diff options
Diffstat (limited to 'sci-chemistry')
814 files changed, 39094 insertions, 0 deletions
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild new file mode 100644 index 000000000000..ef7987d5d03e --- /dev/null +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +if [[ $PV = *9999* ]]; then + scm_eclass=git-2 + EGIT_REPO_URI=" + git://github.com/orbeckst/${PN}.git + https://github.com/orbeckst/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + scm_eclass=vcs-snapshot + SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +inherit eutils distutils-r1 ${scm_eclass} + +DESCRIPTION="Python framework for Gromacs" +HOMEPAGE="http://orbeckst.github.com/GromacsWrapper/" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="" + +DEPEND=" + >=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}] + >=dev-python/RecSQL-0.3[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + " +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/0001-Drop-chmod-hack.patch" +) diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild new file mode 100644 index 000000000000..6d95361ce0f4 --- /dev/null +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +if [[ $PV = *9999* ]]; then + scm_eclass=git-2 + EGIT_REPO_URI=" + git://github.com/orbeckst/${PN}.git + https://github.com/orbeckst/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + scm_eclass=vcs-snapshot + SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +inherit eutils distutils-r1 ${scm_eclass} + +DESCRIPTION="Python framework for Gromacs" +HOMEPAGE="http://orbeckst.github.com/GromacsWrapper/" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="" + +DEPEND=" + >=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}] + >=dev-python/RecSQL-0.3[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + " +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/0001-Drop-chmod-hack.patch" +) diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest new file mode 100644 index 000000000000..4c77ff3c1ead --- /dev/null +++ b/sci-chemistry/GromacsWrapper/Manifest @@ -0,0 +1,2 @@ +DIST GromacsWrapper-0.3.1.tar.gz 1575486 SHA256 ddd2668060668528878370961a9a33257cf3643fd0d9e9191b1d26d4f78e803b SHA512 655dae431bf575963af58a5f75abe6703fe1ecdddba5839b671d9237ddee0e33ab19b528e89bcba4db9063fe30622d44e8f47c7b6452b4d1eed8c7400873a012 WHIRLPOOL 3b848aff931190eabd49426d61186a3c1eef9779a9fabf95b4d21d47793e5543adbcba5ac2b39c8a9af7c2479930a8ea65bb336e2155dfca98378df56ba4cb3e +DIST GromacsWrapper-0.3.2.tar.gz 1592147 SHA256 2fe0173275ca125a4260aa05f82746338f237766fe8aa998e85a5b40cf83e42c SHA512 a9e0abb5e7ad0c6831e23b6a8c09c6e4cc74b33d66cd17df8e00b876dc275dda11c3d3723565d8d58c45bdf6b2b00323bf85e24e2d5324a8d8b597cc3e5d78a4 WHIRLPOOL 852d73d01e1060369521ec5ff5197c86daa30ae98f285fe5e3d392a315cff10c68e2ba54ec9a2659260cf6830cf17cb1e094eecbd63652e9c3f13fff8707a824 diff --git a/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch b/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch new file mode 100644 index 000000000000..8645df77b86e --- /dev/null +++ b/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch @@ -0,0 +1,28 @@ +From 49b8d9662365e0e9b0725682b8a8479de402b272 Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov <alexxy@gentoo.org> +Date: Sat, 23 Mar 2013 16:40:04 +0400 +Subject: [PATCH] Drop chmod hack. + +It doesnt work if wrapper installed system-wide + +Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> +--- + gromacs/config.py | 2 -- + 1 file changed, 2 deletions(-) + +diff --git a/gromacs/config.py b/gromacs/config.py +index cece6fc..2e686e7 100644 +--- a/gromacs/config.py ++++ b/gromacs/config.py +@@ -619,8 +619,6 @@ del g + # Must extract because it is part of a zipped python egg; + # see http://peak.telecommunity.com/DevCenter/PythonEggs#accessing-package-resources + GridMAT_MD = resource_filename(__name__,'external/GridMAT-MD_v1.0.2/GridMAT-MD.pl') +-os.chmod(GridMAT_MD, 0755) +- + + #: 3rd party bundled analysis scripts and tools; this is a list of triplets of + #: +-- +1.8.1.5 + diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml new file mode 100644 index 000000000000..43390c98619e --- /dev/null +++ b/sci-chemistry/GromacsWrapper/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <upstream> + <remote-id type="github">orbeckst/GromacsWrapper</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/PyMca/Manifest b/sci-chemistry/PyMca/Manifest new file mode 100644 index 000000000000..c6899e234b21 --- /dev/null +++ b/sci-chemistry/PyMca/Manifest @@ -0,0 +1 @@ +DIST pymca4.6.2-src.tgz 15979581 SHA256 c50d3a54cad633bac3ec361d1b3b63a78292f1ad4ed976e5206665edd76bc32d SHA512 e33188b446c399e50cf65ebca4bfeef34e1b7d99c331f670dc41ca204284fbba996a1c83bd12a2410a9972927aa9c92b42b5374c58c924b3a8583d4f37be6528 WHIRLPOOL 47f0491aa0e470661bea1aa247d1db730f1db7266f1d2be2272d08f203faa2a084bcb40d579861365ace26d2f94abe03485183eed03139ad7b697cf57bfa5324 diff --git a/sci-chemistry/PyMca/PyMca-4.6.2-r1.ebuild b/sci-chemistry/PyMca/PyMca-4.6.2-r1.ebuild new file mode 100644 index 000000000000..449f9b5ab220 --- /dev/null +++ b/sci-chemistry/PyMca/PyMca-4.6.2-r1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +MY_PV="${PV/_}" + +DESCRIPTION="X-ray Fluorescence Toolkit" +HOMEPAGE="http://pymca.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/pymca/pymca/${PN}${PV/_p1}/pymca${MY_PV}-src.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="X hdf5 matplotlib" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + virtual/opengl + X? ( + dev-python/PyQt4[${PYTHON_USEDEP}] + dev-python/pyqwt[${PYTHON_USEDEP}] + ) + hdf5? ( dev-python/h5py[${PYTHON_USEDEP}] ) + matplotlib? ( dev-python/matplotlib[${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +#S="${WORKDIR}/${PN}${MY_PV}" + +python_prepare_all() { + local PATCHES=( "${FILESDIR}"/${P}-gentoo.patch ) + export SPECFILE_USE_GNU_SOURCE=1 + distutils-r1_python_prepare_all +} diff --git a/sci-chemistry/PyMca/PyMca-4.6.2.ebuild b/sci-chemistry/PyMca/PyMca-4.6.2.ebuild new file mode 100644 index 000000000000..b1e6d2f50524 --- /dev/null +++ b/sci-chemistry/PyMca/PyMca-4.6.2.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_DEPEND="2" +SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.* *-pypy-*" + +inherit distutils eutils + +MY_PV="${PV/_}" + +DESCRIPTION="X-ray Fluorescence Toolkit" +HOMEPAGE="http://pymca.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/pymca/pymca/${PN}${PV/_p1}/pymca${MY_PV}-src.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="X hdf5 matplotlib" + +DEPEND=" + dev-python/numpy + dev-python/sip + virtual/opengl + dev-python/pyopengl + X? ( + dev-python/PyQt4 + dev-python/pyqwt + ) + hdf5? ( dev-python/h5py ) + matplotlib? ( dev-python/matplotlib )" +RDEPEND="${DEPEND}" + +#S="${WORKDIR}/${PN}${MY_PV}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gentoo.patch + export SPECFILE_USE_GNU_SOURCE=1 + distutils_src_prepare +} diff --git a/sci-chemistry/PyMca/files/4.4.1_p1-gentoo.patch b/sci-chemistry/PyMca/files/4.4.1_p1-gentoo.patch new file mode 100644 index 000000000000..487a45963d21 --- /dev/null +++ b/sci-chemistry/PyMca/files/4.4.1_p1-gentoo.patch @@ -0,0 +1,40 @@ +diff --git a/setup.py b/setup.py +index 0b0fa58..a4fdab6 100755 +--- a/setup.py ++++ b/setup.py +@@ -41,34 +41,8 @@ for line in file(os.path.join('PyMca', 'PyMcaMain.py')).readlines(): + print "PyMca X-Ray Fluorescence Toolkit %s" % __version__ + print + +-print "Type 'L' to view the license." +-print "Type 'yes' to accept the terms of the license." +-print "Type 'no' to decline the terms of the license." +-print +- +-while 1: +- try: +- resp = raw_input("Do you accept the terms of the license? ") +- except KeyboardInterrupt: +- raise SystemExit +- except: +- resp = "" +- +- resp = string.lower(string.strip(resp)) +- +- if resp == "yes": +- break +- +- if resp == "no": +- sys.exit(1) +- +- if resp == "l": +- os.system("more LICENSE.GPL") +- +- + # Specify all the required PyMca data +-data_files = [('PyMca', ['LICENSE.GPL', +- 'PyMca/Scofield1973.dict', ++data_files = [('PyMca', ['PyMca/Scofield1973.dict', + 'PyMca/changelog.txt', + 'PyMca/McaTheory.cfg', + 'PyMca/PyMcaSplashImage.png', diff --git a/sci-chemistry/PyMca/files/4.4.1_p1-impl-dec.patch b/sci-chemistry/PyMca/files/4.4.1_p1-impl-dec.patch new file mode 100644 index 000000000000..ea37348066d2 --- /dev/null +++ b/sci-chemistry/PyMca/files/4.4.1_p1-impl-dec.patch @@ -0,0 +1,12 @@ +diff --git a/PyMca/specfile/src/sfwrite.c b/PyMca/specfile/src/sfwrite.c +index 24df907..93c18e9 100755 +--- a/PyMca/specfile/src/sfwrite.c ++++ b/PyMca/specfile/src/sfwrite.c +@@ -55,6 +55,7 @@ + */ + #include <SpecFile.h> + #include <SpecFileP.h> ++#include <unistd.h> + + /* + * Declarations diff --git a/sci-chemistry/PyMca/files/PyMca-4.6.2-gentoo.patch b/sci-chemistry/PyMca/files/PyMca-4.6.2-gentoo.patch new file mode 100644 index 000000000000..81dfaf038fa6 --- /dev/null +++ b/sci-chemistry/PyMca/files/PyMca-4.6.2-gentoo.patch @@ -0,0 +1,16 @@ + setup.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/setup.py b/setup.py +index 0a77cdf..e7ba643 100644 +--- a/setup.py ++++ b/setup.py +@@ -55,7 +55,7 @@ packages = ['PyMca','PyMca.PyMcaPlugins', 'PyMca.tests'] + py_modules = [] + + # Specify all the required PyMca data +-data_files = [(PYMCA_DATA_DIR, ['LICENSE.GPL', ++data_files = [(PYMCA_DATA_DIR, [ + 'PyMca/PyMcaData/Scofield1973.dict', + 'changelog.txt', + 'PyMca/PyMcaData/McaTheory.cfg', diff --git a/sci-chemistry/PyMca/metadata.xml b/sci-chemistry/PyMca/metadata.xml new file mode 100644 index 000000000000..91146f1d585b --- /dev/null +++ b/sci-chemistry/PyMca/metadata.xml @@ -0,0 +1,22 @@ +<?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> +The PyMca Toolkit is a collection of Python tools for visualization and +analysis of energy-dispersive X-ray fluorescence data. It builds its graphic +interface and plotting routines on top of the C++ libraries Qt and Qwt +through their respective Python bindings PyQt and PyQwt. Nevertheless, +the data analysis routines can be used independently of any graphical +interface. +</longdescription> + <use> + <flag name="matplotlib">Support for plotting through matplotlib</flag> + </use> + <upstream> + <remote-id type="sourceforge">pymca</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/acpype/Manifest b/sci-chemistry/acpype/Manifest new file mode 100644 index 000000000000..e1cd9723b479 --- /dev/null +++ b/sci-chemistry/acpype/Manifest @@ -0,0 +1,3 @@ +DIST acpype-366.tar.xz 539408 SHA256 f0c77abea0a5680ecbbecadc1a95c8f851159b7c84d079f6f527336d447e1e9d +DIST acpype-374.tar.xz 521076 SHA256 60a15d1c29ba3254a17c0792ae859444641e7a9375bd24cdd8baccc27920fde3 SHA512 99915299b32878e2139f67503260b491e05f8a592c37c5668e5aea3414822965827a91e09578264cfb48684decbadfb60c833706b756ff277ffde8b15159391e WHIRLPOOL b4e59eec36438eb2ee6d05183a6f08200213923ff50fbff1377cd976c8e39cc24429eb727d890028af2b5b5ad90428c70a10821ae20b50f7fc494ff9163322a8 +DIST acpype-389.tar.xz 524460 SHA256 4fd4036308cd81a480beaa56ae65b43a8c5ee3bbfc64b07b4d0b6649602f529a SHA512 0fbcb83ae8306d6bcc1cfd921d70c67a15e14c443453ab8c4cfd7082c15b95599801abbe31a46313674aa4841c5cd5499b69cc080221acc2793dc808df247987 WHIRLPOOL 21c8ee51c651c7a519716c818b0febd5fd62384aeeb6a5ce0f8dcf877181edba75fdd15be0d5a158b5a22d051765fb231c7c10038b8da1bcd98bede848057e95 diff --git a/sci-chemistry/acpype/acpype-366.ebuild b/sci-chemistry/acpype/acpype-366.ebuild new file mode 100644 index 000000000000..01a804da9cba --- /dev/null +++ b/sci-chemistry/acpype/acpype-366.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +inherit eutils python +PYTHON_DEPEND="2:2.5" + +DESCRIPTION="AnteChamber PYthon Parser interfacE" +HOMEPAGE="http://code.google.com/p/acpype/" +SRC_URI="mirror://gentoo/${P}.tar.xz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="" + +DEPEND="sci-chemistry/ambertools" +RDEPEND="${DEPEND}" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + epatch "${FILESDIR}/${PN}.patch" + python_convert_shebangs -r 2 . +} + +src_install() { + newbin ${PN}.py ${PN} + newbin CcpnToAcpype.py CcpnToAcpype + dodoc NOTE.txt README.txt + insinto /usr/share/${PN} + doins -r ffamber_additions test +} diff --git a/sci-chemistry/acpype/acpype-374.ebuild b/sci-chemistry/acpype/acpype-374.ebuild new file mode 100644 index 000000000000..56036152102c --- /dev/null +++ b/sci-chemistry/acpype/acpype-374.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +PYTHON_DEPEND="2:2.5" + +inherit python + +DESCRIPTION="AnteChamber PYthon Parser interfacE" +HOMEPAGE="http://code.google.com/p/acpype/" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="" + +DEPEND="sci-chemistry/ambertools" +RDEPEND="${DEPEND}" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + python_convert_shebangs -r 2 . +} + +src_install() { + newbin ${PN}.py ${PN} + newbin CcpnToAcpype.py CcpnToAcpype + dodoc NOTE.txt README.txt + insinto /usr/share/${PN} + doins -r ffamber_additions test +} diff --git a/sci-chemistry/acpype/acpype-389.ebuild b/sci-chemistry/acpype/acpype-389.ebuild new file mode 100644 index 000000000000..6ff35e1fcc47 --- /dev/null +++ b/sci-chemistry/acpype/acpype-389.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +DESCRIPTION="AnteChamber PYthon Parser interfacE" +HOMEPAGE="http://code.google.com/p/acpype/" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND=" + ${PYTHON_DEPS} + sci-chemistry/ambertools" +RDEPEND="${DEPEND}" + +src_prepare() { + sed \ + -e '1s:^:#!/usr/bin/python\n\n:g' \ + -i CcpnToAcpype.py || die +} + +src_install() { + python_parallel_foreach_impl python_newscript ${PN}.py ${PN} + python_parallel_foreach_impl python_newscript CcpnToAcpype.py CcpnToAcpype + dodoc NOTE.txt README.txt + insinto /usr/share/${PN} + doins -r ffamber_additions test +} diff --git a/sci-chemistry/acpype/files/acpype.patch b/sci-chemistry/acpype/files/acpype.patch new file mode 100644 index 000000000000..9354527cc8a9 --- /dev/null +++ b/sci-chemistry/acpype/files/acpype.patch @@ -0,0 +1,37 @@ +Index: acpype.py +=================================================================== +--- acpype.py (revision 366) ++++ acpype.py (working copy) +@@ -3020,32 +3020,6 @@ + acMol2FileName = '%s_%s_%s.mol2' % (base, chargeType, atomType) + self.acMol2FileName = acMol2FileName + self.charmmBase = '%s_CHARMM' % base +- # check for which version of antechamber +- if 'amber10' in self.acExe: +- if qprog == 'sqm': +- self.printWarn("SQM is not implemented in AmberTools 1.2") +- self.printWarn("Setting mopac for antechamber") +- qprog = 'mopac' +- elif qprog == 'divcon': +- if not os.path.exists(os.path.join(os.path.dirname(self.acExe), qprog)): +- self.printWarn("DIVCON is not installed") +- self.printWarn("Setting mopac for antechamber") +- qprog = 'mopac' +- elif 'amber11' in self.acExe: +- if qprog == 'divcon': +- self.printWarn("DIVCON is not implemented in AmberTools 1.3 anymore") +- self.printWarn("Setting sqm for antechamber") +- qprog = 'sqm' +- elif qprog == 'mopac': +- if not os.path.exists(os.path.join(os.path.dirname(self.acExe), qprog)): +- self.printWarn("MOPAC is not installed") +- self.printWarn("Setting sqm for antechamber") +- return None +- qprog = 'sqm' +- else: +- self.printWarn("Old version of antechamber. Strongly consider upgrading to AmberTools") +- self.printWarn("Setting mopac for antechamber") +- qprog = 'mopac' + self.qFlag = qDict[qprog] + self.outTopols = [outTopol] + if outTopol == 'all': diff --git a/sci-chemistry/acpype/metadata.xml b/sci-chemistry/acpype/metadata.xml new file mode 100644 index 000000000000..13ef0bf5a17c --- /dev/null +++ b/sci-chemistry/acpype/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest new file mode 100644 index 000000000000..747dbffa95d4 --- /dev/null +++ b/sci-chemistry/ambertools/Manifest @@ -0,0 +1,2 @@ +DIST AmberTools-1.5.tar.bz2 121062582 SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c +DIST ambertools-1.5-bugfix_1-10.patch.xz 31708 SHA256 5773aaa8a2478ad478f0f3afafaa39669002c31ebe755c0d12ff277ce9ab8352 diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild new file mode 100644 index 000000000000..47adf6201db7 --- /dev/null +++ b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild @@ -0,0 +1,144 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 multilib toolchain-funcs + +DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" +HOMEPAGE="http://ambermd.org/#AmberTools" +SRC_URI=" + AmberTools-${PV}.tar.bz2 + mirror://gentoo/${P}-bugfix_1-10.patch.xz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="mpi openmp static-libs X" + +RESTRICT="fetch" + +RDEPEND=" + virtual/cblas + virtual/lapack + sci-libs/clapack + sci-libs/arpack + sci-libs/cifparse-obj + sci-chemistry/mopac7 + sci-libs/netcdf + sci-libs/fftw:2.1 + sci-chemistry/reduce" +DEPEND="${RDEPEND} + dev-util/byacc + dev-libs/libf2c + sys-devel/ucpp + virtual/pkgconfig" +S="${WORKDIR}/amber11" + +pkg_nofetch() { + einfo "Go to ${HOMEPAGE} and get ${A}" + einfo "Place it in ${DISTDIR}" +} + +pkg_setup() { + fortran-2_pkg_setup + if use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" + fi + AMBERHOME="${S}" +} + +src_prepare() { + epatch \ + "${WORKDIR}/${P}-bugfix_1-10.patch" \ + "${FILESDIR}/${P}-gentoo.patch" + cd AmberTools/src + rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die +} + +src_configure() { + cd AmberTools/src + sed \ + -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ + -e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) --libs lapack) -lclapack:g" \ + -e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) --libs