New Addition

(Portage version: 2.2.0_alpha28/cvs/Linux x86_64)

4 files changed, 106 insertions, 0 deletions

diff --git a/sci-chemistry/pymol-plugins-msms/ChangeLog b/sci-chemistry/pymol-plugins-msms/ChangeLog
new file mode 100644
index 000000000000..bf553a656b7a
--- /dev/null
+++ b/sci-chemistry/pymol-plugins-msms/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/pymol-plugins-msms
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol-plugins-msms/ChangeLog,v 1.1 2011/03/22 08:33:08 jlec Exp $
+
+*pymol-plugins-msms-100415 (22 Mar 2011)
+
+  22 Mar 2011; Justin Lecher <jlec@gentoo.org> +files/100415-msms.patch,
+  +pymol-plugins-msms-100415.ebuild, +metadata.xml:
+  New Addition
+
diff --git a/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch
new file mode 100644
index 000000000000..0d26fb31c5f1
--- /dev/null
+++ b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch
@@ -0,0 +1,33 @@
+ pymol-plugins-msms-100415.py |   18 ++++++++++--------
+ 1 files changed, 10 insertions(+), 8 deletions(-)
+
+diff --git a/pymol-plugins-msms-100415.py b/pymol-plugins-msms-100415.py
+index 725934d..7ea00bf 100644
+--- a/pymol-plugins-msms-100415.py
++++ b/pymol-plugins-msms-100415.py
+@@ -99,15 +99,17 @@ class MSMSPlugin:
+         self.cleanup_saved_pymol_sel.set(True) # by default, clean up
+ 
+         self.pdb_fn.set('')
+-        if 'MSMS_BIN' in os.environ:
+-            if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN']
+-            self.msms_bin.set(os.environ['MSMS_BIN'])
+-        else:
+-            if VERBOSE: print 'MSMS_BIN not found in environmental variables.'
+-            self.msms_bin.set('')
++        self.msms_bin.set('GENTOOMSMS')
++##        if 'MSMS_BIN' in os.environ:
++##            if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN']
++##            self.msms_bin.set(os.environ['MSMS_BIN'])
++##        else:
++##            if VERBOSE: print 'MSMS_BIN not found in environmental variables.'
++##            self.msms_bin.set('')
+ ##         self.pdb2xyzr_bin.set('')
+-        if 'PDB2XYZRN' in os.environ:  self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN'])
+-        else:                          self.pdb2xyzrn_bin.set('')
++        self.pdb2xyzrn_bin.set('GENTOOXYZRN')
++##        if 'PDB2XYZRN' in os.environ:  self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN'])
++##        else:                          self.pdb2xyzrn_bin.set('')
+         self.tmp_dir.set('/tmp')
+         self.cleanup_msms_output = Tkinter.BooleanVar()
+         self.cleanup_msms_output.set(True) # by default, clean up msms output
diff --git a/sci-chemistry/pymol-plugins-msms/metadata.xml b/sci-chemistry/pymol-plugins-msms/metadata.xml
new file mode 100644
index 000000000000..53db03dc2118
--- /dev/null
+++ b/sci-chemistry/pymol-plugins-msms/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+<maintainer>
+  <email>jlec@gentoo.org</email>
+</maintainer>
+<longdescription>
+MSMS is an excellent tool for computing protein solvent excluded surface (SES).
+MSMS Plugin for PyMOL provides a graphical user interface for running MSMS and 
+displaying its results in PyMOL. 
+
+1. Citation for this plugin: 
+    Hongbo Zhu. MSMS plugin for PyMOL, 2010, Biotechnology Center (BIOTEC), TU Dresden.
+2. Citation for PyMOL can be found at: http://pymol.sourceforge.net/faq.html#CITE
+</longdescription>
+</pkgmetadata>
diff --git a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415.ebuild b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415.ebuild
new file mode 100644
index 000000000000..cc5c5a579b71
--- /dev/null
+++ b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415.ebuild,v 1.1 2011/03/22 08:33:08 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+SUPPORT_PYTHON_ABIS="1"
+
+inherit eutils python
+
+DESCRIPTION="GUI for MSMS and displaying its results in PyMOL"
+HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/msms_pymol.html"
+SRC_URI="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/pymol_script/msms_pymol.py -> ${P}.py"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="BSD pymol"
+IUSE=""
+
+RDEPEND="
+	sci-chemistry/msms-bin
+	sci-chemistry/pymol"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	mkdir "${S}"
+	cp "${DISTDIR}"/${A} "${S}/"
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-msms.patch
+	sed \
+		-e "s:GENTOOMSMS:${EPREFIX}/opt/bin/msms:g" \
+		-e "s:GENTOOXYZRN:${EPREFIX}/usr/bin/pdb_to_xyzrn:g" \
+		-i ${A} || die
+	python_copy_sources
+}
+
+src_install() {
+	installation() {
+		insinto $(python_get_sitedir)/pmg_tk/startup/
+		doins ${P}.py || die
+	}
+	python_execute_function -s installation
+}