[gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/

[Nicolas Bock]

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@g.o> +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@g.o</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
+}