blas cblas):g" \ + -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ + -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ + -e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \ + -e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \ + -e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \ + -e "s:fc=g77:fc=$(tc-getFC):g" \ + -e "s:\$netcdflib:$($(tc-getPKG_CONFIG) --libs netcdf):g" \ + -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ + -e "s:-O3::g" \ + -i configure || die + sed -e "s:arsecond_:arscnd_:g" \ + -i sff/time.c \ + -i sff/sff.h \ + -i sff/sff.c || die + sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ + -i nss/Makefile || die + + local myconf + + use X || myconf="${myconf} -noX11" + + for x in mpi openmp; do + use ${x} && myconf="${myconf} -${x}" + done + + ./configure \ + ${myconf} \ + -nobintraj \ + -nomdgx \ + -nopython \ + -nomtkpp \ + gnu +# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)') +} + +src_compile() { + cd AmberTools/src + emake +} + +src_install() { + rm -r bin/chemistry bin/MMPBSA_mods + rm bin/ante-MMPBSA.py bin/extractFrcmod.py + for x in bin/* + do dobin ${x} || die + done + rm "${ED}/usr/bin/yacc" + dobin AmberTools/src/antechamber/mopac.sh + sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ + -i "${ED}/usr/bin/mopac.sh" || die + # Make symlinks untill binpath for amber will be fixed + dodir /usr/share/${PN}/bin + cd "${ED}/usr/bin" + for x in *; do + dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} + done + cd "${S}" +# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \ +# -i "${ED}/usr/bin/xleap" \ +# -i "${ED}/usr/bin/tleap" || die + dodoc doc/AmberTools.pdf doc/leap_pg.pdf + + use static-libs && dolib.a lib/* + + insinto /usr/include/${PN} + doins include/* + + insinto /usr/share/${PN} + doins -r dat + + cd AmberTools + doins -r benchmarks examples test + + cat >> "${T}"/99ambertools <<- EOF + AMBERHOME="${EPREFIX}/usr/share/ambertools" + EOF + doenvd "${T}"/99ambertools +} diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch new file mode 100644 index 000000000000..0e41d26d6f9c --- /dev/null +++ b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch @@ -0,0 +1,386 @@ +diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure +--- amber11.orig/AmberTools/src/configure 2011-04-14 15:30:55.000000000 +0300 ++++ amber11/AmberTools/src/configure 2011-06-04 12:26:45.000000000 +0300 +@@ -293,7 +293,8 @@ + echo "Your AMBERHOME environment variable is not set! It should be set to" + echo "$ambhome NOT doing so may cause errors when you compile. Continue" + echo "anyway? (yes or no)" +- read answer ++ #read answer ++ answer='yes' + if [ "$answer" = 'yes' -o "$answer" = 'Yes' -o "$answer" = 'YES' -o "$answer" = 'y' -o "$answer" = 'Y' ]; then + echo "" + echo "Continuing anyway... Setting AMBERHOME to $ambhome temporarily" +@@ -356,11 +357,11 @@ + mpi_flag= + lex=flex + flibs_mkl= +-lapack=install +-blas=install ++lapack=skip ++blas=skip + f2c=skip +-ucpp=install +-cpp="\$(BINDIR)/ucpp -l" ++ucpp=skip ++cpp="\$(EPREFIX)/usr/bin/ucpp -l" + + #----------------------------------- + # skip building of sleap? +@@ -1655,24 +1656,24 @@ + #-------------------------------------------------------------------------- + # Configure fftw-3.2.2: + #-------------------------------------------------------------------------- +- if [ "$mdgx" = 'yes' ]; then +- mdgxflag="--prefix=$AMBERHOME --disable-fortran" +- echo +- echo "Configuring fftw-3.2.2 (may be time-consuming)..." +- echo +- cd fftw-3.2.2 && \ +- env CC="$cc" CFLAGS="$cflags $cnooptflags" \ +- ./configure $mdgxflag > ../fftw3_config.log 2>&1 +- ncerror=$? +- if [ $ncerror -gt 0 ]; then +- echo " Error: FFTW configure returned $ncerror" +- echo " FFTW configure failed! Check the fftw3_config.log file." +- exit 1 +- else +- echo " fftw-3.2.2 configure succeeded." +- fi +- cd .. +- fi ++ #if [ "$mdgx" = 'yes' ]; then ++ # mdgxflag="--prefix=$AMBERHOME --disable-fortran" ++ # echo ++ # echo "Configuring fftw-3.2.2 (may be time-consuming)..." ++ # echo ++ # cd fftw-3.2.2 && \ ++ # env CC="$cc" CFLAGS="$cflags $cnooptflags" \ ++ # ./configure $mdgxflag > ../fftw3_config.log 2>&1 ++ # ncerror=$? ++ # if [ $ncerror -gt 0 ]; then ++ # echo " Error: FFTW configure returned $ncerror" ++ # echo " FFTW configure failed! Check the fftw3_config.log file." ++ # exit 1 ++ # else ++ # echo " fftw-3.2.2 configure succeeded." ++ # fi ++ # cd .. ++ #fi + + #-------------------------------------------------------------------------- + # Configure python +@@ -1792,27 +1793,27 @@ + echo + echo "Configuring fftw-2.1.5 (may be time-consuming)..." + echo +- cd fftw-2.1.5 +- if [ "$mpi" = 'yes' ]; then +- ./configure $rismflag --enable-mpi \ +- CC="$cc" CFLAGS="$cflags $coptflags" \ +- F77="$fc" FFLAGS="$fflags $foptflags" \ +- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 +- else +- ./configure $rismflag \ +- CC="$cc" CFLAGS="$cflags $coptflags" \ +- F77="$fc" FFLAGS="$fflags $foptflags" \ +- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 +- fi +- ncerror=$? +- if [ $ncerror -gt 0 ]; then +- echo " Error: fftw configure returned $ncerror" +- echo " fftw configure failed! Check the fftw2_config.log file." +- exit 1 +- else +- echo " fftw-2.1.5 configure succeeded." +- fi +- cd .. ++ # cd fftw-2.1.5 ++ # if [ "$mpi" = 'yes' ]; then ++ # ./configure $rismflag --enable-mpi \ ++ # CC="$cc" CFLAGS="$cflags $coptflags" \ ++ # F77="$fc" FFLAGS="$fflags $foptflags" \ ++ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 ++ # else ++ # ./configure $rismflag \ ++ # CC="$cc" CFLAGS="$cflags $coptflags" \ ++ # F77="$fc" FFLAGS="$fflags $foptflags" \ ++ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 ++ # fi ++ # ncerror=$? ++ # if [ $ncerror -gt 0 ]; then ++ # echo " Error: fftw configure returned $ncerror" ++ # echo " fftw configure failed! Check the fftw2_config.log file." ++ # exit 1 ++ # else ++ # echo " fftw-2.1.5 configure succeeded." ++ # fi ++ # cd .. + flibs_fftw2="-ldrfftw -ldfftw" + if [ "$mpi" = 'yes' ]; then + flibs_fftw2="-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2" +diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at +--- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at 2011-04-14 15:30:16.000000000 +0300 ++++ amber11/AmberTools/src/cpptraj/src/Makefile_at 2011-05-20 00:45:48.000000000 +0300 +@@ -65,8 +65,8 @@ + -/bin/rm FindDepend.o + -/bin/rm findDepend + +-cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS) +- $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) ++cpptraj$(SFX): $(OBJECTS) ++ $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp + + $(NETCDFLIB): ../../netcdf_config.log + cd ../../netcdf/src && $(MAKE) install +diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile +--- amber11.orig/AmberTools/src/Makefile 2011-04-14 15:30:12.000000000 +0300 ++++ amber11/AmberTools/src/Makefile 2011-05-19 23:36:36.000000000 +0300 +@@ -8,15 +8,15 @@ + + install: $(INSTALLTYPE) + +-serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP) ++serial: configured_serial + @echo "Starting installation of ${AMBERTOOLS} serial at `date`". + # utility routines and libraries: +- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) ++# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) + (cd byacc && $(MAKE) install ) +- (cd arpack && $(MAKE) install ); +- (cd lapack && $(MAKE) $(LAPACK) ) +- (cd blas && $(MAKE) $(BLAS) ) +- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) ++# (cd arpack && $(MAKE) install ); ++# (cd lapack && $(MAKE) $(LAPACK) ) ++# (cd blas && $(MAKE) $(BLAS) ) ++# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) + (cd etc && $(MAKE) install ) + (cd chamber && $(MAKE) install ) + (cd pbsa && $(MAKE) install ) +@@ -32,7 +32,7 @@ + (cd cpptraj && $(MAKE) $(CPPTRAJ)) + + # miscellaneous: +- (cd reduce && $(MAKE) install ) ++# (cd reduce && $(MAKE) install ) + + # leap and gleap: + (cd leap && $(MAKE) install ) +@@ -42,7 +42,7 @@ + (cd rism && $(MAKE) install ) + + # nab: +- (cd cifparse && $(MAKE) install ) ++# (cd cifparse && $(MAKE) install ) + (cd sff && $(MAKE) install ) + (cd pbsa && $(MAKE) libinstall ) + (cd nab && $(MAKE) install ) +@@ -63,19 +63,19 @@ + @echo "Installation of ${AMBERTOOLS} serial is complete at `date`." + @echo "" + +-nabonly: $(NETCDFLIB) ++nabonly: + # utility routines and libraries: +- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) ++# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) + (cd byacc && $(MAKE) install ) +- (cd arpack && $(MAKE) install ); +- (cd lapack && $(MAKE) $(LAPACK) ) +- (cd blas && $(MAKE) $(BLAS) ) +- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) ++# (cd arpack && $(MAKE) install ); ++# (cd lapack && $(MAKE) $(LAPACK) ) ++# (cd blas && $(MAKE) $(BLAS) ) ++# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) + (cd pbsa && $(MAKE) libinstall ) + (cd rism && $(MAKE) install ) + + # nab: +- (cd cifparse && $(MAKE) install ) ++# (cd cifparse && $(MAKE) install ) + (cd sff && $(MAKE) install ) + (cd nab && $(MAKE) install ) + (cd nss && $(MAKE) install ) +diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/src/mdgx/Makefile +--- amber11.orig/AmberTools/src/mdgx/Makefile 2011-04-14 15:30:17.000000000 +0300 ++++ amber11/AmberTools/src/mdgx/Makefile 2011-05-20 12:44:38.000000000 +0300 +@@ -109,7 +109,7 @@ + + FFTW_LIBS = $(LIBDIR)/libfftw3.a + +-mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) ++mdgx$(SFX) : $(MDGX_OBJS) + $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \ + -o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM) + +diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile +--- amber11.orig/AmberTools/src/pbsa/Makefile 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/pbsa/Makefile 2011-05-19 22:27:40.000000000 +0300 +@@ -148,7 +148,7 @@ + ) + + #--------------------------------------------------------------------------- +-pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial ++pbsa$(SFX): $(OBJ) syslib configured_serial + $(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \ + ../lib/nxtsec.o ../lib/random.o \ + $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) +@@ -158,7 +158,7 @@ + ../lib/nxtsec.o ../lib/random.o \ + $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) + +-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex ++simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib + $(FC) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \ + libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) +@@ -194,15 +194,15 @@ + sfflib: + cd ../sff && $(MAKE) install + +-netlib: +- cd ../lapack && $(MAKE) $(LAPACK) +- cd ../blas && $(MAKE) $(BLAS) +- cd ../arpack && $(MAKE) install +- +-c9x-complex: +- @if test $(C9XCOMPLEX) != "skip"; then \ +- cd ../c9x-complex && $(MAKE) libmc.a; \ +- fi ++#netlib: ++# cd ../lapack && $(MAKE) $(LAPACK) ++# cd ../blas && $(MAKE) $(BLAS) ++# cd ../arpack && $(MAKE) install ++ ++#c9x-complex: ++# @if test $(C9XCOMPLEX) != "skip"; then \ ++# cd ../c9x-complex && $(MAKE) libmc.a; \ ++# fi + + %.LIBPBSA.o: %.f + $(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$< +diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile +--- amber11.orig/AmberTools/src/ptraj/Makefile 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/ptraj/Makefile 2011-05-19 23:38:36.000000000 +0300 +@@ -57,25 +57,25 @@ + pubfft.o: pubfft.f + $(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $< + +-rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS) ++rdparm$(SFX): libs $(OBJECTS) + $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ + -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) + +-ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS) ++ptraj$(SFX): libs $(OBJECTS) + $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ + -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) + +-ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS) ++ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS) + $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ + -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM) + + libs: + cd pdb && $(MAKE) +- cd ../arpack && $(MAKE) ++# cd ../arpack && $(MAKE) + +-netlib: +- cd ../lapack && $(MAKE) $(LAPACK) +- cd ../blas && $(MAKE) $(BLAS) ++#netlib: ++# cd ../lapack && $(MAKE) $(LAPACK) ++# cd ../blas && $(MAKE) $(BLAS) + + clean: + cd pdb && $(MAKE) clean +diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h +--- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-05-19 22:30:43.000000000 +0300 +@@ -4,7 +4,7 @@ + # include "../../include/pnetcdf.h" + # define nc_strerror ncmpi_strerror + # else +-# include "../../include/netcdf.h" ++# include <netcdf.h> + # endif + #endif + +diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h +--- amber11.orig/AmberTools/src/ptraj/ptraj.h 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/ptraj/ptraj.h 2011-06-04 13:25:01.000000000 +0300 +@@ -94,7 +94,7 @@ + #define nc_strerror ncmpi_strerror + #include "../../include/pnetcdf.h" + #else +-#include "../../include/netcdf.h" ++#include <netcdf.h> + #endif + #endif + +diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/src/rism/Makefile +--- amber11.orig/AmberTools/src/rism/Makefile 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/rism/Makefile 2011-05-20 01:07:26.000000000 +0300 +@@ -49,7 +49,7 @@ + mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \ + fce_c.o erfcfun.o safemem.o blend.o timer_c.o + +-librism: $(LIBOBJ) $(FLIBS_FFTW2) ++librism: $(LIBOBJ) + $(AR) $(LIBDIR)/$@.a $(LIBOBJ) + $(RANLIB) $(LIBDIR)/$@.a + +diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberTools/src/sff/AmberNetcdf.c +--- amber11.orig/AmberTools/src/sff/AmberNetcdf.c 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/sff/AmberNetcdf.c 2011-05-20 10:49:06.000000000 +0300 +@@ -27,7 +27,7 @@ + #endif + + #ifdef BINTRAJ +-#include "../../include/netcdf.h" ++#include <netcdf.h> + + #define NCFRAME "frame" + #define NCSPATIAL "spatial" +diff -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/src/sff/Makefile +--- amber11.orig/AmberTools/src/sff/Makefile 2011-04-14 15:30:19.000000000 +0300 ++++ amber11/AmberTools/src/sff/Makefile 2011-05-20 09:53:27.000000000 +0300 +@@ -1,7 +1,7 @@ + include ../config.h + + .c.o: +- $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $< ++ $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $< + + OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \ + prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \ +diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile +--- amber11.orig/AmberTools/src/sqm/Makefile 2011-04-14 15:30:20.000000000 +0300 ++++ amber11/AmberTools/src/sqm/Makefile 2011-05-19 22:31:49.000000000 +0300 +@@ -77,7 +77,7 @@ + install: sqm$(SFX) + mv sqm$(SFX) $(BINDIR) + +-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys ++sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys + $(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \ + $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS) + +@@ -94,10 +94,10 @@ + sys: + cd ../lib; $(MAKE) sys.a + +-netlib: +- cd ../lapack; $(MAKE) $(LAPACK) +- cd ../blas; $(MAKE) $(BLAS) +- cd ../arpack && $(MAKE) install ++#netlib: ++# cd ../lapack; $(MAKE) $(LAPACK) ++# cd ../blas; $(MAKE) $(BLAS) ++# cd ../arpack && $(MAKE) install + + clean: + /bin/rm -f *.o _*.f *.mod *.d sqm$(SFX) diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml new file mode 100644 index 000000000000..13ef0bf5a17c --- /dev/null +++ b/sci-chemistry/ambertools/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest new file mode 100644 index 000000000000..fef1437b89f5 --- /dev/null +++ b/sci-chemistry/apbs/Manifest @@ -0,0 +1 @@ +DIST apbs-1.4.1.zip 37999283 SHA256 1156c44fb65bb7c884801f3111ca1cdb1dfba6f5308226587db112aac4969027 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a WHIRLPOOL 6729571f13c953ec0bcf90da73ef0c39cf769f1498a767d3280de3ffbeea18eda718373efca0468436c4b18357fe450865f661daba79eeb66778c572c43ff39a diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild new file mode 100644 index 000000000000..cabbd1e45e92 --- /dev/null +++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild @@ -0,0 +1,128 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +DISTUTILS_SINGLE_IMPL=true + +inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs + +GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65" + +DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems" +HOMEPAGE="http://www.poissonboltzmann.org/apbs/" +#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz" +SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="debug doc examples fast +fetk iapbs mpi openmp python tools" + +REQUIRED_USE=" + iapbs? ( fetk ) + mpi? ( !python ) + python? ( tools fetk iapbs ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/maloc[mpi=] + virtual/blas + sys-libs/readline + fetk? ( + sci-libs/fetk + sci-libs/amd + sci-libs/umfpack + sci-libs/superlu + ) + mpi? ( virtual/mpi ) + python? ( ${PYTHON_DEPS} ) +" +DEPEND="${DEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen ) +" + +S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN} + +PATCHES=( + "${FILESDIR}"/${P}-multilib.patch + "${FILESDIR}"/${P}-manip.patch + "${FILESDIR}"/${P}-python.patch +) + +src_prepare() { + cmake-utils_src_prepare + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + + sed \ + -e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \ + -e "/TOOLS_PATH/d" \ + -i CMakeLists.txt || die + use doc && MAKEOPTS+=" -j1" + if use python; then + unset PATCHES || die + cd tools/python && distutils-r1_src_prepare + fi +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_SKIP_RPATH=ON + -DTOOLS_PATH="${ED}"/usr + -DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir) + -DLIBRARY_INSTALL_PATH=$(get_libdir) + -DFETK_PATH="${EPREFIX}"/usr/ + -DBUILD_SHARED_LIBS=ON + -DENABLE_QUIT=OFF + $(cmake-utils_use_build doc DOC) + $(cmake-utils_use_build tools TOOLS) + -DENABLE_BEM=OFF +# ENABLE_BEM: Boundary element method using TABIPB + $(cmake-utils_use_enable debug DEBUG) + $(cmake-utils_use_enable debug VERBOSE_DEBUG) + $(cmake-utils_use_enable fast FAST) + $(cmake-utils_use_enable fetk FETK) + $(cmake-utils_use_enable mpi MPI) + $(cmake-utils_use_enable python PYTHON) +# ENABLE_TINKER: Enable TINKER support + $(cmake-utils_use_enable iapbs iAPBS) +# MAX_MEMORY: Set the maximum memory (in MB) to be used for a job + ) + cmake-utils_src_configure + if use python; then + cd tools/python && distutils-r1_src_configure + fi +} + +src_compile(){ + cmake-utils_src_compile + if use python; then + append-ldflags -L"${S}"/lib + cd tools/python && distutils-r1_src_compile + fi +} + +src_test() { + python_export_best + cd tests || die + LD_LIBRARY_PATH="${S}"/lib "${PYTHON}" apbs_tester.py -l log || die + grep -q 'FAILED' log && die "Tests failed" +} + +src_install() { + dodir /usr/bin + cmake-utils_src_install + local i + for i in "${ED}"/usr/bin/*; do + if [[ ! "${i}" =~ .