sci-chemistry/parassign: New addition

Package-Manager: portage-2.2.0_alpha176/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

3 files changed, 101 insertions, 2 deletions

diff --git a/sci-chemistry/parassign/Manifest b/sci-chemistry/parassign/Manifest
index 16ac4d920330..5b8125deca02 100644
--- a/sci-chemistry/parassign/Manifest
+++ b/sci-chemistry/parassign/Manifest
@@ -1,4 +1,14 @@
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diff --git a/sci-chemistry/parassign/metadata.xml b/sci-chemistry/parassign/metadata.xml
new file mode 100644
index 000000000000..144ad6d646ca
--- /dev/null
+++ b/sci-chemistry/parassign/metadata.xml
@@ -0,0 +1,27 @@
+<?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>
+The use of paramagnetic NMR data for the refinement of structures of proteins 
+and protein complexes is widespread. However, the power of paramagnetism for 
+protein assignment has not yet been fully exploited. PARAssign is software that 
+uses pseudocontact shift data derived from several paramagnetic centers attached
+to the protein to obtain amide and methyl assignments. The ability of PARAssign 
+to perform assignment when the positions of the paramagnetic centers are known 
+and unknown is demonstrated. PARAssign has been tested using synthetic data for 
+methyl assignment of a 47 kDa protein, and using both synthetic and experimental
+data for amide assignment of a 14 kDa protein. The complex fitting space 
+involved in such an assignment procedure necessitates that good starting 
+conditions are found, both regarding placement and strength of paramagnetic 
+centers. These starting conditions are obtained through automated tensor 
+placement and user-defined tensor parameters. The results presented herein 
+demonstrate that PARAssign is able to successfully perform resonance assignment
+in large systems with a high degree of reliability. This software provides a 
+method for obtaining the assignments of large systems, which may previously have
+been unassignable, by using 2D NMR spectral data and a known protein structure.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-chemistry/parassign/parassign-20130522.ebuild b/sci-chemistry/parassign/parassign-20130522.ebuild
new file mode 100644
index 000000000000..3d3aa5dfcba2
--- /dev/null
+++ b/sci-chemistry/parassign/parassign-20130522.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/parassign/parassign-20130522.ebuild,v 1.1 2013/05/22 11:12:33 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1 python-r1
+
+DESCRIPTION="Assign protein nuclei solely on the basis of pseudocontact shifts (PCS)"
+HOMEPAGE="http://protchem.lic.leidenuniv.nl/software/parassign/registration"
+SRC_URI="PARAssign_Linux_x64_86.tgz"
+
+SLOT="0"
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	dev-python/cython
+	dev-python/matplotlib
+	dev-python/numpy
+	dev-python/scientificpython
+	sci-biology/biopython
+	sci-libs/scipy"
+
+S="${WORKDIR}"/PARAssign_Linux_x64_86/
+
+src_prepare() {
+	sed \
+		-e '1i#!/usr/bin/python2' \
+		-i code/*py || die
+
+	if use x86; then
+		sed \
+			-e "s:munkres64:munkres:g" \
+			-i modules/setup.py || die
+	elif use amd64; then
+		sed \
+			-e "s:munkres:munkres64:g" \
+			-i code/*py || die
+	fi
+	cd modules || die
+	rm *o *c || die
+	distutils-r1_src_prepare
+}
+
+src_compile() {
+	cd modules || die
+	distutils-r1_src_compile
+}
+
+src_install() {
+	python_parallel_foreach_impl python_doscript code/* || die
+
+	dodoc PARAssign_Tutorial.pdf README
+
+	cd modules || die
+	distutils-r1_src_install
+}