pymol -- vmd and numpy support added

4 files changed, 139 insertions, 2 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index c4f61eae7..25218ea21 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*pymol-9999-r1 (09 Jul 2009)
+
+  09 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +pymol-9999-r1.ebuild, metadata.xml:
+  added vmd and numpy support
+
 *pymol-1.2_rc1 (09 Jul 2009)
 
   09 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 77a0c0422..8567d7166 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -11,6 +11,7 @@ DIST apbs_tools.py.090618.bz2 21329 RMD160 80baed718524dfbaff2f0a3b7263fc75c55bf
 EBUILD pymol-1.2_beta8.ebuild 2707 RMD160 8329ceb3b22bbebe66e62d6bb5f78e39edd9ce22 SHA1 062f9887da79aa83325463ae350e290a275dfef4 SHA256 efa34926bd8545b707728c05184b1a5cf8c2bbd2bcd796439577e5e996fe7c4a
 EBUILD pymol-1.2_rc0.ebuild 2701 RMD160 8c96742b4918d7e85ab837058e17de06049928d5 SHA1 b9fc184ab749f041b72055e3854eedd31671bddd SHA256 b92ddfb95ef06c23610563e29f37616005c0191efba5056295d9ae879b5055f8
 EBUILD pymol-1.2_rc1.ebuild 2701 RMD160 3f7e94a8bdbfe402581a90333c5193e74c475bca SHA1 444ec483ea7ce62d2e013c2be2b45885039900c1 SHA256 1aef2304bb1bd6e3a22d463a9f89ee33ac0def10e3d1fe9d5740ba05e79c6f71
+EBUILD pymol-9999-r1.ebuild 2956 RMD160 24c4e12e54b8a9c46b50aa61fa3a671f0a1c1bb5 SHA1 b861bbc4b7581ca9cc91b57655f497a0e4b00b95 SHA256 1e1553260566bf2b60279557f0b1be75c677dec9024b2156835830292281f77b
 EBUILD pymol-9999.ebuild 2683 RMD160 88d12ca9a986ecc0302f61c91bd200586cd436d7 SHA1 b78fc6bdf86093dcc6af7b1f894effc989ca30d5 SHA256 5d2abaa80808a07c74c6dc2145ea15a29bfce17dc0fdd69186ef601c72b0af07
-MISC ChangeLog 3979 RMD160 64323b8913e8c72cf7d4050b4bcf057d6fd479ad SHA1 f4ae54a50688f5564dffb3ba406188d22915d9dd SHA256 d2994678c9bca0550ce178d214bf1fceb799fd67b2a9f3d1910b878f4a93634d
-MISC metadata.xml 297 RMD160 431061f6875f90a251ae90c5fc5be499da78c9d8 SHA1 b01c71fad62ac24b76a45536f6ddeae3904558dd SHA256 fbe32692a4ff6e595966ca094d9d12912952aaeb639d248fdbd0ed2a9a088d75
+MISC ChangeLog 4136 RMD160 e7b63274473188bc315a1cc2c16be60cdfd2deb9 SHA1 0d0e21f3c87ddba0a3d3c5d4c2f17d6be04615a0 SHA256 dee24ceda6a171849e82c3c02a204d2f5e86e61c5e1f42a0185be3ecbcf4f210
+MISC metadata.xml 412 RMD160 9c33c90cdb3bc60af7dbee004b7f1cffd1b43aa6 SHA1 efd4a32d739fe54f0f464edc0843c81e9fb23437 SHA256 ee0056aa8c9e40b6da007fa8c895e15c17cb25004212b91d48dad03f6123483c
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index 1b9609b2a..f4c6f8e38 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -7,5 +7,7 @@
 <use>
   <flag name='apbs'>Pymol supprt for sci-chemistry/apbs</flag>
   <flag name='shaders'>Enable shaders support for Pymol</flag>
+  <flag name='numpy'>Enable numpy support for Pymol</flag>
+  <flag name='vmd'>Builds molfile plugin support</flag>
 </use>
 </pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-9999-r1.ebuild b/sci-chemistry/pymol/pymol-9999-r1.ebuild
new file mode 100644
index 000000000..bc3d4d085
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-9999-r1.ebuild
@@ -0,0 +1,128 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+PYTHON_MODNAME="chempy pmg_tk pymol"
+APBS_PATCH="090618"
+
+inherit distutils subversion flag-o-matic
+
+ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol"
+
+DESCRIPTION="A Python-extensible molecular graphics system."
