graphics/PyMOL: Added (molecular visualization system).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

graphics/PyMOL/PyMOL.SlackBuild

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+#!/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}

graphics/PyMOL/PyMOL.desktop

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+[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

graphics/PyMOL/PyMOL.info

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+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"

graphics/PyMOL/README

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+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.

graphics/PyMOL/doinst.sh

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+if [ -x /usr/bin/update-desktop-database ]; then
+  /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
+fi

graphics/PyMOL/slack-desc

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+# 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: