From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id F38A51381F3 for ; Wed, 31 Jul 2013 16:45:44 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id E78B8E0984; Wed, 31 Jul 2013 16:45:43 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 7091BE0984 for ; Wed, 31 Jul 2013 16:45:43 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 1BA8333E9B9 for ; Wed, 31 Jul 2013 16:45:42 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id AA589E468F for ; Wed, 31 Jul 2013 16:45:40 +0000 (UTC) From: "Nicolas Bock" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Nicolas Bock" Message-ID: <1375178545.e778add7c5e5b9a163df522b00ac5fe85bef0d77.nicolasbock@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/panav/ChangeLog sci-chemistry/panav/metadata.xml sci-chemistry/panav/panav-0.20130730.ebuild X-VCS-Directories: sci-chemistry/panav/ X-VCS-Committer: nicolasbock X-VCS-Committer-Name: Nicolas Bock X-VCS-Revision: e778add7c5e5b9a163df522b00ac5fe85bef0d77 X-VCS-Branch: master Date: Wed, 31 Jul 2013 16:45:40 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: e7e582d9-90c9-42ec-81a2-b3b6f515fc9c X-Archives-Hash: 4aab6a819754edf151562bbc747bf590 commit: e778add7c5e5b9a163df522b00ac5fe85bef0d77 Author: Justin Lecher gentoo org> AuthorDate: Tue Jul 30 10:02:25 2013 +0000 Commit: Nicolas Bock gmail com> CommitDate: Tue Jul 30 10:02:25 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e778add7 sci-chemistry/panav: New addition written by me Package-Manager: portage-2.2.0_alpha190 --- sci-chemistry/panav/ChangeLog | 10 +++++++++ sci-chemistry/panav/metadata.xml | 30 +++++++++++++++++++++++++ sci-chemistry/panav/panav-0.20130730.ebuild | 34 +++++++++++++++++++++++++++++ 3 files changed, 74 insertions(+) diff --git a/sci-chemistry/panav/ChangeLog b/sci-chemistry/panav/ChangeLog new file mode 100644 index 0000000..f6add7e --- /dev/null +++ b/sci-chemistry/panav/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-chemistry/panav +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*panav-0.20130730 (30 Jul 2013) + + 30 Jul 2013; Justin Lecher +panav-0.20130730.ebuild, + +metadata.xml: + New addition written by me + diff --git a/sci-chemistry/panav/metadata.xml b/sci-chemistry/panav/metadata.xml new file mode 100644 index 0000000..3eacfae --- /dev/null +++ b/sci-chemistry/panav/metadata.xml @@ -0,0 +1,30 @@ + + + + sci-chemistry + + jlec@gentoo.org + + +It has been estimated that more than 20% of the proteins in the BMRB are +improperly referenced and that about 1% of all chemical shift assignments are +mis-assigned. These statistics also reflect the likelihood that any newly +assigned protein will have shift assignment or shift referencing errors. The +relatively high frequency of these errors continues to be a concern for the +biomolecular NMR community. While several programs do exist to detect and/or +correct chemical shift mis-referencing or chemical shift mis-assignments, most +can only do one, or the other. The one program (SHIFTCOR) that is capable of +handling both chemical shift mis-referencing and mis-assignments, requires the +3D structure coordinates of the target protein. Given that chemical shift +mis-assignments and chemical shift re-referencing issues should ideally be +addressed prior to 3D structure determination, there is a clear need to develop +a structure-independent approach. Here, we present a new structure-independent +protocol, which is based on using residue-specific and secondary +structure-specific chemical shift distributions calculated over +small (3–6 residue) fragments to identify mis-assigned resonances. The method +is also able to identify and re-reference mis-referenced chemical shift + assignments. Comparisons against existing re-referencing or mis-assignment + detection programs show that the method is as good or superior to existing + approaches. + + diff --git a/sci-chemistry/panav/panav-0.20130730.ebuild b/sci-chemistry/panav/panav-0.20130730.ebuild new file mode 100644 index 0000000..bc3d32c --- /dev/null +++ b/sci-chemistry/panav/panav-0.20130730.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 + +MY_PN="PANAV" + +DESCRIPTION="Probabilistic approach for validating protein NMR chemical shift assignments" +HOMEPAGE="http://link.springer.com/article/10.1007%2Fs10858-010-9407-y/fulltext.html" +SRC_URI="http://www.wishartlab.com/download/${MY_PN}.zip -> ${P}.zip" + +SLOT="0" +LICENSE="all-rights-reserved" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-java/cos + >=virtual/jre-1.6" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_PN} + +src_compile() { :; } + +src_install() { + java-pkg_newjar ${MY_PN}.jar ${PN}.jar + java-pkg_dolauncher + java-pkg_regjar "${EPREFIX}"/usr/share/cos/lib/cos.jar + dodoc README +}