From 490534f6ee7726dfa91ec97fc9a8db9794bfab84 Mon Sep 17 00:00:00 2001 From: Dimitris Zlatanidis Date: Tue, 15 Apr 2014 16:30:55 +0700 Subject: graphics/PyMOL: Added (molecular visualization system). Signed-off-by: Willy Sudiarto Raharjo --- graphics/PyMOL/PyMOL.SlackBuild | 95 ++++++++++++++++++++++++++++++++++++++++ graphics/PyMOL/PyMOL.desktop | 10 +++++ graphics/PyMOL/PyMOL.info | 10 +++++ graphics/PyMOL/README | 4 ++ graphics/PyMOL/doinst.sh | 3 ++ graphics/PyMOL/pymol.png | Bin 0 -> 5331 bytes graphics/PyMOL/slack-desc | 19 ++++++++ 7 files changed, 141 insertions(+) create mode 100644 graphics/PyMOL/PyMOL.SlackBuild create mode 100644 graphics/PyMOL/PyMOL.desktop create mode 100644 graphics/PyMOL/PyMOL.info create mode 100644 graphics/PyMOL/README create mode 100644 graphics/PyMOL/doinst.sh create mode 100644 graphics/PyMOL/pymol.png create mode 100644 graphics/PyMOL/slack-desc diff --git a/graphics/PyMOL/PyMOL.SlackBuild b/graphics/PyMOL/PyMOL.SlackBuild new file mode 100644 index 0000000000..82460f4d97 --- /dev/null +++ b/graphics/PyMOL/PyMOL.SlackBuild @@ -0,0 +1,95 @@ +#!/bin/sh + +# Slackware build script for PyMOL + +# Copyright 2014 Dimitris Zlatanidis Greece-Orestiada +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=PyMOL +SRCNAM=$(echo ${PRGNAM,,}-v) +VERSION=${VERSION:-1.7.0.0} +SRCDIR=$(echo $SRCNAM | cut -c1-5) +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCDIR +tar xvf $CWD/$SRCNAM$VERSION.tar.bz2 +cd $SRCDIR +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +python setup.py build +python setup.py install --root=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/share/applications +install -D -m644 $CWD/$PRGNAM.desktop $PKG/usr/share/applications/$PRGNAM.desktop + +mkdir -p $PKG/usr/share/pixmaps/ +install -D -m644 $CWD/$SRCDIR.png $PKG/usr/share/pixmaps/$SRCDIR.png + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS COPYING ChangeLog LICENSE NEWS README $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/graphics/PyMOL/PyMOL.desktop b/graphics/PyMOL/PyMOL.desktop new file mode 100644 index 0000000000..59624c008f --- /dev/null +++ b/graphics/PyMOL/PyMOL.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Name= PyMOL +Name[he]= PyMOL +Comment= OpenGL based molecular visualization system +Exec=pymol +Icon=pymol +Terminal=false +Type=Application +Categories=Graphics;3DTool; +GenericName=Graphics diff --git a/graphics/PyMOL/PyMOL.info b/graphics/PyMOL/PyMOL.info new file mode 100644 index 0000000000..bce1debf78 --- /dev/null +++ b/graphics/PyMOL/PyMOL.info @@ -0,0 +1,10 @@ +PRGNAM="PyMOL" +VERSION="1.7.0.0" +HOMEPAGE="http://pymol.org" +DOWNLOAD="http://downloads.sourceforge.net/project/pymol/pymol/1.7/pymol-v1.7.0.0.tar.bz2" +MD5SUM="36fc735f6104e59802f109d0d25b6676" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python-pmw" +MAINTAINER="Dimitris Zlatanidis" +EMAIL="d.zlatanidis@gmail.com" diff --git a/graphics/PyMOL/README b/graphics/PyMOL/README new file mode 100644 index 0000000000..f8a79257d1 --- /dev/null +++ b/graphics/PyMOL/README @@ -0,0 +1,4 @@ +PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D +visualization of proteins, small molecules, density, surfaces, and +trajectories. It also includes molecular editing, ray tracing, and +movies. diff --git a/graphics/PyMOL/doinst.sh b/graphics/PyMOL/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/graphics/PyMOL/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/graphics/PyMOL/pymol.png b/graphics/PyMOL/pymol.png new file mode 100644 index 0000000000..6a5f13dc18 Binary files /dev/null and b/graphics/PyMOL/pymol.png differ diff --git a/graphics/PyMOL/slack-desc b/graphics/PyMOL/slack-desc new file mode 100644 index 0000000000..f4f739d944 --- /dev/null +++ b/graphics/PyMOL/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +PyMOL: PyMOL (molecular visualization system) +PyMOL: +PyMOL: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D +PyMOL: visualization of proteins, small molecules, density, surfaces, and +PyMOL: trajectories. It also includes molecular editing, ray tracing, and +PyMOL: movies. +PyMOL: +PyMOL: Homepage: http://pymol.org +PyMOL: +PyMOL: +PyMOL: -- cgit v1.2.3