*apbs$ ]]; then + mv "${i}" "${i}-apbs" || die + fi + done + if use python; then + cd tools/python && distutils-r1_src_install + rm -rf "${ED}"/usr/share/apbs/tools/python || die + fi +} diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch new file mode 100644 index 000000000000..378223397594 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch @@ -0,0 +1,50 @@ + apbs/CMakeLists.txt | 2 +- + apbs/tools/CMakeLists.txt | 4 ---- + apbs/tools/mesh/CMakeLists.txt | 4 ++-- + 4 files changed, 5 insertions(+), 9 deletions(-) + +diff --git a/apbs/CMakeLists.txt b/apbs/CMakeLists.txt +index 8917fc4..5152008 100644 +--- a/apbs/CMakeLists.txt ++++ b/apbs/CMakeLists.txt +@@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF) + + if(ENABLE_FETK) + message(STATUS "Checking for fetk components") +- set(FETK_ENALBED 1) ++ set(FETK_ENABLED 1) + + list(APPEND APBS_LIBS "-lstdc++") + list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") +diff --git a/apbs/tools/manip/CMakeLists.txt b/apbs/tools/manip/CMakeLists.txt +index 937dac7..5768cc5 100644 +--- a/apbs/tools/manip/CMakeLists.txt ++++ b/apbs/tools/manip/CMakeLists.txt +@@ -4,9 +4,9 @@ set(LIBS "") + list(APPEND LIBS "apbs_generic") + list(APPEND LIBS "apbs_mg") + list(APPEND LIBS "apbs_pmgc") +-if(FETK_ENALBED) ++if(FETK_ENABLED) + list(APPEND LIBS "apbs_fem") +-endif(FETK_ENALBED) ++endif(FETK_ENABLED) + + message(STATUS "libraries: ${LIBS}") + +diff --git a/apbs/tools/mesh/CMakeLists.txt b/apbs/tools/mesh/CMakeLists.txt +index 1406377..6e6dfb9 100644 +--- a/apbs/tools/mesh/CMakeLists.txt ++++ b/apbs/tools/mesh/CMakeLists.txt +@@ -4,9 +4,9 @@ set(LIBS "") + list(APPEND LIBS "apbs_generic") + list(APPEND LIBS "apbs_mg") + list(APPEND LIBS "apbs_pmgc") +-if(FETK_ENALBED) ++if(FETK_ENABLED) + list(APPEND LIBS "apbs_fem") +-endif(FETK_ENALBED) ++endif(FETK_ENABLED) + + message(STATUS "libraries: ${LIBS}") + diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch new file mode 100644 index 000000000000..a4e2d1761cf4 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch @@ -0,0 +1,92 @@ + CMakeLists.txt | 18 +++++++++--------- + src/CMakeLists.txt | 1 - + src/fem/CMakeLists.txt | 2 +- + src/pmgc/CMakeLists.txt | 2 +- + 4 files changed, 11 insertions(+), 12 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 75ddbdd..c46f5e7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -61,7 +61,7 @@ set(LIBRARY_OUTPUT_PATH ${APBS_ROOT}/lib) + set(TOOLS_PATH ${APBS_ROOT}/tools) + set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) + +-set(LIBRARY_INSTALL_PATH lib) ++set(LIBRARY_INSTALL_PATH ${CMAKE_INSTALL_LIBDIR}) + set(HEADER_INSTALL_PATH include/apbs) + set(EXECUTABLE_INSTALL_PATH bin) + set(SHARE_INSTALL_PATH share/apbs) +@@ -93,8 +93,6 @@ set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") + list(APPEND CMAKE_INCLUDE_PATH /usr/include) + list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) + +-set(APBS_LIBS "-L${APBS_ROOT}/lib -lapbs_geoflow") +- + ################################################################################ + # Enable ansi pedantic compiling # + ################################################################################ +@@ -193,9 +191,11 @@ if(ENABLE_BEM) + else() + set(TABI_LIBRARY_BASENAME ${CMAKE_STATIC_LIBRARY_PREFIX}${TABI}${CMAKE_STATIC_LIBRARY_SUFFIX}) + endif() +- ++ ++ file(GLOB MODS ${LIBRARY_OUTPUT_PATH}/*.mod) ++ + install( +- FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${LIBRARY_OUTPUT_PATH}/*.mod ++ FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${MODS} + DESTINATION ${LIBRARY_INSTALL_PATH} + ) + set(TABI_LIBRARY ${APBS_ROOT}/${LIBRARY_INSTALL_PATH}/${TABI_LIBRARY_BASENAME}) +@@ -210,7 +210,7 @@ if(ENABLE_BEM) + endif() + get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH) + find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH}) +- list(APPEND APBS_LIBS "-L${APBS_ROOT}/${LIBRARY_INSTALL_PATH} -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" ) ++ list(APPEND APBS_LIBS "-L${APBS_ROOT}/lib -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" ) + endif() # ENABLE_BEM + + find_file( # this should be find path... +@@ -228,7 +228,7 @@ endif() + + + find_library(MALOC_LIBRARY "maloc" +- PATHS ${FETK_PATH}/lib ${CONTRIB_PATH} ++ PATHS ${FETK_PATH}/${CMAKE_INSTALL_LIBDIR} ${CONTRIB_PATH} + DOC "The fetk/maloc library" + ) + if(MALOC_LIBRARY) +@@ -296,9 +296,9 @@ if(ENABLE_FETK) + set(FETK_ENALBED 1) + + list(APPEND APBS_LIBS "-lstdc++") +- list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") ++ list(APPEND APBS_LIBS "-L${FETK_PATH}/${CMAKE_INSTALL_LIBDIR}") + list(APPEND APBS_LIBS -lamd -lpunc -lmc -lgamer -lsuperlu -lumfpack +--lblas -lvf2c -ltetgen -ltriangle -lg2c -lreadline ) ++-lblas -lvf2c -ltetgen -ltriangle -lreadline ) + + SET(HAVE_MC_H YES) + endif() +diff --git a/src/fem/CMakeLists.txt b/src/fem/CMakeLists.txt +index 5a950c2..dc37f48 100644 +--- a/src/fem/CMakeLists.txt ++++ b/src/fem/CMakeLists.txt +@@ -12,4 +12,4 @@ add_items( + vpee.h + ) + +-add_sublibrary(fem) ++add_sublibrary(fem apbs_geoflow) +diff --git a/src/pmgc/CMakeLists.txt b/src/pmgc/CMakeLists.txt +index 85b0c1e..97c95f0 100644 +--- a/src/pmgc/CMakeLists.txt ++++ b/src/pmgc/CMakeLists.txt +@@ -42,4 +42,4 @@ add_items( + mgfasd.h + ) + +-add_sublibrary(pmgc) ++add_sublibrary(pmgc apbs_geoflow) diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch new file mode 100644 index 000000000000..db9f86ba120a --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch @@ -0,0 +1,122 @@ + apbs/contrib/iapbs/src/apbs_driver.c | 6 +++--- + apbs/src/CMakeLists.txt | 1 + + apbs/tools/CMakeLists.txt | 2 +- + apbs/tools/python/CMakeLists.txt | 1 + + apbs/tools/python/apbslib.c | 4 ++-- + apbs/tools/python/apbslib.i | 4 ++-- + apbs/tools/python/setup.py | 16 ++++++++++++++++ + 7 files changed, 26 insertions(+), 8 deletions(-) + +diff --git a/apbs/contrib/iapbs/src/apbs_driver.c b/apbs/contrib/iapbs/src/apbs_driver.c +index c9e443b..e1ad67f 100644 +--- a/apbs/contrib/iapbs/src/apbs_driver.c ++++ b/apbs/contrib/iapbs/src/apbs_driver.c +@@ -595,7 +595,7 @@ int apbsdrv_( + printPBEPARM(pbeparm); + + /* Refine mesh */ +- if (!preRefineFE(i, nosh, feparm, fetk)) { ++ if (!preRefineFE(i, feparm, fetk)) { + Vnm_tprint( 2, "Error pre-refining mesh!\n"); + VJMPERR1(0); + } +@@ -609,7 +609,7 @@ int apbsdrv_( + Vnm_tprint(1, " Beginning solve-estimate-refine cycle:\n"); + for (isolve=0; isolve<feparm->maxsolve; isolve++) { + Vnm_tprint(1, " Solve #%d...\n", isolve); +- if (!solveFE(i, nosh, pbeparm, feparm, fetk)) { ++ if (!solveFE(i, pbeparm, feparm, fetk)) { + Vnm_tprint(2, "ERROR SOLVING EQUATION!\n"); + VJMPERR1(0); + } +@@ -622,7 +622,7 @@ int apbsdrv_( + /* We're not going to refine if we've hit the max number + * of solves */ + if (isolve < (feparm->maxsolve)-1) { +- if (!postRefineFE(i, nosh, feparm, fetk)) break; ++ if (!postRefineFE(i, feparm, fetk)) break; + } + bytesTotal = Vmem_bytesTotal(); + highWater = Vmem_highWaterTotal(); +diff --git a/apbs/src/CMakeLists.txt b/apbs/src/CMakeLists.txt +index 44d20fa..2577343 100644 +--- a/apbs/src/CMakeLists.txt ++++ b/apbs/src/CMakeLists.txt +@@ -68,6 +68,7 @@ configure_file( + + if(ENABLE_iAPBS) + ADD_LIBRARY(apbs_routines routines.c routines.h) ++ target_link_libraries(apbs_routines apbs_mg apbs_fem) + INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH}) + INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH}) + endif() +diff --git a/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt +index 1982a3c..4acbe68 100644 +--- a/apbs/tools/CMakeLists.txt ++++ b/apbs/tools/CMakeLists.txt +@@ -4,5 +4,5 @@ add_subdirectory(mesh) + add_subdirectory(manip) + + if(ENABLE_PYTHON) +- add_subdirectory(manip) ++ add_subdirectory(python) + endif(ENABLE_PYTHON) +diff --git a/apbs/tools/python/CMakeLists.txt b/apbs/tools/python/CMakeLists.txt +new file mode 100644 +index 0000000..8b13789 +--- /dev/null ++++ b/apbs/tools/python/CMakeLists.txt +@@ -0,0 +1 @@ ++ +diff --git a/apbs/tools/python/apbslib.c b/apbs/tools/python/apbslib.c +index fef5cc8..feaaa2c 100644 +--- a/apbs/tools/python/apbslib.c ++++ b/apbs/tools/python/apbslib.c +@@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0}; + #include "maloc/maloc.h" + #include "apbscfg.h" + #include "routines.h" +-#include "apbs/valist.h" +-#include "apbs/vatom.h" ++#include "generic/valist.h" ++#include "generic/vatom.h" + + + #include <limits.h> +diff --git a/apbs/tools/python/apbslib.i b/apbs/tools/python/apbslib.i +index 17fe521..44d05ea 100644 +--- a/apbs/tools/python/apbslib.i ++++ b/apbs/tools/python/apbslib.i +@@ -15,8 +15,8 @@ Header files: + #include "maloc/maloc.h" + #include "apbscfg.h" + #include "routines.h" +-#include "apbs/valist.h" +-#include "apbs/vatom.h" ++#include "generic/valist.h" ++#include "generic/vatom.h" + %} + + /* +diff --git a/apbs/tools/python/setup.py b/apbs/tools/python/setup.py +new file mode 100644 +index 0000000..4a20198 +--- /dev/null ++++ b/apbs/tools/python/setup.py +@@ -0,0 +1,16 @@ ++from distutils.core import setup, Extension ++setup(name='apbs', ++ version='1.4.1', ++ package_dir={'apbs': '', 'vgrid': 'vgrid'}, ++ packages=['apbs', 'vgrid'], ++ py_modules=['apbslib', 'main', 'noinput'], ++ ext_modules=[ ++ Extension( ++ '_apbslib', ++ ['apbslib.i'], ++ swig_opts=['-module', 'apbslib', '-I../include'], ++ include_dirs=["../../src"], ++ libraries=["apbs_generic", "apbs_routines"] ++ ) ++ ], ++ ) diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml new file mode 100644 index 000000000000..f1b8467dd96e --- /dev/null +++ b/sci-chemistry/apbs/metadata.xml @@ -0,0 +1,26 @@ +<?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> + <name>Justin Lecher</name> + <description>Ebuild Crasher</description> + </maintainer> + <use> + <flag name="fetk">Include support for FeTK</flag> + <flag name="fast">APBS fast mode (experimental)</flag> + <flag name="iapbs">C/C++/Fortran interface</flag> + <flag name="tools">Install optional tools</flag> + </use> + <longdescription> +APBS is a software package for modeling biomolecular solvation through solution +of the Poisson-Boltzmann equation (PBE), one of the most popular continuum +models for describing electrostatic interactions between molecular solutes in +salty, aqueous media. Continuum electrostatics plays an important role in +several areas of biomolecular simulation +</longdescription> + <upstream> + <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest new file mode 100644 index 000000000000..7f6594d70fe4 --- /dev/null +++ b/sci-chemistry/aqua/Manifest @@ -0,0 +1,2 @@ +DIST aqua-3.2-nmr_manual.tar.gz 632031 SHA256 89bbc2501831e547fec2fe755bbc0081f672e5e2c7adb83618699e6825f73996 +DIST aqua3.2.tar.gz 688408 SHA256 895291b1771f4db5b4a010ce797400a8c4d84095bf34d660dd3405223419242f diff --git a/sci-chemistry/aqua/aqua-3.2-r2.ebuild b/sci-chemistry/aqua/aqua-3.2-r2.ebuild new file mode 100644 index 000000000000..74fccddc5dd2 --- /dev/null +++ b/sci-chemistry/aqua/aqua-3.2-r2.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="Program suite in this distribution calculates restraint violations" +HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html" +SRC_URI=" + ${PN}${PV}.tar.gz + doc? ( ${P}-nmr_manual.tar.gz )" + +SLOT="0" +LICENSE="procheck" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples" + +RDEPEND="sci-chemistry/procheck" +DEPEND="" + +RESTRICT="fetch" + +S="${WORKDIR}"/${PN}${PV} + +pkg_nofetch() { + elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html" + elog "And follow the instruction for downloading ${PN}${PV}.tar.gz -> ${DISTDIR}/${PN}${PV}.tar.gz." + if use doc; then + elog "nmr_manual.tar.gz -> ${DISTDIR}/${P}-nmr_manual.tar.gz" + fi +} + +src_prepare() { + sed \ + -e 's:nawk:gawk:g' \ + -e "s:/bin/gawk:${EPREFIX}/usr/bin/gawk:g" \ + -e "s:/usr/local/bin/perl:${EPREFIX}/usr/bin/perl:g" \ + -i $(find . -type f) || die + epatch "${FILESDIR}"/${PV}-flags.patch +} + +src_compile() { + pushd src > /dev/null + emake \ + MYROOT="${WORKDIR}" \ + CC="$(tc-getCC)" \ + FC="$(tc-getFC)" \ + CFLAGS="${CFLAGS} -I../sub/lib" \ + FFLAGS="${FFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + exth + emake \ + MYROOT="${WORKDIR}" \ + CC="$(tc-getCC)" \ + FC="$(tc-getFC)" \ + CFLAGS="${CFLAGS} -I../sub/lib" \ + FFLAGS="${FFLAGS}" \ + LDFLAGS="${LDFLAGS}" + popd +} + +src_install() { + rm -f scripts/conv* || die + dobin bin/* scripts/* + dosym AquaWhat /usr/bin/qwhat + dosym AquaHow /usr/bin/qhow + dosym AquaPseudo /usr/bin/qpseudo + dosym AquaDist /usr/bin/qdist + dosym AquaCalc /usr/bin/qcalc + dosym AquaAssign /usr/bin/qassign + dosym AquaRedun /usr/bin/qredun + dosym AquaCompl /usr/bin/qcompl + + dodoc HISTORY HOW_TO_USE NEW README doc/* + dohtml html/* + + insinto /usr/share/${PN} + doins data/* + if use examples; then + doins -r exmpls + fi + + if use doc; then + dohtml -r manual + fi + + cat >> "${T}"/34aqua <<- EOF + AQUADATADIR="${EPREFIX}/usr/share/${PN}" + EOF + doenvd "${T}"/34aqua +} diff --git a/sci-chemistry/aqua/files/3.2-flags.patch b/sci-chemistry/aqua/files/3.2-flags.patch new file mode 100644 index 000000000000..cd12fbb9a324 --- /dev/null +++ b/sci-chemistry/aqua/files/3.2-flags.patch @@ -0,0 +1,84 @@ +diff --git a/src/makefile b/src/makefile +index 3113471..dd7a320 100644 +--- a/src/makefile ++++ b/src/makefile +@@ -176,47 +176,46 @@ nrutil.h: + # Executable files + + $(BIN)/AquaWhat: AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) + + $(BIN)/AquaHow: AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) + + $(BIN)/AquaPseudo: AquaPseudo.o $(OBJECTS) $(R_OBJECTS) +- $(CC) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) + + $(BIN)/AquaDist: AquaDist.o $(OBJECTS) +- $(CC) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) $(LDFLAGS) -lm ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) -lm + + $(BIN)/AquaCalc: AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) -lm ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) -lm + + $(BIN)/AquaAssign: AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) + + $(BIN)/AquaCompl: AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -lm ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -lm + + $(BIN)/AquaRedun: AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) + + $(BIN)/testnew: testnew.o $(OBJECTS) +- $(CC) -o $(BIN)/testnew testnew.o $(OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/testnew testnew.o $(OBJECTS) + + $(BIN)/getproj: getproj.c +- $(CC) -o $(BIN)/getproj -O getproj.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(BIN)/getproj getproj.c + + $(BIN)/AquaPlot: AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o +- $(CC) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o + + $(BIN)/Qext: Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o +- $(CC) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o + + $(BIN)/StarTest: StarTest.o +- $(CC) -o $(BIN)/StarTest StarTest.o $(LDFLAGS) $(STARFLAGS) $(STARLIBS) ++ $(CC) $(LDFLAGS) -o $(BIN)/StarTest StarTest.o $(STARFLAGS) $(STARLIBS) + + exth: exth.f +- f77 -o exth -O2 exth.f +- strip exth ++ $(FC) $(FFLAGS) -o exth -O2 exth.f + + + # Object files +@@ -269,7 +268,7 @@ AquaCommon.o: AquaCommon.c AquaCommon.h nrutil.h \ + $(CC) -c AquaCommon.c $(CFLAGS) + + nrutil.o: nrutil.c nrutil.h +- $(CC) -c nrutil.c -DANSI ++ $(CC) $(CFLAGS) -c nrutil.c -DANSI + + AquaFuncts.o: AquaFuncts.c AquaFuncts.h AquaFuncts_cv.h AquaFuncts_io.h\ + AquaStrucset.h AquaFiles.h\ +@@ -319,7 +318,7 @@ $(LIB)/MenuFuncts.o: $(LIB)/MenuFuncts.c $(LIB)/MenuTypes.h $(LIB)/MenuFuncts.h\ + cd $(LIB); $(CC) -c MenuFuncts.c $(CFLAGS) + + cv_subs.o: cv_subs.f +- f77 -c cv_subs.f $(FFLAGS) ++ $(FC) -c cv_subs.f $(FFLAGS) + + Qext.o: Qext.c Qext.h\ + $(LIB)/MenuFuncts.h $(LIB)/Functs.h $(G_HEADERS) diff --git a/sci-chemistry/aqua/metadata.xml b/sci-chemistry/aqua/metadata.xml new file mode 100644 index 000000000000..1837bbc07a6e --- /dev/null +++ b/sci-chemistry/aqua/metadata.xml @@ -0,0 +1,8 @@ +<?