diff options
Diffstat (limited to 'sci-chemistry/pdb-tools')
| -rw-r--r-- | sci-chemistry/pdb-tools/Manifest | 1 | ||||
| -rw-r--r-- | sci-chemistry/pdb-tools/metadata.xml | 11 | ||||
| -rw-r--r-- | sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild | 80 | ||||
| -rw-r--r-- | sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild | 84 |
4 files changed, 176 insertions, 0 deletions
diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest new file mode 100644 index 000000000000..bf2e4bfa7dce --- /dev/null +++ b/sci-chemistry/pdb-tools/Manifest @@ -0,0 +1 @@ +DIST pdbTools_0.2.1.tar.gz 103835 SHA256 317a5246e806a2b3d0425d080d679646fc77388e3e855412527603f945fa37ae SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 WHIRLPOOL 36d8cf71ba9f9b28e3ad59828539f4e94bbb8bc4514f050ddcbec63857b154ecdc7c32c2945c0d15f4d718c4fe5ab3adcb2e62a4368bfd819b80e9641a9dfd88 diff --git a/sci-chemistry/pdb-tools/metadata.xml b/sci-chemistry/pdb-tools/metadata.xml new file mode 100644 index 000000000000..13e9a3c93979 --- /dev/null +++ b/sci-chemistry/pdb-tools/metadata.xml @@ -0,0 +1,11 @@ +<?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> + <upstream> + <remote-id type="google-code">pdb-tools</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..ad4ab1dec397 --- /dev/null +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +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="http://code.google.com/p/pdb-tools/" +SRC_URI="http://${PN}.googlecode.com/files/${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..e56798f3c95b --- /dev/null +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +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="http://code.google.com/p/pdb-tools/" +SRC_URI="http://${PN}.googlecode.com/files/${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 +} |