proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

4 files changed, 73 insertions, 0 deletions

diff --git a/sci-chemistry/clashlist/Manifest b/sci-chemistry/clashlist/Manifest
new file mode 100644
index 000000000000..3c71b7792037
--- /dev/null
+++ b/sci-chemistry/clashlist/Manifest
@@ -0,0 +1 @@
+DIST molprobity-3.17.tgz 26429898 SHA256 2e70814efb4f566a522762a626f69669c09285cbb6fc26444eb947fde9b30f25 SHA512 a6e986f285ff7e8d167e2d1c935a55b080446c9809d352c95e2ffa32265892b59cd1611730e75ca88aa28387495d3ebd84226e1a9cdd33f0b27b1a8a1b6a469f WHIRLPOOL 3981522eeacaa589530e7d268cda786bebeaf676f7fa5c26508798022126bd1a1c8ea193f65e3c5c739fb3b516b26c3cf24ac0e7898e764a9cffab6637dcd5a9
diff --git a/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild b/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild
new file mode 100644
index 000000000000..7aedd7743f6b
--- /dev/null
+++ b/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+DESCRIPTION="Build lists of van der Waals clashes from an input PDB file"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
+SRC_URI="mirror://gentoo/molprobity-${PV}.tgz"
+
+SLOT="0"
+LICENSE="richardson"
+KEYWORDS="~amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	>=sci-chemistry/cluster-1.3.081231-r1
+	sci-chemistry/probe"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+src_prepare() {
+	sed \
+		-e 's: cluster : molprobity-cluster :g' \
+		-i molprobity3/bin/clashlist || die
+}
+
+src_install() {
+	dobin molprobity3/bin/clashlist
+}
diff --git a/sci-chemistry/clashlist/clashlist-3.17.ebuild b/sci-chemistry/clashlist/clashlist-3.17.ebuild
new file mode 100644
index 000000000000..513a1e024746
--- /dev/null
+++ b/sci-chemistry/clashlist/clashlist-3.17.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+DESCRIPTION="Build lists of van der Waals clashes from an input PDB file"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
+SRC_URI="mirror://gentoo/molprobity-${PV}.tgz"
+
+SLOT="0"
+LICENSE="richardson"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	<=sci-chemistry/cluster-1.3.081231
+	sci-chemistry/probe"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+src_install() {
+	dobin molprobity3/bin/clashlist
+}
diff --git a/sci-chemistry/clashlist/metadata.xml b/sci-chemistry/clashlist/metadata.xml
new file mode 100644
index 000000000000..c96b852229d5
--- /dev/null
+++ b/sci-chemistry/clashlist/metadata.xml
@@ -0,0 +1,16 @@
+<?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>
+Clashlist is a simple UNIX script which uses the awk facility along with
+the programs Probe and Cluster to build lists of van der Waals clashes
+from an input PDB-format molecular data file (with H atoms). These lists
+are organized such that collections of interacting residues are grouped
+together, sorted by the worst clash. For the purposes of this analysis,
+a clash is defined as a van der Waals overlap &gt;= 0.4 A.
+</longdescription>
+</pkgmetadata>