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> +</pkgmetadata> diff --git a/sci-chemistry/aria/Manifest b/sci-chemistry/aria/Manifest new file mode 100644 index 000000000000..28b40aa5c0c8 --- /dev/null +++ b/sci-chemistry/aria/Manifest @@ -0,0 +1 @@ +DIST aria2.3.2_08.26.2013.tar.gz 1878602 SHA256 b9b892de2070a77812733faf4b6a1dbec4bba6dec80e5630088cab8b11cbfaf0 SHA512 a6d8c45218f5d494174587a5f8f1feec940ac8cc4cd7b707dac65b2378219ecf27967e70807e6cb7ae22a7d4aec7239af763f077ad7183c078b1991cac71bc3e WHIRLPOOL 59c0b79fab40201d903c484bf63e8339c235207306efc848965d260c02b00c9a408297df0f211cf45f30d13ec35175bf7d566bb5c6d59b944eb22d9aacf0384d diff --git a/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild b/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild new file mode 100644 index 000000000000..7c4026fb1070 --- /dev/null +++ b/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild @@ -0,0 +1,89 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit eutils python-single-r1 versionator + +MY_P="${PN}$(get_version_component_range 1-2 ${PV})" +DATE="08.26.2013" + +DESCRIPTION="Automated NOE assignment and NMR structure calculation" +HOMEPAGE="http://aria.pasteur.fr/" +SRC_URI="http://aria.pasteur.fr/archives/${MY_P}.2_${DATE}.tar.gz" + +SLOT="0" +LICENSE="cns" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-tcltk/tix + dev-lang/tk + >=dev-python/numpy-1.1[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP},tk] + >=sci-chemistry/cns-1.2.1-r7[aria,openmp] + >=sci-chemistry/ccpn-2.2[${PYTHON_USEDEP}] + sci-chemistry/clashlist + sci-chemistry/procheck + sci-libs/clashscore-db" +DEPEND="${RDEPEND}" + +RESTRICT="fetch" + +S="${WORKDIR}/${MY_P}" + +pkg_nofetch(){ + einfo "Go to http://aria.pasteur.fr/archives/aria2.3.2.tar.gz/view, download ${A}" + einfo "and place it in ${DISTDIR}" +} + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_test(){ + export CCPNMR_TOP_DIR=$(python_get_sitedir) + export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python + ${PYTHON} check.py || die +} + +src_install(){ + python_moduleinto ${PN} + python_domodule src aria2.py + python_moduleinto ${PN}/cns + python_domodule cns/{protocols,toppar,src/helplib} + + if use examples; then + insinto /usr/share/${P}/ + doins -r examples + fi + + # ENV + cat >> "${T}"/20aria <<- EOF + ARIA2="$(python_get_sitedir)/${PN}" + EOF + + doenvd "${T}"/20aria + + # Launch Wrapper + cat >> "${T}"/aria <<- EOF + #!/bin/sh + export CCPNMR_TOP_DIR="$(python_get_sitedir)" + export PYTHONPATH="$(python_get_sitedir)/ccpn/python" + exec "${PYTHON}" -O "\${ARIA2}"/aria2.py \$@ + EOF + + dobin "${T}"/aria + dosym aria /usr/bin/aria2 + + dodoc README + python_optimize "${D}/$(python_get_sitedir)" +} diff --git a/sci-chemistry/aria/files/aria-2.3.2-python.patch b/sci-chemistry/aria/files/aria-2.3.2-python.patch new file mode 100644 index 000000000000..1f9ae1fcc5f6 --- /dev/null +++ b/sci-chemistry/aria/files/aria-2.3.2-python.patch @@ -0,0 +1,30 @@ + src/py/aria/legacy/QualityChecks/Descriptive.py | 5 +++-- + 1 files changed, 3 insertions(+), 2 deletions(-) + +diff --git a/src/py/aria/legacy/QualityChecks/Descriptive.py b/src/py/aria/legacy/QualityChecks/Descriptive.py +index ae5913c..550d20c 100644 +--- a/src/py/aria/legacy/QualityChecks/Descriptive.py ++++ b/src/py/aria/legacy/QualityChecks/Descriptive.py +@@ -1,3 +1,6 @@ ++from math import * ++from numpy import * ++ + class Descriptive: + """ + some basic statistics +@@ -55,7 +58,6 @@ class Descriptive: + + def getStdDev(self): + if( len(self.myData) == 0): return None +- from math import * + if( (self.count - 1) > 0 ): + return sqrt( self.pseudoVariance/ (self.count - 1)) + else: +@@ -89,7 +91,6 @@ class Descriptive: + def getMedian(self): + if( len(self.myData) == 0): return None + if( self.median == None ): +- from numpy import * + sort(self.myData) + if( self.count%2 == 1): + self.median = self.myData[(self.count-1)/2] diff --git a/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch b/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch new file mode 100644 index 000000000000..6a363d098632 --- /dev/null +++ b/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch @@ -0,0 +1,139 @@ + src/py/aria/exportToCcpn.py | 24 +++++++++++------------- + src/py/aria/importFromCcpn.py | 32 ++++++++++++-------------------- + 2 files changed, 23 insertions(+), 33 deletions(-) + +diff --git a/src/py/aria/exportToCcpn.py b/src/py/aria/exportToCcpn.py +index c742a88..aae7b7d 100644 +--- a/src/py/aria/exportToCcpn.py ++++ b/src/py/aria/exportToCcpn.py +@@ -1,5 +1,5 @@ + from ccpnmr.analysis.core.ConstraintBasic import makeNmrConstraintStore, makeStructureGeneration, getFixedResonance +-from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims ++from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims, getThroughSpaceDataDims + from ccpnmr.analysis.core.AssignmentBasic import assignAtomsToRes, assignResToDim + from ccpnmr.analysis.core.PeakBasic import pickPeak, setManualPeakIntensity + from ccpnmr.analysis.core.MoleculeBasic import DEFAULT_ISOTOPES +@@ -791,12 +791,13 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None, + ariaDims = ariaDimDict.get(spectrum) + if not ariaDims: + ariaDims = [] #[0,1,2] ++ throughSpaceDataDims = getThroughSpaceDataDims(spectrum) + + dataDims = spectrum.sortedDataDims() + if len(dataDims) == 3: + for dataDim in dataDims: + expDimRef = dataDim.findFirstDataDimRef().expDimRef +- if '1H' in expDimRef.isotopeCodes: # 0 or 2 ++ if dataDim in throughSpaceDataDims: # 0 or 2 + if onebondDims.get(dataDim.dim): + if ppmX1 is None: + ariaDims.append(2) +@@ -816,21 +817,18 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None, + ariaDims.append(1) + + else: +- transfer = spectrum.experiment.findFirstExpTransfer(transferType='through-space') or \ +- spectrum.experiment.findFirstExpTransfer(transferType='NOESY') + ++ i = 0 + for dataDim in dataDims: +- expDimRefs = [dataDimRef.expDimRef for dataDimRef in dataDim.dataDimRefs] +- i = 0 +- for expDimRef in transfer.sortedExpDimRefs(): +- if expDimRef in expDimRefs: +- ariaDims.append(i) +- boundDim = onebondDims.get(dataDim.dim) +- if boundDim: +- ariaDims.append(i+1) +- ++ if dataDim in throughSpaceDataDims: ++ ariaDims.append(i) ++ boundDim = onebondDims.get(dataDim.dim) ++ if boundDim: ++ ariaDims.append(i+1) ++ + i += 2 + ++ + ariaDimDict[spectrum] = ariaDims + + if namesDict: +diff --git a/src/py/aria/importFromCcpn.py b/src/py/aria/importFromCcpn.py +index a65ae3e..f63ba16 100644 +--- a/src/py/aria/importFromCcpn.py ++++ b/src/py/aria/importFromCcpn.py +@@ -165,7 +165,7 @@ def getStructureEnsembles(project, ccpChains): + + return ensembles + +-def getNoesyPeakLists(project, molSystem=None): ++def getNoesyPeakLists(project, molSystem=None, excludeSimulated=True): + """Descrn: Get the NOE peak lists from a CCPN project. Can filter if appropriate to a given + molecular system if passed in. + Inputs: Implementation.Project, ccp.molecule.MolSystem.MolSystem +@@ -196,19 +196,10 @@ def getNoesyPeakLists(project, molSystem=None): + + for spectrum in experiment.dataSources: + if (spectrum.dataType == 'processed') and (spectrum.numDim > 1): +- +- isotopes = [] +- for dataDim in spectrum.dataDims: +- for expDimRef in dataDim.expDim.expDimRefs: +- if expDimRef.measurementType in ('shift','Shift'): +- isotope = ','.join(expDimRef.isotopeCodes) +- isotopes.append(isotope) +- break +- +- if isotopes.count('1H') > 1: +- for peakList in spectrum.peakLists: +- if peakList.findFirstPeak(): +- peakLists.append(peakList) ++ for peakList in spectrum.sortedPeakLists(): ++ if excludeSimulated and peakList.isSimulated: ++ continue ++ peakLists.append(peakList) + + + return peakLists +@@ -490,7 +481,10 @@ def makeAriaChain(ccpChain): + # Does below work for DNA/RNA? + + aria_settings = ChainSettings() +- aria_settings['type'] = chainTypeMapping[ccpChain.molecule.molType] ++ # wb104: below changed 31 Oct 2011 to try and get around case when molType is None ++ #aria_settings['type'] = chainTypeMapping[ccpChain.molecule.molType] ++ molType = ccpChain.molecule.molType or 'protein' ++ aria_settings['type'] = chainTypeMapping[molType] + + aria_chain = Chain(settings=aria_settings, segid=string_to_segid(ccpChain.code)) + +@@ -952,8 +946,6 @@ def makeAriaSpectrum(peakList, ariaMolecule, filterRejected=True): + expDimRefDict = {} + + for expDimRef in transfer.sortedExpDimRefs(): +- if expDimRef.isotopeCodes != ('1H',): +- raise Exception('Not an H-H experiment') + + onebondTransfer = expDimRef.findFirstExpTransfer(transferType='onebond') + +@@ -1095,7 +1087,7 @@ def getAriaAtomsFromResonance(resonance, ariaMolecule, cache={}): + + # TJS modify to return just a list of atoms, rather than a list of list + ariaAtoms = [] +- for atom in atomSet.sortedAtoms(): ++ for atom in atomSet.atoms: + ariaAtom = ariaResidue.atoms.get(atom.name) + if not ariaAtom: + messager.warning('Could not find ARIA Atom for CCPN atom %d%s %s' % (residue.seqCode,residue.ccpCode, atom.name)) +@@ -1256,9 +1248,9 @@ def getAriaDistanceRestraintsList(constraint_list, constraint_type, aria_mol): + restraint.setWeight(weight) + + +- for constrItem in distConstr.sortedItems(): ++ for constrItem in distConstr.items: + +- reso1, reso2 = constrItem.sortedResonances() ++ reso1, reso2 = constrItem.resonances + + # TJS fix for mapping prochirals + # always use real resonnances where possible diff --git a/sci-chemistry/aria/files/aria-2.3.2-through-space.patch b/sci-chemistry/aria/files/aria-2.3.2-through-space.patch new file mode 100644 index 000000000000..bda76aa11c80 --- /dev/null +++ b/sci-chemistry/aria/files/aria-2.3.2-through-space.patch @@ -0,0 +1,118 @@ + src/py/aria/exportToCcpn.py | 24 +++++++++++------------- + src/py/aria/importFromCcpn.py | 25 +++++++------------------ + 2 files changed, 18 insertions(+), 31 deletions(-) + +diff --git a/src/py/aria/exportToCcpn.py b/src/py/aria/exportToCcpn.py +index c742a88..aae7b7d 100644 +--- a/src/py/aria/exportToCcpn.py ++++ b/src/py/aria/exportToCcpn.py +@@ -1,5 +1,5 @@ + from ccpnmr.analysis.core.ConstraintBasic import makeNmrConstraintStore, makeStructureGeneration, getFixedResonance +-from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims ++from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims, getThroughSpaceDataDims + from ccpnmr.analysis.core.AssignmentBasic import assignAtomsToRes, assignResToDim + from ccpnmr.analysis.core.PeakBasic import pickPeak, setManualPeakIntensity + from ccpnmr.analysis.core.MoleculeBasic import DEFAULT_ISOTOPES +@@ -791,12 +791,13 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None, + ariaDims = ariaDimDict.get(spectrum) + if not ariaDims: + ariaDims = [] #[0,1,2] ++ throughSpaceDataDims = getThroughSpaceDataDims(spectrum) + + dataDims = spectrum.sortedDataDims() + if len(dataDims) == 3: + for dataDim in dataDims: + expDimRef = dataDim.findFirstDataDimRef().expDimRef +- if '1H' in expDimRef.isotopeCodes: # 0 or 2 ++ if dataDim in throughSpaceDataDims: # 0 or 2 + if onebondDims.get(dataDim.dim): + if ppmX1 is None: + ariaDims.append(2) +@@ -816,21 +817,18 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None, + ariaDims.append(1) + + else: +- transfer = spectrum.experiment.findFirstExpTransfer(transferType='through-space') or \ +- spectrum.experiment.findFirstExpTransfer(transferType='NOESY') + ++ i = 0 + for dataDim in dataDims: +- expDimRefs = [dataDimRef.expDimRef for dataDimRef in dataDim.dataDimRefs] +- i = 0 +- for expDimRef in transfer.sortedExpDimRefs(): +- if expDimRef in expDimRefs: +- ariaDims.append(i) +- boundDim = onebondDims.get(dataDim.dim) +- if boundDim: +- ariaDims.append(i+1) +- ++ if dataDim in throughSpaceDataDims: ++ ariaDims.append(i) ++ boundDim = onebondDims.get(dataDim.dim) ++ if boundDim: ++ ariaDims.append(i+1) ++ + i += 2 + ++ + ariaDimDict[spectrum] = ariaDims + + if namesDict: +diff --git a/src/py/aria/importFromCcpn.py b/src/py/aria/importFromCcpn.py +index a65ae3e..91ad123 100644 +--- a/src/py/aria/importFromCcpn.py ++++ b/src/py/aria/importFromCcpn.py +@@ -196,19 +196,10 @@ def getNoesyPeakLists(project, molSystem=None): + + for spectrum in experiment.dataSources: + if (spectrum.dataType == 'processed') and (spectrum.numDim > 1): +- +- isotopes = [] +- for dataDim in spectrum.dataDims: +- for expDimRef in dataDim.expDim.expDimRefs: +- if expDimRef.measurementType in ('shift','Shift'): +- isotope = ','.join(expDimRef.isotopeCodes) +- isotopes.append(isotope) +- break +- +- if isotopes.count('1H') > 1: +- for peakList in spectrum.peakLists: +- if peakList.findFirstPeak(): +- peakLists.append(peakList) ++ for peakList in spectrum.sortedPeakLists(): ++ if excludeSimulated and peakList.isSimulated: ++ continue ++ peakLists.append(peakList) + + + return peakLists +@@ -952,8 +943,6 @@ def makeAriaSpectrum(peakList, ariaMolecule, filterRejected=True): + expDimRefDict = {} + + for expDimRef in transfer.sortedExpDimRefs(): +- if expDimRef.isotopeCodes != ('1H',): +- raise Exception('Not an H-H experiment') + + onebondTransfer = expDimRef.findFirstExpTransfer(transferType='onebond') + +@@ -1095,7 +1084,7 @@ def getAriaAtomsFromResonance(resonance, ariaMolecule, cache={}): + + # TJS modify to return just a list of atoms, rather than a list of list + ariaAtoms = [] +- for atom in atomSet.sortedAtoms(): ++ for atom in atomSet.atoms: + ariaAtom = ariaResidue.atoms.get(atom.name) + if not ariaAtom: + messager.warning('Could not find ARIA Atom for CCPN atom %d%s %s' % (residue.seqCode,residue.ccpCode, atom.name)) +@@ -1256,9 +1245,9 @@ def getAriaDistanceRestraintsList(constraint_list, constraint_type, aria_mol): + restraint.setWeight(weight) + + +- for constrItem in distConstr.sortedItems(): ++ for constrItem in distConstr.items: + +- reso1, reso2 = constrItem.sortedResonances() ++ reso1, reso2 = constrItem.resonances + + # TJS fix for mapping prochirals + # always use real resonnances where possible diff --git a/sci-chemistry/aria/metadata.xml b/sci-chemistry/aria/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/aria/metadata.xml @@ -0,0 +1,8 @@ +<?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> +</pkgmetadata> diff --git a/sci-chemistry/arp-warp-bin/Manifest b/sci-chemistry/arp-warp-bin/Manifest new file mode 100644 index 000000000000..739b86dac839 --- /dev/null +++ b/sci-chemistry/arp-warp-bin/Manifest @@ -0,0 +1 @@ +DIST arp_warp_7.5.tar.gz 198643246 SHA256 d16fc6775905e56e5159f4a658f654b98d94f78143a2537ba67bffaed7ef1ad8 SHA512 351ed4bad863bac63005d128c693b7dde60c03ca5e8bd449ea602646f7f856c022070e542bcacae2793fbde88d67e7b5639bedeec55eeb191017a2ec19d03768 WHIRLPOOL d4ea42179a8a406508c82320567dc39ce419a2cba8b9e6ed05739dbbf0c9aba072b720c56987c4c94806ba2772f9c8787bde898f7c76543cc4702f00b7f16532 diff --git a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild new file mode 100644 index 000000000000..ef10d0ab3d5d --- /dev/null +++ b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils prefix + +MY_P="arp_warp_${PV}" + +DESCRIPTION="Improvement and interpretation of crystallographic electron density maps" +SRC_URI="${MY_P}.tar.gz" +HOMEPAGE="http://www.embl-hamburg.de/ARP/" + +LICENSE="ArpWarp" +SLOT="0" +KEYWORDS="-* amd64 x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_sse2" + +REQUIRED_USE="cpu_flags_x86_sse2" + +RDEPEND=" + app-shells/tcsh + sci-chemistry/refmac + virtual/awk + virtual/jre + virtual/opengl + x11-libs/libX11" +DEPEND="" + +RESTRICT="fetch" + +S="${WORKDIR}/${MY_P}" + +QA_PREBUILT="opt/arp-warp-bin/bin/*" + +pkg_nofetch(){ + elog "Fill out the form at http://www.embl-hamburg.de/ARP/" + elog "and place ${A} in ${DISTDIR}" +} + +src_prepare() { + epatch "${FILESDIR}"/7.3-setup.patch + eprefixify "${S}"/share/arpwarp_setup_base.* + + sed -e '/exit/d' -i "${S}"/share/arpwarp_setup_base.