vmd and numpy added to IUSE

apbs plugin support now depends on sci-chemistry/pymol-apbs-plugin
(Portage version: 2.2_rc62/cvs/Linux x86_64)

4 files changed, 151 insertions, 1 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 8e3da3dcf330..ce97881c561c 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.51 2010/02/01 20:42:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.52 2010/02/01 21:48:57 jlec Exp $
+
+*pymol-1.2.2-r1 (01 Feb 2010)
+
+  01 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +pymol-1.2.2-r1.ebuild, +files/pymol-1.2.2-vmd.patch, metadata.xml:
+  vmd and numpy added to IUSE
+  apbs plugin support now depends on sci-chemistry/pymol-apbs-plugin
 
   01 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org> pymol-1.2.1.ebuild,
   pymol-1.2.2.ebuild:
diff --git a/sci-chemistry/pymol/files/pymol-1.2.2-vmd.patch b/sci-chemistry/pymol/files/pymol-1.2.2-vmd.patch
new file mode 100644
index 000000000000..1355abe22093
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.2.2-vmd.patch
@@ -0,0 +1,33 @@
+Index: setup.py
+===================================================================
+--- setup.py	(revision 3887)
++++ setup.py	(working copy)
+@@ -123,8 +123,8 @@
+               "/usr/include/freetype2",
+ #                 "/users/warren/ext/include",
+ # VMD plugin support
+-#              "contrib/uiuc/plugins/include",
+-#              "contrib/uiuc/plugins/molfile_plugin/src",
++              "contrib/uiuc/plugins/include",
++              "contrib/uiuc/plugins/molfile_plugin/src",
+               ]
+     libs=["GL","GLU","glut","png","z","freetype",
+ #          "Xxf86vm"
+@@ -143,7 +143,7 @@
+ # Numeric Python support                    
+ #                ("_PYMOL_NUMPY",None),
+ # VMD plugin support           
+-#               ("_PYMOL_VMD_PLUGINS",None)
++               ("_PYMOL_VMD_PLUGINS",None)
+                 ]
+     ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
+     ext_link_args=[]
+@@ -290,7 +290,7 @@
+     "layer5/main.c"
+ # VMD plugin support
+     # switch the 0 to 1 to activate the additional source code
+-    ] + 0 * [
++    ] + 1 * [
+ # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
+     'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
+     'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index 41c9ec230233..4a1b6bfe8bb6 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -7,6 +7,8 @@
 </maintainer>
 <use>
 		<flag name="apbs">Install the apbs plugin</flag>
+		<flag name="numpy">Compile numpy support</flag>
 		<flag name="shaders">Build with Shaders support - good for high-end 3D video cards.</flag>
+		<flag name="vmd">Enable vmd module for trajectories</flag>
 </use>
 </pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-1.2.2-r1.ebuild b/sci-chemistry/pymol/pymol-1.2.2-r1.ebuild
new file mode 100644
index 000000000000..82d774f32f18
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.2.2-r1.ebuild
@@ -0,0 +1,108 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.2.2-r1.ebuild,v 1.1 2010/02/01 21:48:57 jlec Exp $
+
+EAPI="2"
+
+inherit distutils
+
+PYTHON_MODNAME="chempy pmg_tk pymol"
+REV="3859"
+
+DESCRIPTION="A Python-extensible molecular graphics system."
+HOMEPAGE="http://pymol.sourceforge.net/"
+SRC_URI="http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol.tar.gz?view=tar&pathrev=${REV} -> ${P}.tar.gz"
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="apbs numpy shaders vmd"
+
+DEPEND=">=dev-lang/python-2.4[tk]
+		dev-python/numpy
+		dev-python/pmw
+		media-libs/freetype:2
+		media-libs/libpng
+		media-video/mpeg-tools
+		sys-libs/zlib
+		virtual/glut
+		apbs? (
+			dev-libs/maloc
+			sci-chemistry/apbs
+			sci-chemistry/pdb2pqr
+			sci-chemistry/pymol-apbs-plugin
+		)"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+pkg_setup(){
+	python_version
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/1.2.1/${PN}-1.2.1-data-path.patch \
+		|| die "Failed to apply data-path.patch"
+
+	# Turn off splash screen.  Please do make a project contribution
+	# if you are able though. #299020
+	epatch "${FILESDIR}"/1.2.1/nosplash-gentoo.patch
+
+	# Respect CFLAGS
+	sed -i \
+		-e "s:\(ext_comp_args=\).*:\1[]:g" \
+		"${S}"/setup.py || die "Failed running sed on setup.py"
+
+	use shaders && epatch "${FILESDIR}"/${P}-shaders.patch
+
+	if use apbs; then
+		cp -f "${WORKDIR}"/apbs_tools.py.${APBS_PATCH} modules/pmg_tk/startup/apbs_tools.py \
+			|| die "Failed to copy apbs_tools.py"
+
+		sed "s:LIBANDPYTHON:$(python_get_libdir):g" \
+			-i modules/pmg_tk/startup/apbs_tools.py \
+				|| die "Failed running sed on apbs_tools.py"
+	fi
+
+	use vmd && epatch "${FILESDIR}"/${P}-vmd.patch
+
+	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)/${PN}
+		PYMOL_DATA="/usr/share/pymol/data"
+		PYMOL_SCRIPTS="/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${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."
+
+	rm "${D}"$(python_get_sitedir)/pmg_tk/startup/apbs_tools.py
+}