2b --- /dev/null +++ b/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Cross conversion environment of NMR spectra" +HOMEPAGE="http://fermi.pharm.hokudai.ac.jp/olivia/api/index.php/Xyza2pipe_src" +SRC_URI="http://fermi.pharm.hokudai.ac.jp/olivia/documents/xyza2pipe.tgz -> ${P}.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="olivia" +IUSE="" + +S="${WORKDIR}"/${PN} + +src_prepare() { + epatch "${FILESDIR}"/${P}-gentoo.patch + tc-export CC + mkdir bin +} + +src_install() { + local i + dodoc README FEEDBACK + cd bin || die + for i in *; do + newbin ${i}{,-olivia} + done +} |