* || die +} + +src_install(){ + m_type=$(uname -m) + os_type=$(uname) + + exeinto /opt/${PN}/bin/bin-${m_type}-${os_type} + doexe "${S}"/bin/bin-${m_type}-${os_type}/* "${S}"/share/*{pl,sh} + + insinto /opt/${PN}/bin/bin-${m_type}-${os_type} + doins "${S}"/share/*{gif,bmp,XYZ,bash,csh,dat,lib,tbl,llh,prm} + + insinto /etc/profile.d/ + newins "${S}"/share/arpwarp_setup_base.csh 90arpwarp_setup.csh + newins "${S}"/share/arpwarp_setup_base.bash 90arpwarp_setup.sh + + dodoc "${S}"/README manual/UserGuide${PV}.pdf + dohtml -r "${S}"/manual/html/* +} + +pkg_postinst(){ + testcommand=$(echo 3 2 | awk '{printf"%3.1f",$1/$2}') + if [ $testcommand == "1,5" ];then + ewarn "*** ERROR ***" + ewarn " 3/2=" $testcommand + ewarn "Invalid decimal separator (must be ".")" + ewarn "You need to set this correctly!!!" + echo + ewarn "One way of setting the decimal separator is:" + ewarn "setenv LC_NUMERIC C' in your .cshrc file" + ewarn "\tor" + ewarn "export LC_NUMERIC=C' in your .bashrc file" + ewarn "Otherwise please consult your system manager" + fi +} diff --git a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch b/sci-chemistry/arp-warp-bin/files/7.3-setup.patch new file mode 100644 index 000000000000..faed9c1102fd --- /dev/null +++ b/sci-chemistry/arp-warp-bin/files/7.3-setup.patch @@ -0,0 +1,30 @@ +diff --git a/share/arpwarp_setup_base.bash b/share/arpwarp_setup_base.bash +index 29e769c..0b8a51e 100644 +--- a/share/arpwarp_setup_base.bash ++++ b/share/arpwarp_setup_base.bash +@@ -13,10 +13,10 @@ else + identifier=${nameprocessor}'-'${namesystem} + fi + # +-arpwarphome="$1X" ++arpwarphome="@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin" + # + export warpbin=${arpwarphome}/bin/bin-${identifier} +-export warpdoc=${arpwarphome}/manual ++export warpdoc=@GENTOO_PORTAGE_EPREFIX@/usr/share/doc/arp-warp-bin-7.1/html/ + export PATH=${warpbin}:${PATH} + # + # Checks for existence of $warpbin directory +diff --git a/share/arpwarp_setup_base.csh b/share/arpwarp_setup_base.csh +index 41b11e9..a4edcff 100644 +--- a/share/arpwarp_setup_base.csh ++++ b/share/arpwarp_setup_base.csh +@@ -13,7 +13,7 @@ else + set identifier = ${nameprocessor}'-'${namesystem} + endif + # +-set arpwarphome = '$1X' ++set arpwarphome = '@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin' + # + setenv warpbin ${arpwarphome}/bin/bin-${identifier} + # diff --git a/sci-chemistry/arp-warp-bin/metadata.xml b/sci-chemistry/arp-warp-bin/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/arp-warp-bin/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest new file mode 100644 index 000000000000..422cb216787f --- /dev/null +++ b/sci-chemistry/autodock/Manifest @@ -0,0 +1 @@ +DIST autodocksuite-4.2.6-src.tar.gz 35438010 SHA256 4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4 SHA512 75b8878f948c4f6bc28adb442997192dad0c36bbede2fd698623903cb27b06b4df3ba038bfc70fc13b4bdee864fd2344f0f7208be2020da4e01a00b842b46bbb WHIRLPOOL 18230783d13c2d82ad6427711a48dec0c6695301a52dcf419cf4feefb0b5f41bac5de53824313e75d9040ac8623915ba266e764e92ecad9869d845053ec60b93 diff --git a/sci-chemistry/autodock/autodock-4.2.6.ebuild b/sci-chemistry/autodock/autodock-4.2.6.ebuild new file mode 100644 index 000000000000..10d018292e93 --- /dev/null +++ b/sci-chemistry/autodock/autodock-4.2.6.ebuild @@ -0,0 +1,102 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools eutils python-any-r1 versionator + +MY_PN="autodocksuite" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="A suite of automated docking tools" +HOMEPAGE="http://autodock.scripps.edu/" +SRC_URI="http://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(delete_all_version_separators)/${MY_P}-src.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples openmp test" + +RDEPEND="" +DEPEND="test? ( ${PYTHON_DEPS} )" + +S="${WORKDIR}/src" + +PATCHES=( + "${FILESDIR}"/${P}-buildsystem.patch +) + +src_prepare() { + local i + + epatch ${PATCHES[@]} + + sed \ + -e "s/\tcsh/\tsh/" \ + -i auto{dock,grid}/Makefile.am || die + for i in autodock autogrid; do + pushd $i &>/dev/null + eautoreconf + popd &>/dev/null + done +} + +src_configure() { + local i + for i in autodock autogrid; do + pushd $i &>/dev/null + econf $(use_enable openmp) + popd &>/dev/null + done +} + +src_compile() { + emake -C autodock + emake -C autogrid +} + +src_test() { + elog "Testing autodock" + cd "${S}/autodock/Tests" || die + cp ../*.dat . || die + ${EPYTHON} test_autodock4.py || die "AutoDock tests failed." + einfo "Testing autogrid" + cd "${S}/autogrid/Tests" || die + ${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed." +} + +src_install() { + if use openmp; then + newbin autodock/autodock4.omp ${PN}4 + dobin autogrid/autogrid4 + else + dobin autodock/autodock4 autogrid/autogrid4 + fi + + insinto /usr/share/${PN} + doins -r \ + autodock/{AD4_parameters.dat,AD4_PARM99.dat} \ + $(usex examples "autodoc/EXAMPLES" "") + + DOCS=( + RELEASENOTES + autodock/{AUTHORS,README} + autodock/USERGUIDES/AutoDock4.{0,1,2}_UserGuide.doc + autodock/USERGUIDES/AutoDock4.2_UserGuide.pdf + ) + einstalldocs +} + +pkg_postinst() { + elog "The AutoDock development team requests all users to fill out the" + elog "registration form at:" + echo + elog "\thttp://autodock.scripps.edu/downloads/autodock-registration" + echo + elog "The number of unique users of AutoDock is used by Prof. Arthur J." + elog "Olson and the Scripps Research Institude to support grant" + elog "applications." +} diff --git a/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch b/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch new file mode 100644 index 000000000000..b9eb3c409c64 --- /dev/null +++ b/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch @@ -0,0 +1,10 @@ +--- autodocksuite-4.0.1.orig/src/autogrid/check_size.cpp 2008-08-04 22:44:46.000000000 -0700 ++++ autodocksuite-4.0.1/src/autogrid/check_size.cpp 2008-08-04 22:45:12.000000000 -0700 +@@ -27,6 +27,7 @@ + + #include <iostream> + #include <math.h> ++#include <cstdlib> + #include "autogrid.h" + + diff --git a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch new file mode 100644 index 000000000000..ae44ffeb3159 --- /dev/null +++ b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch @@ -0,0 +1,44 @@ + src/autodock/Makefile.am | 6 +++--- + src/autogrid/Makefile.am | 4 ++-- + 2 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/src/autodock/Makefile.am b/src/autodock/Makefile.am +index 799a3c4..911897b 100644 +--- a/src/autodock/Makefile.am ++++ b/src/autodock/Makefile.am +@@ -459,7 +459,8 @@ endif + + BUILT_SOURCES = $(autodock4_SOURCES) default_parameters.h + +-AM_CXXFLAGS = -O3 # Agressive optimization ++AM_CXXFLAGS = ++#AM_CXXFLAGS = -O3 # Agressive optimization + #AM_CXXFLAGS = -g # debug + + # if gnu c++ compiler +@@ -488,8 +489,7 @@ endif + AM_CPPFLAGS = -DNOSQRT \ + -DUSE_DOUBLE \ + -DUSE_8A_NBCUTOFF \ +- -DUSE_INT_AS_FOURBYTELONG \ +- -O3 ++ -DUSE_INT_AS_FOURBYTELONG + # AM_LDFLAGS = -g # -g is MP debug + + +diff --git a/src/autogrid/Makefile.am b/src/autogrid/Makefile.am +index b531099..b78b380 100644 +--- a/src/autogrid/Makefile.am ++++ b/src/autogrid/Makefile.am +@@ -94,9 +94,9 @@ autogrid4_SOURCES = main.cpp \ + BUILT_SOURCES = default_parameters.h + + +-AM_CFLAGS = -Wall -O3 # All warnings, Agressive optimization ++AM_CFLAGS = -Wall # All warnings, Agressive optimization + +-AM_CPPFLAGS = -Wall -O3 -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization ++AM_CPPFLAGS = -Wall -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization + AM_CPPFLAGS += -Wno-write-strings # increase compatibility with pre 4.x compilers for string handling + # M Pique - add USE_8A_NBCUTOFF + AM_CPPFLAGS += -DUSE_8A_NBCUTOFF diff --git a/sci-chemistry/autodock/metadata.xml b/sci-chemistry/autodock/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/autodock/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest new file mode 100644 index 000000000000..a2f7882e9d79 --- /dev/null +++ b/sci-chemistry/autodock_vina/Manifest @@ -0,0 +1 @@ +DIST autodock_vina_1_1_2.tgz 67366 SHA256 b86412d316960b1e4e319401719daf57ff009229d91654d623c3cf09339f6776 SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9 WHIRLPOOL b68f3bb81fe957fddb6674f71e0c63d1425eb5b4de0615258545ba8e241b347380c8745ee47bd2ee2257f29916191773440e3dd4e9ce857b83a947074eae8d45 diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild new file mode 100644 index 000000000000..aea218f8faf9 --- /dev/null +++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils flag-o-matic versionator + +MY_P="${PN}_$(replace_all_version_separators _)" + +DESCRIPTION="Program for drug discovery, molecular docking and virtual screening" +HOMEPAGE="http://vina.scripps.edu/" +SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz" + +SLOT="0" +KEYWORDS="amd64 x86" +LICENSE="Apache-2.0" +IUSE="debug" + +RDEPEND="dev-libs/boost" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_P}/build/linux/release + +src_prepare() { + cd "${WORKDIR}"/${MY_P} || die + epatch \ + "${FILESDIR}"/${PV}-gentoo.patch \ + "${FILESDIR}"/${P}-boost-filesystem.patch +} + +src_compile() { + local c_options + + use debug || c_options="-DNDEBUG" + + append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 + + emake \ + BASE="${EPREFIX}"/usr/ \ + GPP="$(tc-getCXX)" \ + C_OPTIONS="${c_options}" +} + +src_install() { + dobin vina{,_split} +} diff --git a/sci-chemistry/autodock_vina/files/1.1.1-gentoo.patch b/sci-chemistry/autodock_vina/files/1.1.1-gentoo.patch new file mode 100644 index 000000000000..356ae2ee547d --- /dev/null +++ b/sci-chemistry/autodock_vina/files/1.1.1-gentoo.patch @@ -0,0 +1,68 @@ +diff --git a/build/linux/debug/Makefile b/build/linux/debug/Makefile +index d2c2d3b..d1f02e5 100644 +--- a/build/linux/debug/Makefile ++++ b/build/linux/debug/Makefile +@@ -1,6 +1,6 @@ + BASE=/usr/local + BOOST_VERSION=1_41 +-C_PLATFORM=-static-libgcc -pthread ++C_PLATFORM=-pthread + GPP=/usr/bin/g++ + C_OPTIONS= -g + BOOST_LIB_VERSION= +diff --git a/build/linux/release/Makefile b/build/linux/release/Makefile +index bfbcc1e..c9fd630 100644 +--- a/build/linux/release/Makefile ++++ b/build/linux/release/Makefile +@@ -1,6 +1,6 @@ + BASE=/usr/local + BOOST_VERSION=1_41 +-C_PLATFORM=-static-libgcc -pthread ++C_PLATFORM=-pthread + GPP=/usr/bin/g++ + C_OPTIONS= -O3 -DNDEBUG + BOOST_LIB_VERSION= +diff --git a/build/makefile_common b/build/makefile_common +index 885935c..e72142d 100644 +--- a/build/makefile_common ++++ b/build/makefile_common +@@ -1,30 +1,30 @@ +-BOOST_INCLUDE = $(BASE)/include/boost-${BOOST_VERSION} ++BOOST_INCLUDE = $(BASE)/include/boost + + LIBOBJ = cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manifold.o model.o monte_carlo.o mutate.o my_pid.o naive_non_cache.o non_cache.o parallel_mc.o parse_pdbqt.o pdb.o quasi_newton.o quaternion.o random.o ssd.o terms.o weighted_terms.o + MAINOBJ = main.o + SPLITOBJ = split.o + +-INCFLAGS = -I $(BOOST_INCLUDE) ++INCFLAGS = -I$(BOOST_INCLUDE) + +-CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS) ++CC = ${GPP} ${C_PLATFORM} ${C_OPTIONS} $(INCFLAGS) + +-LDFLAGS = -L$(BASE)/lib -L. ++LDFLAGS += -L. + +-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread ++LIBS = -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem -lboost_program_options -lpthread + + .SUFFIXES: .cpp .o + + %.o : ../../../src/lib/%.cpp +- $(CC) $(CFLAGS) -o $@ -c $< ++ $(CC) $(CXXFLAGS) -o $@ -c $< + + %.o : ../../../src/design/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + %.o : ../../../src/main/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + %.o : ../../../src/split/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + all: vina vina_split + diff --git a/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch new file mode 100644 index 000000000000..61ae8bec36f5 --- /dev/null +++ b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch @@ -0,0 +1,72 @@ + build/linux/debug/Makefile | 2 +- + build/linux/release/Makefile | 2 +- + build/makefile_common | 14 +++++++------- + 3 files changed, 9 insertions(+), 9 deletions(-) + +diff --git a/build/linux/debug/Makefile b/build/linux/debug/Makefile +index 6a41cfc..8097fb9 100644 +--- a/build/linux/debug/Makefile ++++ b/build/linux/debug/Makefile +@@ -1,7 +1,7 @@ + BASE=/usr/local + BOOST_VERSION=1_41 + BOOST_INCLUDE = $(BASE)/include +-C_PLATFORM=-static -pthread ++C_PLATFORM=-pthread + GPP=/usr/local/bin/g++ + C_OPTIONS= -g + BOOST_LIB_VERSION= +diff --git a/build/linux/release/Makefile b/build/linux/release/Makefile +index 1de1063..ded8133 100644 +--- a/build/linux/release/Makefile ++++ b/build/linux/release/Makefile +@@ -1,7 +1,7 @@ + BASE=/usr/local + BOOST_VERSION=1_41 + BOOST_INCLUDE = $(BASE)/include +-C_PLATFORM=-static -pthread ++C_PLATFORM=-pthread + GPP=/usr/local/bin/g++ + C_OPTIONS= -O3 -DNDEBUG + BOOST_LIB_VERSION= +diff --git a/build/makefile_common b/build/makefile_common +index a940329..96336e8 100644 +--- a/build/makefile_common ++++ b/build/makefile_common +@@ -2,29 +2,29 @@ LIBOBJ = cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manif + MAINOBJ = main.o + SPLITOBJ = split.o + +-INCFLAGS = -I $(BOOST_INCLUDE) ++INCFLAGS = -I$(BOOST_INCLUDE) + + # -pedantic fails on Mac with Boost 1.41 (syntax problems in their headers) + #CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS) + CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS) + +-LDFLAGS = -L$(BASE)/lib -L. ++LDFLAGS += -L. + +-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread ++LIBS = -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem -lboost_program_options -lpthread + + .SUFFIXES: .cpp .o + + %.o : ../../../src/lib/%.cpp +- $(CC) $(CFLAGS) -o $@ -c $< ++ $(CC) $(CXXFLAGS) -o $@ -c $< + + %.o : ../../../src/design/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + %.o : ../../../src/main/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + %.o : ../../../src/split/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + all: vina vina_split + diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch new file mode 100644 index 000000000000..298aaa9ab993 --- /dev/null +++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch @@ -0,0 +1,79 @@ + src/main/main.cpp | 10 +++++++++- + src/split/split.cpp | 11 ++++++++++- + 2 files changed, 19 insertions(+), 2 deletions(-) + +diff --git a/src/main/main.cpp b/src/main/main.cpp +index f49c8f5..b566aa2 100644 +--- a/src/main/main.cpp ++++ b/src/main/main.cpp +@@ -47,7 +47,7 @@ + using boost::filesystem::path;
+
+ path make_path(const std::string& str) {
+- return path(str, boost::filesystem::native);
++ return path(str);
+ }
+
+ void doing(int verbosity, const std::string& str, tee& log) {
+@@ -661,7 +661,11 @@ Thank you!\n"; + cpu, seed, verbosity, max_modes_sz, energy_range, log);
+ }
+ catch(file_error& e) {
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#else
+ std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#endif
+ return 1;
+ }
+ catch(boost::filesystem::filesystem_error& e) {
+@@ -673,7 +677,11 @@ Thank you!\n"; + return 1;
+ }
+ catch(parse_error& e) {
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n';
++#else
+ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++#endif
+ return 1;
+ }
+ catch(std::bad_alloc&) {
+diff --git a/src/split/split.cpp b/src/split/split.cpp +index 54c614b..bc5530e 100644 +--- a/src/split/split.cpp ++++ b/src/split/split.cpp +@@ -38,7 +38,7 @@ + using boost::filesystem::path;
+
+ path make_path(const std::string& str) {
+- return path(str, boost::filesystem::native);
++ return path(str);
+ }
+
+ std::string default_prefix(const std::string& input_name, const std::string& add) {
+@@ -208,7 +208,12 @@ Thank you!\n"; + write_multimodel_pdbqt(tmp, ligand_prefix, flex_prefix);
+ }
+ catch(file_error& e) {
++
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#else
+ std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#endif
+ return 1;
+ }
+ catch(boost::filesystem::filesystem_error& e) {
+@@ -220,7 +225,11 @@ Thank you!\n"; + return 1;
+ }
+ catch(parse_error& e) {
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n';
++#else
+ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++#endif
+ return 1;
+ }
+ catch(std::bad_alloc&) {
diff --git a/sci-chemistry/autodock_vina/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml new file mode 100644 index 000000000000..3f44e973345a --- /dev/null +++ b/sci-chemistry/autodock_vina/metadata.xml @@ -0,0 +1,29 @@ +<?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> +AutoDock Vina is a new open-source program for drug discovery, molecular +docking and virtual screening, offering multi-core capability, high +performance and enhanced accuracy and ease of use. [1] +AutoDock Vina has been designed and implemented by Dr. Oleg Trott +in the Molecular Graphics Lab at The Scripps Research Institute. +If you used AutoDock Vina in your work, please cite: +O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy +of docking with a new scoring function, efficient optimization and +multithreading +Journal of Computational Chemistry 31 (2010) 455-461 +</longdescription> + <!-- +<use> + <flag name='flag'>Description of how USE='flag' affects this package</flag> + <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this + package</flag> + <flag name='aspell'>Uses <pkg>app-text/aspell</pkg> for spell checking. + Requires an installed dictionary from <cat>app-dicts</cat></flag> +</use> +--> +</pkgmetadata> diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest new file mode 100644 index 000000000000..aad0cb8f1ba9 --- /dev/null +++ b/sci-chemistry/avogadro/Manifest @@ -0,0 +1,2 @@ +DIST avogadro-1.0.3.tar.bz2 4971989 SHA256 efb6fda223da3c027436f0c218a47ce804f7469c58b41134230e9ebad1c98468 SHA512 49e7b8ca43f0f52a65efc7bf9dc45670ae5a5de5d1aa6bf7b58b8368e816be30fe6529c45fa658d7337d4a69327bb0aa8799d8d4b4805860aace28011cc74210 WHIRLPOOL c835ac24b317a1fa310bf3ea75bae4002d01f364d4754e6a7d841594dcce321435c827d60e125d9410f05670a94c887cc250bf49759d02cde34a5839d2324c92 +DIST avogadro-1.1.0.tar.bz2 10741835 SHA256 6b4eaf57ae52bf43df9b103c77e6abae71e067053d5c99f82acbce9855ecceb0 SHA512 d621dd3ea9e9223d3a29c6b0c0eec89a935837d0c587fcaaa549f91274a76f78a8c60c2a68a67d2f3aa2e107826befb6658be601c46c5bc0760c95bf7284540a WHIRLPOOL c81e866e60b3383a58de515317c754e3982e716c27974ce43ca0c1209d24544949361a7f2f93a4a940d73fd7a18b184f68c7a1856fea89ae5eba75db74b1012d diff --git a/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild b/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild new file mode 100644 index 000000000000..ae73ee50ac4e --- /dev/null +++ b/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils eutils python-single-r1 + +DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" +HOMEPAGE="http://avogadro.openmolecules.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~ppc ~x86" +IUSE="+glsl python cpu_flags_x86_sse2" + +RDEPEND=" + >=sci-chemistry/openbabel-2.2.3 + >=dev-qt/qtgui-4.5.3:4 + >=dev-qt/qtopengl-4.5.3:4 + x11-libs/gl2ps + glsl? ( >=media-libs/glew-1.5.0 ) + python? ( + >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND} + dev-cpp/eigen:2" + +PATCHES=( + "${FILESDIR}"/1.0.1-gl2ps.