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jlec 13/05/22 11:12:33 |
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|
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Added: metadata.xml ChangeLog parassign-20130522.ebuild |
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Manifest |
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Log: |
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sci-chemistry/parassign: New addition |
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|
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(Portage version: 2.2.0_alpha176/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916) |
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|
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Revision Changes Path |
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1.1 sci-chemistry/parassign/metadata.xml |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/parassign/metadata.xml?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/parassign/metadata.xml?rev=1.1&content-type=text/plain |
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|
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Index: metadata.xml |
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=================================================================== |
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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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<pkgmetadata> |
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<herd>sci-chemistry</herd> |
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<maintainer> |
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<email>jlec@g.o</email> |
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</maintainer> |
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<longdescription> |
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The use of paramagnetic NMR data for the refinement of structures of proteins |
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and protein complexes is widespread. However, the power of paramagnetism for |
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protein assignment has not yet been fully exploited. PARAssign is software that |
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uses pseudocontact shift data derived from several paramagnetic centers attached |
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to the protein to obtain amide and methyl assignments. The ability of PARAssign |
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to perform assignment when the positions of the paramagnetic centers are known |
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and unknown is demonstrated. PARAssign has been tested using synthetic data for |
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methyl assignment of a 47 kDa protein, and using both synthetic and experimental |
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data for amide assignment of a 14 kDa protein. The complex fitting space |
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involved in such an assignment procedure necessitates that good starting |
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conditions are found, both regarding placement and strength of paramagnetic |
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centers. These starting conditions are obtained through automated tensor |
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placement and user-defined tensor parameters. The results presented herein |
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demonstrate that PARAssign is able to successfully perform resonance assignment |
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in large systems with a high degree of reliability. This software provides a |
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method for obtaining the assignments of large systems, which may previously have |
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been unassignable, by using 2D NMR spectral data and a known protein structure. |
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</longdescription> |
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</pkgmetadata> |
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|
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1.1 sci-chemistry/parassign/ChangeLog |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/parassign/ChangeLog?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/parassign/ChangeLog?rev=1.1&content-type=text/plain |
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|
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Index: ChangeLog |
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=================================================================== |
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# ChangeLog for sci-chemistry/parassign |
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# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/parassign/ChangeLog,v 1.1 2013/05/22 11:12:33 jlec Exp $ |
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|
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*parassign-20130522 (22 May 2013) |
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|
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22 May 2013; Justin Lecher <jlec@g.o> +parassign-20130522.ebuild, |
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+metadata.xml: |
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New addition |
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1.1 sci-chemistry/parassign/parassign-20130522.ebuild |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/parassign/parassign-20130522.ebuild?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/parassign/parassign-20130522.ebuild?rev=1.1&content-type=text/plain |
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|
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Index: parassign-20130522.ebuild |
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=================================================================== |
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# Copyright 1999-2013 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/parassign/parassign-20130522.ebuild,v 1.1 2013/05/22 11:12:33 jlec Exp $ |
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|
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EAPI=5 |
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|
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PYTHON_COMPAT=( python{2_6,2_7} ) |
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|
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inherit distutils-r1 python-r1 |
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|
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DESCRIPTION="Assign protein nuclei solely on the basis of pseudocontact shifts (PCS)" |
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HOMEPAGE="http://protchem.lic.leidenuniv.nl/software/parassign/registration" |
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SRC_URI="PARAssign_Linux_x64_86.tgz" |
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|
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SLOT="0" |
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LICENSE="Apache-2.0" |
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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IUSE="" |
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|
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RDEPEND="" |
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DEPEND="${RDEPEND} |
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dev-python/cython |
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dev-python/matplotlib |
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dev-python/numpy |
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dev-python/scientificpython |
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sci-biology/biopython |
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sci-libs/scipy" |
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|
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S="${WORKDIR}"/PARAssign_Linux_x64_86/ |
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|
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src_prepare() { |
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sed \ |
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-e '1i#!/usr/bin/python2' \ |
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-i code/*py || die |
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|
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if use x86; then |
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sed \ |
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-e "s:munkres64:munkres:g" \ |
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-i modules/setup.py || die |
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elif use amd64; then |
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sed \ |
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-e "s:munkres:munkres64:g" \ |
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-i code/*py || die |
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fi |
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cd modules || die |
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rm *o *c || die |
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distutils-r1_src_prepare |
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} |
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|
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src_compile() { |
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cd modules || die |
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distutils-r1_src_compile |
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} |
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|
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src_install() { |
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python_parallel_foreach_impl python_doscript code/* || die |
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|
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dodoc PARAssign_Tutorial.pdf README |
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|
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cd modules || die |
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distutils-r1_src_install |
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} |
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1.1 sci-chemistry/parassign/Manifest |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/parassign/Manifest?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/parassign/Manifest?rev=1.1&content-type=text/plain |
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|
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Index: Manifest |
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=================================================================== |
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DIST PARAssign_Linux_x64_86.tgz 76693208 SHA256 56a322a8825c13cd3e7d90998471c47fb6062e79e2d20108b4fb6ed24664c89d SHA512 63018b0f1e3ce7821cebb90cd59ef5fdfa44b7ce6776956184b55a6247009f5e9df435332772dfa0db7294308c4d930ff0104daf45a46df709fb132dac10bd79 WHIRLPOOL 87ae85974f2a84c3814d261390e011f7ef2a012881df15f0f8ba4a7b5e88992e7932f12566847eaa38958394f7a243a4f0d536375e4640377d6f183e793bccc5 |
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EBUILD parassign-20130522.ebuild 1225 SHA256 af822a83a42e4d4efdd0706fc6b2946c9b579f82aac5aa22180b24623940b8a9 SHA512 1a0184774eaacb001c52b2ddd4a6859c1ecf40685385be2184331c6466be1b34c8c2a9f56c405725bb1b4e315ff267ebfa69f486e2a37ac9989579092b93b978 WHIRLPOOL cb906e6f701d99217554808895f6b346308e8e16fe8062d50999fb6a0a2dda0b0949baf98e038ba68fff86df13ce1fc30e5b3ace18d50b01e723789720cc816a |
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MISC ChangeLog 267 SHA256 79266c77471973648834778a6ccd1fe58b7c63777ed4f7b9df635d966af7ba60 SHA512 d74d2220b04c0f02f05f582a952e783a2d1316989c88958d6ee61929a55aa9067f737a92b6cfedb99266a6ff159eeeab54ad339b770e45432db5f44f65ad1767 WHIRLPOOL ef06c4e2ba6ec1554d13c67e4bdfe032cc4afce2d449a7ee13f97971be8cf30274d6bdf510402828ce0cd998c1ee2a84c6d43c0f6181b0097bd160f5d6f9870b |
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MISC metadata.xml 1609 SHA256 afb0540b0835deed76b8b623e187067d7c329d7823a5309b8e621be83c486be8 SHA512 d06fad8456c4d326d8f194fdbf60a28addd79d57cf74c6c43538993535ff236f32af827701973c6d6f09107cc938e661fc823fd076bca662e2ada938bde43b2e WHIRLPOOL c678b21cbf0303393b4d490e1e329438520259b5dadf16981764f751d4cecb06cc87ba80a4f0811824875aadd41b5be2df97388bcf7ea424de5df7a86eb0b4ca |
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