From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-chemistry/numbat/Manifest | 1 + .../numbat/files/numbat-0.999-gnuplot.patch | 42 +++++++++++++++++ sci-chemistry/numbat/metadata.xml | 19 ++++++++ sci-chemistry/numbat/numbat-0.999-r1.ebuild | 53 ++++++++++++++++++++++ 4 files changed, 115 insertions(+) create mode 100644 sci-chemistry/numbat/Manifest create mode 100644 sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch create mode 100644 sci-chemistry/numbat/metadata.xml create mode 100644 sci-chemistry/numbat/numbat-0.999-r1.ebuild (limited to 'sci-chemistry/numbat') 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 @@ + + + + sci-chemistry + + jlec@gentoo.org + + +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. + + 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 +} -- cgit v1.2.3-65-gdbad