sci-chemistry/parassign: New addition

(Portage version: 2.2.0_alpha176/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

4 files changed, 103 insertions, 0 deletions

diff --git a/sci-chemistry/parassign/ChangeLog b/sci-chemistry/parassign/ChangeLog
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+# ChangeLog for sci-chemistry/parassign
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/parassign/ChangeLog,v 1.1 2013/05/22 11:12:33 jlec Exp $
+
+*parassign-20130522 (22 May 2013)
+
+  22 May 2013; Justin Lecher <jlec@gentoo.org> +parassign-20130522.ebuild,
+  +metadata.xml:
+  New addition
+
diff --git a/sci-chemistry/parassign/Manifest b/sci-chemistry/parassign/Manifest
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index 000000000000..16ac4d920330
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+++ b/sci-chemistry/parassign/Manifest
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+DIST PARAssign_Linux_x64_86.tgz 76693208 SHA256 56a322a8825c13cd3e7d90998471c47fb6062e79e2d20108b4fb6ed24664c89d SHA512 63018b0f1e3ce7821cebb90cd59ef5fdfa44b7ce6776956184b55a6247009f5e9df435332772dfa0db7294308c4d930ff0104daf45a46df709fb132dac10bd79 WHIRLPOOL 87ae85974f2a84c3814d261390e011f7ef2a012881df15f0f8ba4a7b5e88992e7932f12566847eaa38958394f7a243a4f0d536375e4640377d6f183e793bccc5
+EBUILD parassign-20130522.ebuild 1225 SHA256 af822a83a42e4d4efdd0706fc6b2946c9b579f82aac5aa22180b24623940b8a9 SHA512 1a0184774eaacb001c52b2ddd4a6859c1ecf40685385be2184331c6466be1b34c8c2a9f56c405725bb1b4e315ff267ebfa69f486e2a37ac9989579092b93b978 WHIRLPOOL cb906e6f701d99217554808895f6b346308e8e16fe8062d50999fb6a0a2dda0b0949baf98e038ba68fff86df13ce1fc30e5b3ace18d50b01e723789720cc816a
+MISC ChangeLog 267 SHA256 79266c77471973648834778a6ccd1fe58b7c63777ed4f7b9df635d966af7ba60 SHA512 d74d2220b04c0f02f05f582a952e783a2d1316989c88958d6ee61929a55aa9067f737a92b6cfedb99266a6ff159eeeab54ad339b770e45432db5f44f65ad1767 WHIRLPOOL ef06c4e2ba6ec1554d13c67e4bdfe032cc4afce2d449a7ee13f97971be8cf30274d6bdf510402828ce0cd998c1ee2a84c6d43c0f6181b0097bd160f5d6f9870b
+MISC metadata.xml 1609 SHA256 afb0540b0835deed76b8b623e187067d7c329d7823a5309b8e621be83c486be8 SHA512 d06fad8456c4d326d8f194fdbf60a28addd79d57cf74c6c43538993535ff236f32af827701973c6d6f09107cc938e661fc823fd076bca662e2ada938bde43b2e WHIRLPOOL c678b21cbf0303393b4d490e1e329438520259b5dadf16981764f751d4cecb06cc87ba80a4f0811824875aadd41b5be2df97388bcf7ea424de5df7a86eb0b4ca
diff --git a/sci-chemistry/parassign/metadata.xml b/sci-chemistry/parassign/metadata.xml
new file mode 100644
index 000000000000..144ad6d646ca
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+++ b/sci-chemistry/parassign/metadata.xml
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+<?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
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+++ b/sci-chemistry/parassign/parassign-20130522.ebuild
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+# 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
+}