+HOMEPAGE="http://pymol.sourceforge.net/"
+SRC_URI="apbs? ( http://dev.gentooexperimental.org/~jlec/distfiles/apbs_tools.py.${APBS_PATCH}.bz2 )"
+
+LICENSE="PSF-2.2"
+IUSE="apbs numpy shaders vmd"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/pmw
+		dev-python/numpy
+		>=dev-lang/python-2.4[tk]
+		media-libs/libpng
+		sys-libs/zlib
+		virtual/glut
+		apbs? ( dev-libs/maloc
+				sci-chemistry/apbs
+				sci-chemistry/pdb2pqr
+		)"
+DEPEND="${RDEPEND}"
+
+pkg_setup(){
+	python_version
+}
+
+src_unpack() {
+	use apbs && unpack ${A}
+	subversion_src_unpack
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-data-path.patch || die
+
+	# Turn off splash screen.  Please do make a project contribution
+	# if you are able though.
+	[[ -n ${WANT_SPLASH} ]] || epatch "${FILESDIR}"/nosplash-gentoo.patch
+
+	# Respect CFLAGS
+	sed -i \
+		-e "s:\(ext_comp_args=\).*:\1[]:g" \
+		"${S}"/setup.py
+
+	use shaders && \
+		sed \
+			-e '/PYMOL_OPENGL_SHADERS/s:^#::g' \
+			-i setup.py
+
+	if use apbs; then
+		cp -f "${WORKDIR}"/apbs_tools.py.${APBS_PATCH} modules/pmg_tk/startup/apbs_tools.py || die
+		sed "s:LIBANDPYTHON:$(python_get_libdir):g" \
+			-i modules/pmg_tk/startup/apbs_tools.py || die
+	fi
+
+	use vmd && \
+		sed \
+			-e 's:\] + 0 \* \[:] + 1 * [:g' \
+			-e '/contrib\/uiuc\/plugins/s:^#::g' \
+			-e '/PYMOL_VMD_PLUGINS/s:^#::g' \
+			-i setup.py
+
+	use numpy && \
+		sed \
+			-e '/PYMOL_NUMPY/s:^#::g' \
+			-i setup.py
+}
+
+src_configure() {
+	:
+}
+
+src_install() {
+	distutils_src_install
+
+	# 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)/${PN}
+		PYMOL_DATA="/usr/share/pymol/data"
+		PYMOL_SCRIPTS="/usr/share/pymol/scripts"
+	EOF
+
+	use apbs && \
+	echo "APBS_PSIZE=$(python_get_sitedir)/pdb2pqr/src/psize.py" >> "${T}"/20pymol
+
+	doenvd "${T}"/20pymol || die "Failed to install env.d file."
+
+	cat >> "${T}"/pymol <<- EOF
+	#!/bin/sh
+	${python} -O \${PYMOL_PATH}/__init__.py \$*
+	EOF
+
+	dobin "${T}"/pymol || die "Failed to install wrapper."
+
+	insinto /usr/share/pymol
+	doins -r test data scripts || die "no shared data"
+
+	insinto /usr/share/pymol/examples
+	doins -r examples || die "Failed to install docs."
+
+	dodoc DEVELOPERS README || die "Failed to install docs."
+
+	if ! use apbs; then
+		rm "${D}"$(python_get_sitedir)/pmg_tk/startup/apbs_tools.py
+	fi
+}
+
+pkg_postinst(){
+	distutils_pkg_postinst
+
+	# The apbs ebuild was just corrected and not bumped #213616
+	if use apbs; then
+		[ -e /usr/share/apbs-0.5* ] && \
+		ewarn "You need to reemerge sci-chemistry/apbs!"
+	fi
+}