reinit the tree, so we can have metadata

3 files changed, 96 insertions, 0 deletions

diff --git a/sci-chemistry/parassign/Manifest b/sci-chemistry/parassign/Manifest
new file mode 100644
index 000000000000..94dee25bb160
--- /dev/null
+++ b/sci-chemistry/parassign/Manifest
@@ -0,0 +1,5 @@
+DIST PARAssign_Linux_x64_86.tgz 76693208 SHA256 56a322a8825c13cd3e7d90998471c47fb6062e79e2d20108b4fb6ed24664c89d SHA512 63018b0f1e3ce7821cebb90cd59ef5fdfa44b7ce6776956184b55a6247009f5e9df435332772dfa0db7294308c4d930ff0104daf45a46df709fb132dac10bd79 WHIRLPOOL 87ae85974f2a84c3814d261390e011f7ef2a012881df15f0f8ba4a7b5e88992e7932f12566847eaa38958394f7a243a4f0d536375e4640377d6f183e793bccc5
+EBUILD parassign-20130522.ebuild 1375 SHA256 8ba3200b371f0f2141a2e1788b5fe978b6f3f27d95c15b77dec75d330f6ad5c1 SHA512 7634d41463024be7606e63cd6fda1a9645c5fea48922232e1b404fe486416e89a454ea63220772ba75a327cf4c03140beef332f857c3a283063cd4687abadd46 WHIRLPOOL 552338a64f5cd36be567776b526e47a1a7fcbdd5311d6f16093c6a4df677046fc8c24bf5727e2ae0fe495b0e5b94ef488ca86461dfc2314c9460d2807a3eda47
+MISC ChangeLog 2932 SHA256 d0e349b0bda85091938cb845231989794f49603a5e7e857593cd6d010066df22 SHA512 065c8ce78bc6213d5a75803ddc9fbf1b511d4bcf06ef02ca055d93e3f34fdaafdfea55b418be6a35c6d83d081e6898f849960f4eb21bdcc61a43eff824b61ad4 WHIRLPOOL 1c4e9a6f969e55612331750dc0badddae00e0c95df8f5f0af48134b5563a51db253b3fbdfb3268ee90d30cedd15c981c36256ae2ea66bfbf9bc80085af84ea9d
+MISC ChangeLog-2015 710 SHA256 6120da15577d59fc164364e020f944e51c230c3f09d900ba49cfc6c4518de06a SHA512 3c8bfb6d578c3e2c12662e5f5a21432712016a2acbba7ad1c30dbf05d15d3d17f4416bf573d81a60b8106bafe2230beb37db0c9c52a294a4614403bb552fe038 WHIRLPOOL dd4794621e710997f9ee6617fd84b6a79f0afabcc76934ce9181882cbf94e3ad3d3961f16372886c01e79a80b6a1dee05b2c08cf49d64436e6a09360455d6dba
+MISC metadata.xml 1646 SHA256 4164a2b198ae08c9bd405ee3a0e09283a0462dcbd8cb8c464924a3a5a2175013 SHA512 73b07789bffc4fb45c5c3ca5c6b3e7fc75e358fc8a73b2cc2d76e8faf5bc1f2765fb1dcbdb2dcc34a21123d3f99bd8fc61ec3ca4a10e6887f26863b93fc1db1f WHIRLPOOL 32ece752cc3205c5b79045fff756ab926bbbe26a06c05722d2c60554e1d1856f9c2f4cc894292905bd276c17f9bf4e5a5c8af271ce2e88b79c9ec2c9597dc28d
diff --git a/sci-chemistry/parassign/metadata.xml b/sci-chemistry/parassign/metadata.xml
new file mode 100644
index 000000000000..f230593f73e9
--- /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>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </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..c49d09b2ab0a
--- /dev/null
+++ b/sci-chemistry/parassign/parassign-20130522.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_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"
+RESTRICT="fetch"
+
+SLOT="0"
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}"
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/scientificpython[${PYTHON_USEDEP}]
+	sci-biology/biopython[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]"
+
+S="${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_foreach_impl python_doscript code/* || die
+
+	dodoc PARAssign_Tutorial.pdf README
+
+	cd modules || die
+	distutils-r1_src_install
+}