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

5 files changed, 147 insertions, 0 deletions

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
+}