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DENABLE_THREADGL=OFF + -DENABLE_RPATH=OFF + -DENABLE_UPDATE_CHECKER=OFF + -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs" + -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs + $(cmake-utils_use_enable glsl) + $(cmake-utils_use_with cpu_flags_x86_sse2 SSE2) + $(cmake-utils_use_enable python) + ) + + cmake-utils_src_configure +} diff --git a/sci-chemistry/avogadro/avogadro-1.1.0.ebuild b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild new file mode 100644 index 000000000000..0de1b83085b6 --- /dev/null +++ b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils eutils python-single-r1 + +DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" +HOMEPAGE="http://avogadro.openmolecules.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86" +IUSE="+glsl python cpu_flags_x86_sse2 test" + +RDEPEND=" + >=sci-chemistry/openbabel-2.3.0 + >=dev-qt/qtgui-4.5.3:4 + >=dev-qt/qtopengl-4.5.3:4 + x11-libs/gl2ps + glsl? ( >=media-libs/glew-1.5.0 ) + python? ( + >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND} + dev-cpp/eigen:2" + +# https://sourceforge.net/p/avogadro/bugs/653/ +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/${P}-textrel.patch + "${FILESDIR}"/${P}-xlibs.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DENABLE_THREADGL=OFF + -DENABLE_RPATH=OFF + -DENABLE_UPDATE_CHECKER=OFF + -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs" + -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs + $(cmake-utils_use_enable glsl) + $(cmake-utils_use_enable test TESTS) + $(cmake-utils_use_with cpu_flags_x86_sse2 SSE2) + $(cmake-utils_use_enable python) + ) + + cmake-utils_src_configure +} diff --git a/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch new file mode 100644 index 000000000000..d8a0c0f758e1 --- /dev/null +++ b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch @@ -0,0 +1,39 @@ +diff --git a/avogadro/src/CMakeLists.txt b/avogadro/src/CMakeLists.txt +index 75b6dfb..d87ac2c 100644 +--- a/avogadro/src/CMakeLists.txt ++++ b/avogadro/src/CMakeLists.txt +@@ -45,7 +45,7 @@ endif(ENABLE_UPDATE_CHECKER) + FILE(GLOB projectDelegates_SRCS "projectdelegates/*.cpp") + set(avogadro_SRCS ${avogadro_SRCS} ${projectDelegates_SRCS}) + # Add GL2PS to the executable +-set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c") ++#set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c") + + if( WIN32 ) + set(avogadro_SRCS ${avogadro_SRCS} windows/avogadro.rc) +diff --git a/avogadro/src/mainwindow.cpp b/avogadro/src/mainwindow.cpp +index 66785fd..2933953 100644 +--- a/avogadro/src/mainwindow.cpp ++++ b/avogadro/src/mainwindow.cpp +@@ -51,7 +51,7 @@ + //#endif + + // Include the GL2PS header +-#include "../gl2ps/gl2ps.h" ++#include <gl2ps.h> + + #include <avogadro/pluginmanager.h> + +diff --git a/libavogadro/src/CMakeLists.txt b/libavogadro/src/CMakeLists.txt +index cce8ece..cc084fb 100644 +--- a/libavogadro/src/CMakeLists.txt ++++ b/libavogadro/src/CMakeLists.txt +@@ -152,7 +152,7 @@ endforeach(headerFile ${libavogadro_HDRS}) + add_library(avogadro SHARED ${libavogadro_SRCS} ${libavogadro_QM} ${pythontool_RC_SRCS}) + set_target_properties(avogadro + PROPERTIES VERSION ${Avogadro_VERSION_FULL} SOVERSION 1 ) +-target_link_libraries(avogadro ${AVO_LINK_LIBRARIES}) ++target_link_libraries(avogadro ${AVO_LINK_LIBRARIES} gl2ps) + + install(TARGETS avogadro DESTINATION ${LIB_INSTALL_DIR}) + install(FILES ${libavogadro_HDRS} diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch new file mode 100644 index 000000000000..6d4536ef7c9b --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch @@ -0,0 +1,29 @@ + libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt | 2 +- + libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt +index fb88316..2ddcfdf 100644 +--- a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt ++++ b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt +@@ -20,6 +20,6 @@ add_library(spglib STATIC ${spglib_SRCS}) + set_target_properties(spglib PROPERTIES COMPILE_FLAGS "-w") + + # Set -fPIC on x86_64 +-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") ++if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" ) + endif() +diff --git a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt +index 0cd0c3e..9e89daf 100644 +--- a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt ++++ b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt +@@ -19,7 +19,7 @@ add_library(tubegen STATIC ${tubegen_SRCS}) + set_target_properties(tubegen PROPERTIES COMPILE_FLAGS "-w") + + # Set -fPIC on x86_64 +-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") ++if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" ) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC" ) + endif() diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch new file mode 100644 index 000000000000..74a5889ec8ae --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch @@ -0,0 +1,16 @@ + * Info: Using [gentoo] (https://bugs.gentoo.org/xmlrpc.cgi) + * Info: Getting attachment 403034 + * Info: Viewing attachment: "X11.patch" +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 60ec98f..03443a7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -225,6 +225,7 @@ set(I18N_LANGUAGE "" CACHE STRING "Build i18n only for selected language") + + find_package(Qt4 4.6.0 REQUIRED) # find and setup Qt4 for this project + find_package(OpenGL REQUIRED) # find and setup OpenGL ++find_package(X11 REQUIRED) + find_package(Linguist) # find and setup Linguist + if(NOT Linguist_FOUND) + message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations") + diff --git a/sci-chemistry/avogadro/metadata.xml b/sci-chemistry/avogadro/metadata.xml new file mode 100644 index 000000000000..bacd1480b120 --- /dev/null +++ b/sci-chemistry/avogadro/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> + Avogadro is an advanced molecular editor designed for cross-platform use in + computational chemistry, molecular modeling, bioinformatics, materials + science, and related areas. It offers flexible rendering and a powerful + plugin architecture. + </longdescription> + <use> + <flag name="glsl">Enable glsl features via GLEW.</flag> + </use> + <upstream> + <remote-id type="sourceforge">avogadro</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/azara/Manifest b/sci-chemistry/azara/Manifest new file mode 100644 index 000000000000..700d6abb6ece --- /dev/null +++ b/sci-chemistry/azara/Manifest @@ -0,0 +1 @@ +DIST azara-2.8-src.tgz 638120 SHA256 1f9b86d368ca3b4818c88490c40b2055c7a6d1732e746e4c117e045a73269a98 SHA512 61a913b041f8ed7dade9d452ca0d99804ffcea0c678f23ad8357c1e7188996eecde9402201399306fcb32a504b17c3d61997f50ce57794f876c9f8d492ca500c WHIRLPOOL b7512fe29ad97830d2f96811e71c2ab74e9e71c62354f65a499484a1a57fbe8b74a8ecd27a0b72c48cf0ec5bb48c78148433e32f4f2a880c6317d516f3aa644a diff --git a/sci-chemistry/azara/azara-2.8-r4.ebuild b/sci-chemistry/azara/azara-2.8-r4.ebuild new file mode 100644 index 000000000000..2b5f3bd6f0b8 --- /dev/null +++ b/sci-chemistry/azara/azara-2.8-r4.ebuild @@ -0,0 +1,98 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +PYTHON_DEPEND="python? 2" +SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.* *-jython 2.7-pypy-*" + +inherit eutils python toolchain-funcs + +DESCRIPTION="A suite of programmes to process and view NMR data" +HOMEPAGE="http://www.bio.cam.ac.uk/azara/" +SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${PN}/${P}-src.tgz" + +LICENSE="AZARA" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="python xpm X" + +RDEPEND=" + x11-libs/libX11 + x11-libs/motif:0 + xpm? ( x11-libs/libXpm )" +DEPEND="${RDEPEND}" + +src_prepare() { + cat > ENVIRONMENT <<- EOF + CC=$(tc-getCC) + CFLAGS = ${CFLAGS} + LFLAGS = ${LDFLAGS} + MATH_LIB = -lm + X11_INCLUDE_DIR = -I"${EPREFIX}/usr/X11R6/include" + MOTIF_INCLUDE_DIR = -I"${EPREFIX}/usr/include" -I../global + X11_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)" + MOTIF_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)" + X11_LIB = -lX11 + MOTIF_LIB = -lXm -lXt + SHARED_FLAGS = -shared + ENDIAN_FLAG = -DBIG_ENDIAN_DATA -DWRITE_ENDIAN_PAR + PIC = -fPIC + EOF + + use xpm && echo "XPMUSE=\"XPM_FLAG=-DUSE_XPM XPM_LIB=-lXpm\"" >> ENVIRONMENT + + epatch \ + "${FILESDIR}"/${PV}-prll.patch \ + "${FILESDIR}"/${PV}-impl-dec.patch \ + "${FILESDIR}"/${PV}-python.patch \ + "${FILESDIR}"/${PV}-64bit.patch +} + +src_compile() { + local mymake + local makeflags + + mymake="${mymake} help nongui" + use X && mymake="${mymake} gui" + + emake ${mymake} || die + + compilation() { + emake DataRows_clean || die + emake \ + PYTHON_INCLUDE_DIR="-I${EPREFIX}/$(python_get_includedir)" \ + PYTHON_LIB="$(python_get_library -l)" \ + DataRows || die + } + use python && python_execute_function compilation +} + +src_install() { + rm bin/pythonAzara || die + if ! use X; then + rm bin/plot* || die + fi + + dodoc CHANGES* README* || die + dohtml -r html/* || die + + installation() { + insinto $(python_get_sitedir) + doins lib/DataRows.so || die + } + use python && python_execute_function installation + + cd bin + dobin ${PN}|| die + rm ${PN} + for bin in *; do + newbin ${bin} ${bin}-${PN} || die "failed to install ${bin}" + done +} + +pkg_postinst() { + einfo "Due to collision we moved all binary to *-${PN}" +} diff --git a/sci-chemistry/azara/azara-2.8-r5.ebuild b/sci-chemistry/azara/azara-2.8-r5.ebuild new file mode 100644 index 000000000000..4b90f2ccbd2b --- /dev/null +++ b/sci-chemistry/azara/azara-2.8-r5.ebuild @@ -0,0 +1,99 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 toolchain-funcs + +DESCRIPTION="A suite of programmes to process and view NMR data" +HOMEPAGE="http://www.bio.cam.ac.uk/azara/" +SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${PN}/${P}-src.tgz" + +LICENSE="AZARA" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="xpm X" + +RDEPEND=" + x11-libs/libX11 + x11-libs/motif:0 + xpm? ( x11-libs/libXpm )" +DEPEND="${RDEPEND}" + +src_prepare() { + cat > ENVIRONMENT <<- EOF + CC=$(tc-getCC) + CFLAGS = ${CFLAGS} + LFLAGS = ${LDFLAGS} + MATH_LIB = -lm + X11_INCLUDE_DIR = -I"${EPREFIX}/usr/X11R6/include" + MOTIF_INCLUDE_DIR = -I"${EPREFIX}/usr/include" -I../global + X11_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)" + MOTIF_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)" + X11_LIB = -lX11 + MOTIF_LIB = -lXm -lXt + SHARED_FLAGS = -shared + ENDIAN_FLAG = -DBIG_ENDIAN_DATA -DWRITE_ENDIAN_PAR + PIC = -fPIC + EOF + + use xpm && echo "XPMUSE=\"XPM_FLAG=-DUSE_XPM XPM_LIB=-lXpm\"" >> ENVIRONMENT + + epatch \ + "${FILESDIR}"/${PV}-prll.patch \ + "${FILESDIR}"/${PV}-impl-dec.patch \ + "${FILESDIR}"/${PV}-python.patch \ + "${FILESDIR}"/${PV}-64bit.patch +} + +src_compile() { + local mymake + local makeflags + + mymake="${mymake} help nongui" + use X && mymake="${mymake} gui" + + emake ${mymake} + + compilation() { + python_export PYTHON_CFLAGS PYTHON_LIBS + cd "${BUILD_DIR}" || die + emake DataRows_clean + emake \ + PYTHON_INCLUDE_DIR="${PYTHON_CFLAGS}" \ + PYTHON_LIB="${PYTHON_LIBS}" \ + DataRows + } + python_copy_sources + python_foreach_impl compilation +} + +src_install() { + rm bin/pythonAzara || die + if ! use X; then + rm bin/plot* || die + fi + + dodoc CHANGES* README* + dohtml -r html/* + + cd bin || die + dobin ${PN} + rm ${PN} || die + for bin in *; do + newbin ${bin} ${bin}-${PN} + done + + installation() { + cd "${BUILD_DIR}" || die + python_domodule lib/DataRows.so + } + python_foreach_impl installation +} + +pkg_postinst() { + einfo "Due to collision we moved all binary to *-${PN}" +} diff --git a/sci-chemistry/azara/files/2.8-64bit.patch b/sci-chemistry/azara/files/2.8-64bit.patch new file mode 100644 index 000000000000..c65e075c1d30 --- /dev/null +++ b/sci-chemistry/azara/files/2.8-64bit.patch @@ -0,0 +1,85 @@ +diff --git a/global/par.c b/global/par.c +index ac87c88..fecfe35 100644 +--- a/global/par.c ++++ b/global/par.c +@@ -562,9 +562,9 @@ static Status get_varian_header(FILE *fp, String error_msg) + return OK; + } + +-static long get_varian_long(int offset) ++static int get_varian_int(int offset) + { +- long x; ++ int x; + + if (swapped) + { +@@ -572,7 +572,7 @@ static long get_varian_long(int offset) + SWAP(varian_header[offset+1], varian_header[offset+2], char); + } + +- x = *((long *) (varian_header + offset)); ++ x = *((int *) (varian_header + offset)); + + return x; + } +@@ -591,7 +591,7 @@ static short get_varian_short(int offset) + + static Status check_varian_header(String error_msg) + { +- long nblocks, ntraces, np, ebytes, tbytes, /*bbytes,*/ d; ++ int nblocks, ntraces, np, ebytes, tbytes, /*bbytes,*/ d; + short status; + FILE *fp; + +@@ -605,17 +605,19 @@ static Status check_varian_header(String error_msg) + FCLOSE(fp); + + /* numbers in parentheses are offsets into header */ +- nblocks = get_varian_long(0); /* number of blocks in file */ +- ntraces = get_varian_long(4); /* number of traces per block */ +- np = get_varian_long(8); /* number of elements per trace */ +- ebytes = get_varian_long(12); /* number of bytes per element */ +- tbytes = get_varian_long(16); /* number of bytes per trace */ +- /*bbytes = get_varian_long(20);*/ /* number of bytes per block */ ++ nblocks = get_varian_int(0); /* number of blocks in file */ ++ printf("nblocks = %d\n", nblocks); ++ ntraces = get_varian_int(4); /* number of traces per block */ ++ printf("ntraces = %d\n", ntraces); ++ np = get_varian_int(8); /* number of elements per trace */ ++ ebytes = get_varian_int(12); /* number of bytes per element */ ++ tbytes = get_varian_int(16); /* number of bytes per trace */ ++ /*bbytes = get_varian_int(20);*/ /* number of bytes per block */ + /* short starting at 24 is software version */ + status = get_varian_short(26); /* status of whole file */ + /* long starting at 28 is number of block headers */ + +- if (ntraces != 1L) ++ if (ntraces != 1) + RETURN_ERROR_MSG("can only process Varian data with #traces = 1"); + + if (np != npoints[0]) +@@ -646,12 +648,12 @@ static Status check_varian_header(String error_msg) + + if (integer) + { +- if (ebytes == 2L) ++ if (ebytes == 2) + { + if (status & (1<<2)) + RETURN_ERROR_MSG("Varian header has inconsistent byte information"); + } +- else if (ebytes == 4L) ++ else if (ebytes == 4) + { + if (!(status & (1<<2))) + RETURN_ERROR_MSG("Varian header has inconsistent byte information"); +@@ -666,7 +668,7 @@ static Status check_varian_header(String error_msg) + } + else /* !integer, i.e. floating point */ + { +- if (ebytes != 4L) ++ if (ebytes != 4) + RETURN_ERROR_MSG("Varian header has inconsistent byte information"); + } + diff --git a/sci-chemistry/azara/files/2.8-impl-dec.patch b/sci-chemistry/azara/files/2.8-impl-dec.patch new file mode 100644 index 000000000000..62e8c7d6873b --- /dev/null +++ b/sci-chemistry/azara/files/2.8-impl-dec.patch @@ -0,0 +1,226 @@ +diff --git a/DataRows/data_rows.c b/DataRows/data_rows.c +index 054fa1f..a07eedc 100644 +--- a/DataRows/data_rows.c ++++ b/DataRows/data_rows.c +@@ -1,4 +1,5 @@ + #include "data_rows.h" ++#include "utility.h" + + #include "par.h" + +diff --git a/DataRows/py_data_rows.c b/DataRows/py_data_rows.c +index fc8b3c8..985e6c3 100644 +--- a/DataRows/py_data_rows.c ++++ b/DataRows/py_data_rows.c +@@ -1,4 +1,6 @@ + #include "Python.h" /* Python header files */ ++#include "modsupport.h" ++#include "intobject.h" + + #include "data_rows.h" + +diff --git a/connect/crosspeak.c b/connect/crosspeak.c +index 0de57bf..7b016e1 100644 +--- a/connect/crosspeak.c ++++ b/connect/crosspeak.c +@@ -1,4 +1,5 @@ + #include "crosspeak.h" ++#include "utility.h" + + #include "atom.h" + #include "table.h" +diff --git a/connect/shift.c b/connect/shift.c +index f54ba9f..a880001 100644 +--- a/connect/shift.c ++++ b/connect/shift.c +@@ -1,4 +1,5 @@ + #include "shift.h" ++#include "utility.h" + + #include "atom.h" + #include "table.h" +diff --git a/global/macros.h b/global/macros.h +index 43fc43e..bb1d267 100644 +--- a/global/macros.h ++++ b/global/macros.h +@@ -8,6 +8,7 @@ + #include <math.h> + #include <string.h> + #include <stdlib.h> ++#include <ctype.h> + + #ifdef WIN32 + #include <ctype.h> +diff --git a/global/parser.c b/global/parser.c +index 007d926..0f19575 100644 +--- a/global/parser.c ++++ b/global/parser.c +@@ -1,4 +1,5 @@ + #include "parser.h" ++#include "utility.h" + + #define MAX_NARGS 20 + +diff --git a/peak/fitter.c b/peak/fitter.c +index ba6b175..b58f573 100644 +--- a/peak/fitter.c ++++ b/peak/fitter.c +@@ -1,4 +1,5 @@ + #include "fitter.h" ++#include "data.h" + + #include "nonlinear_model.h" + +diff --git a/peak/peak_fit.c b/peak/peak_fit.c +index 92c69a8..5b9791f 100644 +--- a/peak/peak_fit.c ++++ b/peak/peak_fit.c +@@ -6,6 +6,7 @@ + #include "output.h" + #include "ref.h" + #include "script_fit.h" ++#include "fitter.h" + + #define MEGAWORD (1024 * 1024) + #define DEFAULT_STORE (2 * MEGAWORD) +diff --git a/plot1/draw.c b/plot1/draw.c +index 4fdce96..a2a2e8a 100644 +--- a/plot1/draw.c ++++ b/plot1/draw.c +@@ -1,4 +1,5 @@ + #include "draw.h" ++#include "ticks.h" + + #include "color.h" + #include "data.h" +diff --git a/plot1/object.c b/plot1/object.c +index 973897c..e043a53 100644 +--- a/plot1/object.c ++++ b/plot1/object.c +@@ -1,4 +1,5 @@ + #include "object.h" ++#include "script.h" + + #include "color.h" + #include "parser.h" +diff --git a/plot1/output_popup.c b/plot1/output_popup.c +index 0794584..e73976e 100644 +--- a/plot1/output_popup.c ++++ b/plot1/output_popup.c +@@ -1,4 +1,5 @@ + #include "output_popup.h" ++#include "script.h" + + #include "output.hlp" + +diff --git a/plot1/plots.c b/plot1/plots.c +index 3790f5b..7ac58df 100644 +--- a/plot1/plots.c ++++ b/plot1/plots.c +@@ -1,4 +1,5 @@ + #include "plots.h" ++#include "script.h" + + #include "data.h" + #include "input.h" +diff --git a/plot1/region_popup.c b/plot1/region_popup.c +index 68b3930..f049d29 100644 +--- a/plot1/region_popup.c ++++ b/plot1/region_popup.c +@@ -1,4 +1,5 @@ + #include "region_popup.h" ++#include "data.h" + + #include "region.hlp" + +diff --git a/plot2/data_popup.c b/plot2/data_popup.c +index 851b1d4..1c9026e 100644 +--- a/plot2/data_popup.c ++++ b/plot2/data_popup.c +@@ -1,4 +1,5 @@ + #include "data_popup.h" ++#include "rowcol_popup.h" + + #include "data.hlp" + +diff --git a/plot2/extract_popup.c b/plot2/extract_popup.c +index 416aab0..a7fcbf3 100644 +--- a/plot2/extract_popup.c ++++ b/plot2/extract_popup.c +@@ -1,4 +1,5 @@ + #include "extract_popup.h" ++#include "script.h" + + #include "extract.hlp" + +diff --git a/plot2/levels_popup.c b/plot2/levels_popup.c +index 197cf2c..e1ac22c 100644 +--- a/plot2/levels_popup.c ++++ b/plot2/levels_popup.c +@@ -1,4 +1,5 @@ + #include "levels_popup.h" ++#include "levels_func.h" + + #include "levels.hlp" + +diff --git a/plot2/plot2.c b/plot2/plot2.c +index 9ca91c3..0c10d5a 100644 +--- a/plot2/plot2.c ++++ b/plot2/plot2.c +@@ -1,4 +1,6 @@ + #include "plot2.h" ++#include "object_popup.h" ++#include "prop_popup.h" + + #include "baseline_popup.h" + #include "callback.h" +diff --git a/plot2/rowcol_popup.c b/plot2/rowcol_popup.c +index e9f4843..6c50426 100644 +--- a/plot2/rowcol_popup.c ++++ b/plot2/rowcol_popup.c +@@ -1,4 +1,5 @@ + #include "rowcol_popup.h" ++#include "ref_popup.h" + + #include "rowcol.hlp" + +diff --git a/plot2/script.c b/plot2/script.c +index 2f55182..d7d886f 100644 +--- a/plot2/script.c ++++ b/plot2/script.c +@@ -1,4 +1,5 @@ + #include "script.h" ++#include "macros.h" + + #include "param.h" + #include "stack.h" +diff --git a/plot2/slice_popup.c b/plot2/slice_popup.c +index b601834..1b1e686 100644 +--- a/plot2/slice_popup.c ++++ b/plot2/slice_popup.c +@@ -1,4 +1,5 @@ + #include "slice_popup.h" ++#include "rowcol_func.h" + + #include "baseline.h" + #include "baseline_popup.h" +diff --git a/process/files.c b/process/files.c +index e09127e..d95d681 100644 +--- a/process/files.c ++++ b/process/files.c +@@ -1,4 +1,5 @@ + #include "files.h" ++#include "macros.h" + + #include <sys/types.h> + #include <sys/stat.h> +diff --git a/project/project.c b/project/project.c +index 92b70e3..a3e6d94 100644 +--- a/project/project.c ++++ b/project/project.c +@@ -1,4 +1,5 @@ + #include "project.h" ++#include "utility.h" + + #include "block.h" + #include "par.h" diff --git a/sci-chemistry/azara/files/2.8-prll.patch b/sci-chemistry/azara/files/2.8-prll.patch new file mode 100644 index 000000000000..4720bb659445 --- /dev/null +++ b/sci-chemistry/azara/files/2.8-prll.patch @@ -0,0 +1,387 @@ +diff --git a/DataRows/makefile b/DataRows/makefile +index 587e710..4e0a312 100644 +--- a/DataRows/makefile ++++ b/DataRows/makefile +@@ -28,7 +28,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-DataRows.so: locals globals ++DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) +diff --git a/azara/makefile b/azara/makefile +index 3ba0cd9..f7b4ce5 100644 +--- a/azara/makefile ++++ b/azara/makefile +@@ -12,7 +12,7 @@ LOCAL_OBJS = \ + GLOBAL_OBJS = \ + $(GLOBAL_DIR)/help.o + +-azara: locals globals ++azara: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/combine/makefile b/combine/makefile +index a855236..7a83d8f 100644 +--- a/combine/makefile ++++ b/combine/makefile +@@ -20,7 +20,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-combine: locals globals ++combine: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/connect/makefile b/connect/makefile +index d75e7da..d238507 100644 +--- a/connect/makefile ++++ b/connect/makefile +@@ -23,7 +23,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-connect: locals globals ++connect: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/contours/makefile b/contours/makefile +index 5b832b8..49175dd 100644 +--- a/contours/makefile ++++ b/contours/makefile +@@ -19,7 +19,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-contours: locals globals ++contours: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/deflate/makefile b/deflate/makefile +index 4c4e02e..42d5c30 100644 +--- a/deflate/makefile ++++ b/deflate/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-deflate: locals globals ++deflate: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/extract/makefile b/extract/makefile +index 3212cb9..fed874b 100644 +--- a/extract/makefile ++++ b/extract/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-extract: locals globals ++extract: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/global/makefile b/global/makefile +index 364fa41..5272a31 100644 +--- a/global/makefile ++++ b/global/makefile +@@ -42,6 +42,31 @@ LINPACK_OBJS = \ + AZARA_OBJS = \ + help.o + ++all: \ ++ azara_objects \ ++ decay_objects \ ++ simulate_objects \ ++ viewer_objects \ ++ components_objects \ ++ shuffle_objects \ ++ connect_objects \ ++ slides_objects \ ++ peak_find_objects \ ++ peak_fit_objects \ ++ plot1_objects \ ++ reflate_objects \ ++ deflate_objects \ ++ combine_objects \ ++ unblock_objects \ ++ extract_objects \ ++ project_objects \ ++ contours_objects \ ++ plot2_nog_objects \ ++ plot2_objects \ ++ process_objects \ ++ python_objects \ ++ integrate_objects ++ + azara_objects: $(AZARA_OBJS) + + DECAY_OBJS = \ +diff --git a/help/makefile b/help/makefile +index 9e99a7c..59a86a3 100644 +--- a/help/makefile ++++ b/help/makefile +@@ -39,7 +39,7 @@ globals: + + .c.o:; $(CC) -c $(CFLAGS) $< + +-hlp: ++hlp: txt2hlp + $(TXT2HLP) azara + $(TXT2HLP) combine + $(TXT2HLP) connect +@@ -78,7 +78,7 @@ hlp: + $(TXT2HLP) plot1/text + $(TXT2HLP) DataRows + +-html: ++html: txt2html + $(TXT2HTML) azara + $(TXT2HTML) combine + $(TXT2HTML) connect +diff --git a/makefile b/makefile +index 9965b07..f4383af 100644 +--- a/makefile ++++ b/makefile +@@ -14,7 +14,7 @@ all: help nongui DataRows gui + help: \ + help_program + +-nongui: \ ++nongui: help \ + process_program \ + plot2_nog_program \ + peak_program \ +@@ -29,63 +29,66 @@ nongui: \ + connect_program \ + azara_program + +-gui: \ ++gui: help \ + plot2_program \ + plot1_program + +-DataRows: \ ++DataRows: help \ + DataRows + +-process_program: +- cd process; $(MAKE) ++global: ++ $(MAKE) -C global + +-plot2_program: +- cd plot2; $(MAKE) plot2 ++process_program: global ++ $(MAKE) -C process + +-plot2_nog_program: +- cd plot2; $(MAKE) plot2_nog ++plot2_program: global ++ $(MAKE) -C plot2 + +-plot1_program: +- cd plot1; $(MAKE) ++plot2_nog_program: global ++ $(MAKE) -C plot2 plot2_nog + +-peak_program: +- cd peak; $(MAKE) ++plot1_program: global ++ $(MAKE) -C plot1 + +-extract_program: +- cd extract; $(MAKE) ++peak_program: global process_program ++ $(MAKE) -C peak + +-project_program: +- cd project; $(MAKE) ++extract_program: global ++ $(MAKE) -C extract + +-unblock_program: +- cd unblock; $(MAKE) ++project_program: global ++ $(MAKE) -C project + +-contours_program: +- cd contours; $(MAKE) ++unblock_program: global ++ $(MAKE) -C unblock + +-combine_program: +- cd combine; $(MAKE) ++contours_program: global ++ $(MAKE) -C contours + +-deflate_program: +- cd deflate; $(MAKE) ++combine_program: global ++ $(MAKE) -C combine + +-reflate_program: +- cd reflate; $(MAKE) ++deflate_program: global ++ $(MAKE) -C deflate + +-utility_program: +- cd utility; $(MAKE) ++reflate_program: global ++ $(MAKE) -C reflate + +-connect_program: +- cd connect; $(MAKE) ++utility_program: global ++ $(MAKE) -C utility + +-help_program: +- cd help; $(MAKE) ++connect_program: global ++ $(MAKE) -C connect + +-azara_program: +- cd azara; $(MAKE) ++help_program: global ++ $(MAKE) -C help + +-DataRows: +- cd DataRows; $(MAKE) ++azara_program: global ++ $(MAKE) -C azara ++ ++DataRows: global ++ $(MAKE) -C DataRows + + clean: \ + global_clean \ +@@ -227,3 +230,5 @@ azara_realclean: + DataRows_realclean: + cd DataRows; $(MAKE) realclean + ++ ++.PHONY: global process_program +diff --git a/peak/makefile b/peak/makefile +index f3c13b7..4211221 100644 +--- a/peak/makefile ++++ b/peak/makefile +@@ -97,13 +97,13 @@ COMMAND_OBJS = \ + + all: peak_find peak_fit + +-peak_find: local_find global_find ++peak_find: $(LOCAL_FIND_OBJS) $(GLOBAL_FIND_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_FIND_OBJS) \ + $(GLOBAL_FIND_OBJS) \ + $(LIB) $(MATH_LIB) + +-peak_fit: local_fit global_fit commands ++peak_fit: $(LOCAL_FIT_OBJS) $(GLOBAL_FIT_OBJS) $(COMMAND_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_FIT_OBJS) \ + $(GLOBAL_FIT_OBJS) \ +diff --git a/plot1/makefile b/plot1/makefile +index d1dce2d..e729443 100644 +--- a/plot1/makefile ++++ b/plot1/makefile +@@ -95,7 +95,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/utility.o \ + $(GLOBAL_DIR)/window.o + +-plot1: locals globals ++plot1: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +@@ -110,7 +110,7 @@ locals: + globals: + cd $(GLOBAL_DIR); $(MAKE) plot1_objects + +-.c.o:; $(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) $< ++.c.o:; $(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) -I../plot2 $< + + clean: + rm -f *.o +diff --git a/plot2/makefile b/plot2/makefile +index a6b7b4a..98e286e 100644 +--- a/plot2/makefile ++++ b/plot2/makefile +@@ -129,7 +129,7 @@ GLOBAL_PLOT2_NOG_OBJS = \ + + all: plot2 plot2_nog + +-plot2: local_plot2 global_plot2 ++plot2: $(LOCAL_PLOT2_OBJS) $(GLOBAL_PLOT2_OBJS) + $(CC) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_PLOT2_OBJS) \ + $(GLOBAL_PLOT2_OBJS) \ +@@ -137,7 +137,7 @@ plot2: local_plot2 global_plot2 + $(LIB) $(MATH_LIB) \ + $(MOTIF_LIB) $(X11_LIB) $(XPM_LIB) + +-plot2_nog: local_plot2_nog global_plot2_nog ++plot2_nog: $(LOCAL_PLOT2_NOG_OBJS) $(GLOBAL_PLOT2_NOG_OBJS) + $(CC) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_PLOT2_NOG_OBJS) \ + $(GLOBAL_PLOT2_NOG_OBJS) \ +diff --git a/process/makefile b/process/makefile +index 22ceeed..72d587b 100644 +--- a/process/makefile ++++ b/process/makefile +@@ -72,7 +72,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/utility.o \ + $(LINPACK_OBJS) + +-process: locals globals ++process: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/project/makefile b/project/makefile +index 78143fc..ed0f296 100644 +--- a/project/makefile ++++ b/project/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-project: locals globals ++project: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/reflate/makefile b/reflate/makefile +index 079a3fc..01ec311 100644 +--- a/reflate/makefile ++++ b/reflate/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-reflate: locals globals ++reflate: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/unblock/makefile b/unblock/makefile +index 510dc9e..d9a0f2b 100644 +--- a/unblock/makefile ++++ b/unblock/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-unblock: locals globals ++unblock: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ diff --git a/sci-chemistry/azara/files/2.8-python.patch b/sci-chemistry/azara/files/2.8-python.patch new file mode 100644 index 000000000000..9834c77a77dc --- /dev/null +++ b/sci-chemistry/azara/files/2.8-python.patch @@ -0,0 +1,44 @@ +diff --git a/DataRows/makefile b/DataRows/makefile +index 4e0a312..ce261ab 100644 +--- a/DataRows/makefile ++++ b/DataRows/makefile +@@ -22,16 +22,17 @@ LOCAL_OBJS = \ + data_rows.o + + GLOBAL_OBJS = \ +- $(GLOBAL_DIR)/block_io.o \ +- $(GLOBAL_DIR)/par.o \ +- $(GLOBAL_DIR)/parse.o \ +- $(GLOBAL_DIR)/ref.o \ +- $(GLOBAL_DIR)/utility.o ++ block_io.o \ ++ par.o \ ++ parse.o \ ++ ref.o \ ++ utility.o + + DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_OBJS) \ +- $(GLOBAL_OBJS) ++ $(GLOBAL_OBJS) \ ++ $(PYTHON_LIB) + + local_objects: $(LOCAL_OBJS) + +@@ -42,9 +43,13 @@ globals: + cd $(GLOBAL_DIR); $(MAKE) python_objects + + py_data_rows.o: py_data_rows.c +- $(CC) -c $(CFLAGS) $(PYTHON_INCLUDE_DIR) $< ++ $(CC) -c $(CFLAGS) $(PIC) $(PYTHON_INCLUDE_DIR) $< + +-.c.o:; $(CC) -c $(CFLAGS) $< ++data_rows.o: data_rows.c ++ $(CC) -c $(CFLAGS) $(PIC) $< ++ ++%.o: $(GLOBAL_DIR)/%.c ++ $(CC) -c $(CFLAGS) $(PIC) $< + + clean: + rm -f *.o diff --git a/sci-chemistry/azara/metadata.xml b/sci-chemistry/azara/metadata.xml new file mode 100644 index 000000000000..c0432fefe855 --- /dev/null +++ b/sci-chemistry/azara/metadata.xml @@ -0,0 +1,9 @@ +<?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> + <name>Justin Lecher (jlec)</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/babel/Manifest b/sci-chemistry/babel/Manifest new file mode 100644 index 000000000000..c710a51eca7e --- /dev/null +++ b/sci-chemistry/babel/Manifest @@ -0,0 +1 @@ +DIST babel-1.6.tar.Z 242341 SHA256 132a800cfe0c15b47391c809481a7ca174bbd1402aac7486e0973da0fd4db948 SHA512 60336f695b8ee3ec87433b003da38d55365162bbe87244cb175eabec6c0a470c475dac66f85f24525a61b16fa933bdc3eea5ddd0452b6573bcb046ab774b3229 WHIRLPOOL f6dee4fe6409aed0dfae3f672c826ccdb45f0f5d743421faf6622e1258435caf7d9259ece83ab711754a7964bca0c21af42ed179af23b056329d8b800bd95e80 diff --git a/sci-chemistry/babel/babel-1.6-r1.ebuild b/sci-chemistry/babel/babel-1.6-r1.ebuild new file mode 100644 index 000000000000..1905b34846f0 --- /dev/null +++ b/sci-chemistry/babel/babel-1.6-r1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils + +DESCRIPTION="Interconvert file formats used in molecular modeling" +HOMEPAGE="http://smog.com/chem/babel/" +SRC_URI="http://smog.com/chem/babel/files/${P}.tar.Z" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="amd64 ppc x86" +RESTRICT="mirror bindist" + +#Doesn't really seem to depend on anything (?) +DEPEND="!sci-chemistry/openbabel" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-gcc32.diff \ + "${FILESDIR}"/${P}-makefile.patch + tc-export CC +} + +src_install () { + emake DESTDIR="${D}"/usr/bin install + + insinto /usr/share/${PN} + doins *.lis + + doenvd "${FILESDIR}"/10babel + dodoc README.1ST +} diff --git a/sci-chemistry/babel/files/10babel b/sci-chemistry/babel/files/10babel new file mode 100644 index 000000000000..69f3397638dd --- /dev/null +++ b/sci-chemistry/babel/files/10babel @@ -0,0 +1 @@ +BABEL_DIR=/usr/share/babel diff --git a/sci-chemistry/babel/files/babel-1.6-gcc32.diff b/sci-chemistry/babel/files/babel-1.6-gcc32.diff new file mode 100644 index 000000000000..ba0964af5352 --- /dev/null +++ b/sci-chemistry/babel/files/babel-1.6-gcc32.diff @@ -0,0 +1,28 @@ +--- block.c.orig Sun Sep 15 04:51:13 2002 ++++ block.c Sun Sep 15 04:58:04 2002 +@@ -99,7 +99,12 @@ + void *array; + + /* calc how much space we are gonna need */ ++#ifdef __va_copy ++ __va_copy (ap, initap); ++#else + ap = initap; ++#endif ++ + size = 0; + for(i=0; types[i] != '\0'; i++) + { +@@ -116,7 +121,12 @@ + /* set up the ptrs if we can alloc the memory */ + if(*handle != NULL) + { ++#ifdef __va_copy ++ __va_copy (ap, initap); ++#else + ap = initap; ++#endif ++ + ptr = 0; + for(i=0; types[i] != '\0'; i++) + { diff --git a/sci-chemistry/babel/files/babel-1.6-gentoo.diff b/sci-chemistry/babel/files/babel-1.6-gentoo.diff new file mode 100644 index 000000000000..77e2cb47ef03 --- /dev/null +++ b/sci-chemistry/babel/files/babel-1.6-gentoo.diff @@ -0,0 +1,28 @@ +--- Makefile.orig Tue Oct 23 00:20:54 2001 ++++ Makefile Tue Oct 23 00:33:36 2001 +@@ -1,11 +1,15 @@ +-CFLAGS = -O ++#Commented out to pull CFLAGS from make.conf ++#CFLAGS = -O + + LIBFLAGS = -O -DLIBRARY + +-CC = cc ++#Probably not necessary to specify gcc ++CC = gcc + + PROGRAM = babel + ++DEST = ${DESTDIR}/$(PROGRAM) ++ + LDFLAGS = + + LIBS = +@@ -334,6 +338,7 @@ + index:; ctags -wx $(HDRS) $(SRCS) + + install: $(PROGRAM) ++ install -d ${DESTDIR} + install -s $(PROGRAM) $(DEST) + + print:; $(PRINT) $(HDRS) $(SRCS) diff --git a/sci-chemistry/babel/files/babel-1.6-makefile.patch b/sci-chemistry/babel/files/babel-1.6-makefile.patch new file mode 100644 index 000000000000..33b158d1b2cf --- /dev/null +++ b/sci-chemistry/babel/files/babel-1.6-makefile.patch @@ -0,0 +1,33 @@ +diff -Naur babel-1.6/Makefile babel-1.6.new/Makefile +--- babel-1.6/Makefile 1997-01-21 10:53:05.000000000 -0500 ++++ babel-1.6.new/Makefile 2008-10-19 10:41:42.000000000 -0400 +@@ -1,12 +1,16 @@ +-CFLAGS = -O ++#Commented out to pull CFLAGS from make.conf ++#CFLAGS = -O + + LIBFLAGS = -O -DLIBRARY + +-CC = cc ++#Probably not necessary to specify gcc ++#CC = gcc + + PROGRAM = babel + +-LDFLAGS = ++DEST = ${DESTDIR}/$(PROGRAM) ++ ++#LDFLAGS = + + LIBS = + +@@ -334,7 +338,8 @@ + index:; ctags -wx $(HDRS) $(SRCS) + + install: $(PROGRAM) +- install -s $(PROGRAM) $(DEST) ++ install -d ${DESTDIR} ++ install $(PROGRAM) $(DEST) + + print:; $(PRINT) $(HDRS) $(SRCS) + diff --git a/sci-chemistry/babel/metadata.xml b/sci-chemistry/babel/metadata.xml new file mode 100644 index 000000000000..e42d0af60f42 --- /dev/null +++ b/sci-chemistry/babel/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/balbes/Manifest b/sci-chemistry/balbes/Manifest new file mode 100644 index 000000000000..ac3f2cd87d87 --- /dev/null +++ b/sci-chemistry/balbes/Manifest @@ -0,0 +1,2 @@ +DIST balbes-1.0.0_p100317.tar.gz 506464 SHA256 c5bf6c2086e1a3d7d380e5501c0cffdb91cbf77c74d2951dd345273f21921d0c +DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 diff --git a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild new file mode 100644 index 000000000000..5334207c0229 --- /dev/null +++ b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +CCP4VER="6.1.3" +PYTHON_DEPEND="2" + +inherit eutils fortran-2 python toolchain-funcs + +DESCRIPTION="Automated molecular replacement (MR) pipeline" +HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/index.html" +SRC_URI=" + mirror://gentoo/${P}.tar.gz + ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-core-src.tar.gz" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +# bundled PyXML is modified and cannot be replaced + +COMMON_DEPEND="sci-libs/ccp4-libs" +RDEPEND="${COMMON_DEPEND} + ~sci-libs/balbes-db-${CCP4VER} + !