reinit the tree, so we can have metadata

4 files changed, 180 insertions, 0 deletions

diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest
new file mode 100644
index 000000000000..5aeed090a90e
--- /dev/null
+++ b/sci-chemistry/pdb-tools/Manifest
@@ -0,0 +1,6 @@
+DIST pdbTools_0.2.1.tar.gz 103835 SHA256 317a5246e806a2b3d0425d080d679646fc77388e3e855412527603f945fa37ae SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 WHIRLPOOL 36d8cf71ba9f9b28e3ad59828539f4e94bbb8bc4514f050ddcbec63857b154ecdc7c32c2945c0d15f4d718c4fe5ab3adcb2e62a4368bfd819b80e9641a9dfd88
+EBUILD pdb-tools-0.2.1-r1.ebuild 1675 SHA256 435fb08c68c9c04fd62d0c0cdd926fc2d7ced72df71cdf85d53abdb167c63202 SHA512 f356c319d545920d550bdee48fd84ceebc7ad022d3dc58c28c79060da2aeb953c87328b3faeb08b6b8c4973ee9dd2b97a42a857ef51b1b4949b91a5333f9d147 WHIRLPOOL 46939042237121eba404f029f92cce7dcf28776e79b7cfce7636846bb95e6be8873710b28a83284c003a9ea2230b45604efaf901925206a48d5c3398b71bdb74
+EBUILD pdb-tools-0.2.1-r2.ebuild 1740 SHA256 106af905d17dbb6449279519913ea60667e46f70e4f67363ee6febcab8f494ce SHA512 06ce18d1f7aaa9b2e4e1f8c29fa7e187737af741ee53570a65b41b28c9bdb3ba23e8cda4b37d70fb169eed84829ebf425c22193bef587dbc87dbbdfec2a8f30b WHIRLPOOL c2306ed61a9c8ffabe0360c00533c2a66a28ac6ec7bce7a2f8ae6600a82d2a0b1a02fbf0669ed110acdf506b432ae21fb164094349073ce0376b73c5fc7ebded
+MISC ChangeLog 3379 SHA256 43a935f6490ec1e126bb9ec2e611971bd7752059c512b563a0491cda1f24687f SHA512 7b03f3807c361f84aca9a0788cbd59057991a7598b525e72522f3e3a0fd9efaab5bec335211a9733f302e93d1392fbe9f6088dbd3276063431871b2d0a092da7 WHIRLPOOL fc3ee4b9d62c2e21d7b8fc02b0148d424e0e1b55fd4813b2e1cabe3aef9e96f73b105789a5880ed3e418fd3d7fb5b7ccc296944aa41b208587efeed940e84805
+MISC ChangeLog-2015 3211 SHA256 286ecae6758c4a581103511115c76269aa93dc0cf75581e3c3cd68a880286ace SHA512 3152a37dd8ed05293941c2a01bb40f02988222706871b0459f2aea3de8c45607350553137839f3c2559ec5ad62a5aa0510deb79498751b515ec9614a9d2ba6cc WHIRLPOOL 8f98eaecbdc391768e2f98ea8e3c626cbae8fb6eb2fe3ec12f800c4297ff0e0ab738b522762bab0bf3bce8b504d90ed8bedb14f17878b2441f7fe291bf0bc08d
+MISC metadata.xml 413 SHA256 bc95368bb1cf8894d12449e7b03caa3ac05f7a8fd661343a643a96c2229a8b37 SHA512 74abf290517514aa17fadf8271d2af124fef766b473199502959a662d3bf7a8fed59746b43b3084b83bc14f8d5b9048b419f59d901dec100cbdd81975864cce2 WHIRLPOOL 1983ce37297a5d9bb911c0f1c598a03d03e770746a276e0095de84134cd76434f04dd74f8bf9dfa9038671f92ed5bae7724122a772d77ea59d27fa34f9a77891
diff --git a/sci-chemistry/pdb-tools/metadata.xml b/sci-chemistry/pdb-tools/metadata.xml
new file mode 100644
index 000000000000..25095bc4b42e
--- /dev/null
+++ b/sci-chemistry/pdb-tools/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="google-code">pdb-tools</remote-id>
+    <remote-id type="github">harmslab/pdbtools</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild
new file mode 100644
index 000000000000..88c1f246e8a2
--- /dev/null
+++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 pypy )
+
+inherit fortran-2 python-single-r1 toolchain-funcs
+
+MY_PN="pdbTools"
+
+DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files"
+HOMEPAGE="https://github.com/harmslab/pdbtools"
+SRC_URI="https://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${MY_PN}_${PV}
+
+pkg_setup() {
+	python-single-r1_pkg_setup
+	fortran-2_pkg_setup
+}
+
+src_prepare() {
+	sed \
+		-e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \
+		-i pdb_sasa.py || die
+	sed \
+		-e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \
+		-i pdb_satk.py || die
+	sed \
+		-e 's:> %:>%:g' \
+		-i pdb_seq.py || die
+}
+
+src_compile() {
+	mkdir bin
+	cd satk
+	for i in *.f; do
+		einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}"
+		$(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die
+		$(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die
+		sed \
+			-e "s:${i/.f}.out:${i/.f}:g" \
+			-i ../pdb_satk.py || die
+	done
+}
+
+src_install() {
+	local script
+	insinto /usr/share/${PN}
+	doins -r pdb_data/peptides
+	rm -rf pdb_data/peptides || die
+
+	python_domodule helper pdb_data
+
+	python_moduleinto ${PN/-/_}
+	python_domodule *.py
+
+	for i in pdb_*.py; do
+		cat > ${i/.py} <<- EOF
+		#!${EPREFIX}/bin/bash
+		${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@
+		EOF
+		dobin ${i/.py}
+	done
+
+	dobin bin/*
+	dodoc README
+}
diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild
new file mode 100644
index 000000000000..35910807746f
--- /dev/null
+++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit fortran-2 python-single-r1 toolchain-funcs
+
+MY_PN="pdbTools"
+
+DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files"
+HOMEPAGE="https://github.com/harmslab/pdbtools"
+SRC_URI="https://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${MY_PN}_${PV}
+
+pkg_setup() {
+	python-single-r1_pkg_setup
+	fortran-2_pkg_setup
+}
+
+src_prepare() {
+	sed \
+		-e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \
+		-i pdb_sasa.py || die
+	sed \
+		-e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \
+		-i pdb_satk.py || die
+	sed \
+		-e 's:> %:>%:g' \
+		-i pdb_seq.py || die
+
+	sed \
+		-e "/import/s:helper:${PN/-/_}.helper:g" \
+		-i *.py || die
+}
+
+src_compile() {
+	mkdir bin
+	cd satk
+	for i in *.f; do
+		einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}"
+		$(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die
+		$(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die
+		sed \
+			-e "s:${i/.f}.out:${i/.f}:g" \
+			-i ../pdb_satk.py || die
+	done
+}
+
+src_install() {
+	local script
+	insinto /usr/share/${PN}
+	doins -r pdb_data/peptides
+	rm -rf pdb_data/peptides || die
+
+	python_domodule pdb_data
+
+	python_moduleinto ${PN/-/_}
+	python_domodule helper *.py
+
+	for i in pdb_*.py; do
+		cat > ${i/.py} <<- EOF
+		#!${EPREFIX}/bin/bash
+		${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@
+		EOF
+		dobin ${i/.py}
+	done
+
+	dobin bin/*
+	dodoc README
+}