From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-chemistry/parassign/Manifest | 5 ++ sci-chemistry/parassign/metadata.xml | 27 ++++++++++ sci-chemistry/parassign/parassign-20130522.ebuild | 64 +++++++++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 sci-chemistry/parassign/Manifest create mode 100644 sci-chemistry/parassign/metadata.xml create mode 100644 sci-chemistry/parassign/parassign-20130522.ebuild (limited to 'sci-chemistry/parassign') 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 @@ + + + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + +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. + + 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 +} -- cgit v1.2.3