From: "Nicolas Bock" <nicolasbock@gmail.com>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/
Date: Wed, 31 Jul 2013 16:45:40 +0000 (UTC) [thread overview]
Message-ID: <1375178545.e778add7c5e5b9a163df522b00ac5fe85bef0d77.nicolasbock@gentoo> (raw)
commit: e778add7c5e5b9a163df522b00ac5fe85bef0d77
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jul 30 10:02:25 2013 +0000
Commit: Nicolas Bock <nicolasbock <AT> gmail <DOT> 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 <jlec@gentoo.org> +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 @@
+<?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>
+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.
+</longdescription>
+</pkgmetadata>
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
+}
next reply other threads:[~2013-07-31 16:45 UTC|newest]
Thread overview: 6+ messages / expand[flat|nested] mbox.gz Atom feed top
2013-07-31 16:45 Nicolas Bock [this message]
-- strict thread matches above, loose matches on Subject: below --
2015-09-21 17:44 [gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/ Justin Lecher
2015-10-06 21:11 Marius Brehler
2021-01-10 18:37 Andrew Ammerlaan
2021-01-19 16:56 Andrew Ammerlaan
2021-02-04 8:05 Andrew Ammerlaan
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