<=sci-chemistry/ccp4-apps-6.1.3-r1" +DEPEND="${COMMON_DEPEND}" + +S="${WORKDIR}"/src + +pkg_setup() { + fortran-2_pkg_setup + python_set_active_version 2 +} + +src_unpack() { + unpack ${P}.tar.gz + tar xvzf "${DISTDIR}"/ccp4-${CCP4VER}-core-src.tar.gz \ + ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \ + ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 + python_convert_shebangs 2 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes +} + +src_prepare() { + mkdir "${WORKDIR}"/bin || die + epatch "${FILESDIR}"/${PV}-makefile.patch + cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/ + epatch "${FILESDIR}"/pyxml-0.8.4-python-2.6.patch +} + +src_compile() { + emake \ + BLANC_FORT="$(tc-getFC) ${FFLAGS}" || die + cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 + find build -delete + $(PYTHON) setup.py build + find xml/xslt test -delete +} + +src_install() { + insinto /usr/share/balbes/BALBES_0.0.1/ + doins -r \ + "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \ + "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 || die + dobin \ + "${WORKDIR}"/bin/* \ + "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes \ + || die +} + +pkg_postinst() { + python_mod_optimize /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4} +} + +pkg_postrm() { + python_mod_cleanup /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4} +} diff --git a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch b/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch new file mode 100644 index 000000000000..da17240642d7 --- /dev/null +++ b/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch @@ -0,0 +1,107 @@ +diff --git a/makefile b/makefile +index baaceb5..85a7baf 100755 +--- a/makefile ++++ b/makefile +@@ -70,6 +70,15 @@ OBJDB_G = get_pdb_list.o + + #OBJDB_Z = blanc2mtz.o libutils.o + ++# incomplete targets: ++# dimer_search_db domain_search_db domain align3 ++all: search_db get_structure_db manage_db search_dm dom2ch \ ++ save_si get_pdb_list_db update_db \ ++ update_dom_db bl2mtz check_file_db fobs2cif sol_check \ ++ get_trns p2s check_cell alt_sg \ ++ align cell_list create_bins \ ++ get_pdb_list_db get_ch get_nm get_mod ++ + search_db: sdb_l + + get_structure_db: tdb_l +@@ -201,58 +210,58 @@ save_seg_id.o: save_seg_id.f + $(BLANC_FORT) -c save_seg_id.f + + sdb_l: $(OBJDB_S) +- $(BLANC_FORT) -o ../bin/search_DB $(OBJDB_S) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DB $(OBJDB_S) + tdb_l: $(OBJDB_T) +- $(BLANC_FORT) -o ../bin/get_structure_DB $(OBJDB_T) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_structure_DB $(OBJDB_T) + mdb_l: $(OBJDB_M) +- $(BLANC_FORT) -o ../bin/manage_DB $(OBJDB_M) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/manage_DB $(OBJDB_M) + mdm_l: $(OBJDB_MD) +- $(BLANC_FORT) -o ../bin/search_DOM $(OBJDB_MD) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DOM $(OBJDB_MD) + d2c_l: $(OBJDB_A) +- $(BLANC_FORT) -o ../bin/domain2chain $(OBJDB_A) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain2chain $(OBJDB_A) + upd_l: $(OBJDB_U) +- $(BLANC_FORT) -o ../bin/update_DB $(OBJDB_U) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_DB $(OBJDB_U) + dom_l: $(OBJDB_V) +- $(BLANC_FORT) -o ../bin/update_domain_DB $(OBJDB_V) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_domain_DB $(OBJDB_V) + ddb_l: $(OBJDB_D) +- $(BLANC_FORT) -o ../bin/dimer_search $(OBJDB_D) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/dimer_search $(OBJDB_D) + dmdb_l: $(OBJDB_N) +- $(BLANC_FORT) -o ../bin/domain_search $(OBJDB_N) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain_search $(OBJDB_N) + gdb_l: $(OBJDB_G) +- $(BLANC_FORT) -o ../bin/get_pdb_list $(OBJDB_G) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_pdb_list $(OBJDB_G) + b2m_l: blanc2mtz.o libutils.o +- $(BLANC_FORT) -o ../bin/blanc2mtz blanc2mtz.o libutils.o $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/blanc2mtz blanc2mtz.o libutils.o -lccp4f -lccp4c + f2c_l: f2cif.o libutils.o +- $(BLANC_FORT) -o ../bin/f2cif f2cif.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/f2cif f2cif.o libutils.o + chf_l: check_file_DB.o libutils.o +- $(BLANC_FORT) -o ../bin/check_file_DB check_file_DB.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_file_DB check_file_DB.o libutils.o + chc_l: check_cell_sg.o libutils.o +- $(BLANC_FORT) -o ../bin/check_cell_sg check_cell_sg.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_cell_sg check_cell_sg.o libutils.o + asl_l: alt_sg_list.o libutils.o +- $(BLANC_FORT) -o ../bin/alt_sg_list alt_sg_list.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/alt_sg_list alt_sg_list.o libutils.o + sc_l: $(OBJDB_C) +- $(BLANC_FORT) -o ../bin/solution_check $(OBJDB_C) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/solution_check $(OBJDB_C) + gt_l: $(OBJDB_R) +- $(BLANC_FORT) -o ../bin/get_trans $(OBJDB_R) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_trans $(OBJDB_R) + dmn_l: domain.o libutils.o +- $(BLANC_FORT) -o ../bin/domain domain.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain domain.o libutils.o + pack: pdb_pack.o libutils.o +- $(BLANC_FORT) -o ../bin/pdb_pack pdb_pack.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb_pack pdb_pack.o libutils.o + p2s_l: $(OBJDB_P) +- $(BLANC_FORT) -o ../bin/pdb2s $(OBJDB_P) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb2s $(OBJDB_P) + aln_l: align_DB.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/align_DB align_DB.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB align_DB.o DB_subr.o libutils.o + aln3_l: align_DB_new.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o + cell_l: create_cell_list.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o + getch_l: get_chain.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/get_chain get_chain.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_chain get_chain.o DB_subr.o libutils.o + getnmr_l: get_nmr.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o + getmod_l: get_model.o libutils.o +- $(BLANC_FORT) -o ../bin/get_model get_model.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_model get_model.o libutils.o + crb_l: create_binaries.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o + save_si_l: save_seg_id.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o diff --git a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch new file mode 100644 index 000000000000..d29b0b6a9eb2 --- /dev/null +++ b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch @@ -0,0 +1,28 @@ +diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py +--- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:54:36.000000000 +0900 ++++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:57:02.000000000 +0900 +@@ -24,8 +24,8 @@ class ParsedAbbreviatedAbsoluteLocationP + self._rel = rel + nt = ParsedNodeTest.ParsedNodeTest('node', '') + ppl = ParsedPredicateList.ParsedPredicateList([]) +- as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') +- self._step = ParsedStep.ParsedStep(as, nt, ppl) ++ as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') ++ self._step = ParsedStep.ParsedStep(as_, nt, ppl) + return + + def evaluate(self, context): +diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py +--- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:54:36.000000000 +0900 ++++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:58:58.000000000 +0900 +@@ -28,8 +28,8 @@ class ParsedAbbreviatedRelativeLocationP + self._right = right + nt = ParsedNodeTest.ParsedNodeTest('node','') + ppl = ParsedPredicateList.ParsedPredicateList([]) +- as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') +- self._middle = ParsedStep.ParsedStep(as, nt, ppl) ++ as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') ++ self._middle = ParsedStep.ParsedStep(as_, nt, ppl) + + def evaluate(self, context): + res = [] diff --git a/sci-chemistry/balbes/metadata.xml b/sci-chemistry/balbes/metadata.xml new file mode 100644 index 000000000000..4bb6be5e5d0c --- /dev/null +++ b/sci-chemistry/balbes/metadata.xml @@ -0,0 +1,18 @@ +<?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> + BALBES is a system for solving protein structures using x-ray + crystalographic data. Molecular Replacement(MR) is its core + scientific method. BALBES aims to integrate all components, + necessary for finding a solution structure by MR, into one system. + It consists of a database, scientific programs and a python + pipeline. The system is automated so that it needs no user's + intervention when running complicated combination of jobs such + as model searching, molecular replacement and refinement. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/ball/Manifest b/sci-chemistry/ball/Manifest new file mode 100644 index 000000000000..f7919da9098f --- /dev/null +++ b/sci-chemistry/ball/Manifest @@ -0,0 +1 @@ +DIST BALL-1.4.2.tar.xz 16080664 SHA256 053931b2e050d7d5bceaa21ad3617a1ad0af00f94de56076ce02d544383cbf91 SHA512 c719af4ef2dc1076818d59b72350b704fbffea06bd44737519fb50d88da113ea509333d407f2330aa59bf1c4e6b81adfd3d28e05459f66d7c9707f8d85db7a87 WHIRLPOOL ba7ae340833ea5703d047a9dbc0ce50d9b9dc2b0047a0c6d9f9a17946956c684a09e0860f25c7214a2aa0adee9beb1d01eac38b0ab08259a2934f97cbef91379 diff --git a/sci-chemistry/ball/ball-1.4.2.ebuild b/sci-chemistry/ball/ball-1.4.2.ebuild new file mode 100644 index 000000000000..bc1005204c0b --- /dev/null +++ b/sci-chemistry/ball/ball-1.4.2.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils python-single-r1 + +DESCRIPTION="Biochemical Algorithms Library" +HOMEPAGE="http://www.ball-project.org/" +SRC_URI="http://www.ball-project.org/Downloads/v${PV}/BALL-${PV}.tar.xz" + +SLOT="0" +LICENSE="LGPL-2 GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda mpi +python sql test +threads +webkit" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/boost + dev-qt/qtcore:4 + dev-qt/qtgui:4 + dev-qt/qtopengl:4 + dev-qt/qttest:4 + dev-qt/qtwebkit:4 + media-libs/glew + sci-libs/fftw:3.0[threads?] + sci-libs/gsl + sci-libs/libsvm + sci-mathematics/lpsolve + virtual/opengl + x11-libs/libX11 + cuda? ( dev-util/nvidia-cuda-toolkit ) + mpi? ( virtual/mpi ) + python? ( ${PYTHON_DEPS} ) + sql? ( dev-qt/qtsql:4 ) + webkit? ( dev-qt/qtwebkit:4 )" +DEPEND="${RDEPEND} + dev-python/sip + sys-devel/bison + virtual/yacc" + +S="${WORKDIR}"/BALL-${PV} + +PATCHES=( + "${FILESDIR}"/${PN}-1.4.1-multilib.patch + "${FILESDIR}"/${PN}-1.4.1-missing-signed.patch + "${FILESDIR}"/${P}-PDBFile-Fix-compilation-with-gcc-4.8.patch + "${FILESDIR}"/${P}-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch + "${FILESDIR}"/${PN}-1.4.1-BondOrder.xml.patch + "${FILESDIR}"/${P}-Fix-compilation-of-sipModularWidget.patch + "${FILESDIR}"/${P}-underlinking.patch + ) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_use threads FFTW_THREADS) + $(cmake-utils_use cuda MT_ENABLE_CUDA) + $(cmake-utils_use mpi MT_ENABLE_MPI) + $(cmake-utils_use sql BALL_HAS_QTSQL) + $(cmake-utils_use_use webkit USE_QTWEBKIT) + $(cmake-utils_use python BALL_PYTHON_SUPPORT) + ) + cmake-utils_src_configure + local i + for i in "${S}"/data/*; do + ln -sf "${i}" "${BUILD_DIR}"/source/TEST/ || die + ln -sf "${i}" "${S}"/source/TEST/ || die + done +} + +src_compile() { + cmake-utils_src_compile + use test && cmake-utils_src_make build_tests +} diff --git a/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch b/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch new file mode 100644 index 000000000000..51e592806999 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch @@ -0,0 +1,30 @@ + source/STRUCTURE/assignBondOrderProcessor.C | 2 +- + source/TEST/AssignBondOrderProcessor_test.C | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/source/STRUCTURE/assignBondOrderProcessor.C b/source/STRUCTURE/assignBondOrderProcessor.C +index f8acc4f..035fffc 100644 +--- a/source/STRUCTURE/assignBondOrderProcessor.C ++++ b/source/STRUCTURE/assignBondOrderProcessor.C +@@ -100,7 +100,7 @@ namespace BALL + const bool AssignBondOrderProcessor::Default::KEKULIZE_RINGS = true; + + const char* AssignBondOrderProcessor::Option::INIFile = "iniFile"; +- const String AssignBondOrderProcessor::Default::INIFile = "/bond_lengths/BondOrder.xml"; ++ const String AssignBondOrderProcessor::Default::INIFile = "bond_lengths/BondOrder.xml"; + + const char* AssignBondOrderProcessor::Option::MAX_BOND_ORDER = "max_bond_order"; + const int AssignBondOrderProcessor::Default::MAX_BOND_ORDER = 3; +diff --git a/source/TEST/AssignBondOrderProcessor_test.C b/source/TEST/AssignBondOrderProcessor_test.C +index 6dfafcc..3405ef5 100644 +--- a/source/TEST/AssignBondOrderProcessor_test.C ++++ b/source/TEST/AssignBondOrderProcessor_test.C +@@ -1834,7 +1834,7 @@ CHECK(Option::INIFile) + // There is really not much we can test here, so we just execute the processor + // to have a chance of catching bugs with valgrind if they sneak in + AssignBondOrderProcessor abop; +- abop.options.set(AssignBondOrderProcessor::Option::INIFile, "/bond_lengths/BondOrderGAFF.xml"); ++ abop.options.set(AssignBondOrderProcessor::Option::INIFile, "bond_lengths/BondOrderGAFF.xml"); + + System sys40; + MOL2File mol40(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_C4_input.mol2), std::ios::in); diff --git a/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch b/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch new file mode 100644 index 000000000000..6868871b3dc4 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch @@ -0,0 +1,26 @@ +Index: ball/include/BALL/DATATYPE/hashGrid.h +=================================================================== +--- ball.orig/include/BALL/DATATYPE/hashGrid.h 2011-12-09 13:49:26.000000000 +0100 ++++ ball/include/BALL/DATATYPE/hashGrid.h 2011-12-09 13:51:09.000000000 +0100 +@@ -37,7 +37,7 @@ + { + namespace __private + { +- extern const char BALL_EXPORT neighbour_table_[27][3]; ++ extern const signed char BALL_EXPORT neighbour_table_[27][3]; + } + + template <typename Item> class HashGrid3; +Index: ball/source/DATATYPE/hashGrid.C +=================================================================== +--- ball.orig/source/DATATYPE/hashGrid.C 2011-12-09 13:49:26.000000000 +0100 ++++ ball/source/DATATYPE/hashGrid.C 2011-12-09 13:50:49.000000000 +0100 +@@ -9,7 +9,7 @@ + { + namespace __private + { +- const char neighbour_table_[27][3] = ++ const signed char neighbour_table_[27][3] = + { + { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 }, + { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 }, diff --git a/sci-chemistry/ball/files/ball-1.4.1-multilib.patch b/sci-chemistry/ball/files/ball-1.4.1-multilib.patch new file mode 100644 index 000000000000..317c4029c678 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.1-multilib.patch @@ -0,0 +1,39 @@ +From 5b8f4e58b4e54bcdfa6f287e01f91d9dfd4e5a14 Mon Sep 17 00:00:00 2001 +From: Justin Lecher <jlec@gentoo.org> +Date: Sun, 25 Mar 2012 14:12:21 +0200 +Subject: [PATCH] Correct path for multilib installation. + +Libraries should go into lib64 not lib on native 64bit. Therefore we can use the LIBDIR detected by cmake. +--- + CMakeLists.txt | 8 ++++---- + 1 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 940ebf4..7eb3db4 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -426,8 +426,8 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin") + ## These variables are used in all install-targets + IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + SET(BALL_RUNTIME_INSTALL_DIRECTORY "bin") +- SET(BALL_LIBRARY_INSTALL_DIRECTORY "lib") +- SET(BALL_ARCHIVE_INSTALL_DIRECTORY "lib") ++ SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) ++ SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) + SET(BALL_HEADER_INSTALL_DIRECTORY ".") + SET(BALL_DATA_INSTALL_DIRECTORY "share/BALL") + SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY "share/BALL/doc") +@@ -435,8 +435,8 @@ IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + SET(BALL_PYTHON_INSTALL_DIRECTORY "bin") + SET(BALL_PLUGIN_INSTALL_DIRECTORY "bin") + ELSE() +- SET(BALL_PYTHON_INSTALL_DIRECTORY "lib") +- SET(BALL_PLUGIN_INSTALL_DIRECTORY "lib") ++ SET(BALL_PYTHON_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) ++ SET(BALL_PLUGIN_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) + ENDIF() + ELSE() + SET(BALL_BUNDLE_INSTALL_DIRECTORY "Applications") +-- +1.7.8.5 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch b/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch new file mode 100644 index 000000000000..3ec2f6e983a8 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch @@ -0,0 +1,40 @@ +From da49802f8620562f91ac2c947520dccd223ee26b Mon Sep 17 00:00:00 2001 +From: Andreas Hildebrandt <andreas.hildebrandt@uni-mainz.de> +Date: Wed, 15 Jan 2014 17:42:01 +0100 +Subject: [PATCH] Fix compilation of sipModularWidget + +--- + source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip | 10 +++++----- + 1 file changed, 5 insertions(+), 5 deletions(-) + +diff --git a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip +index 522b0ed..7b8ba3e 100644 +--- a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip ++++ b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip +@@ -22,18 +22,18 @@ class ModularWidget + static Size countInstances(); + static ModularWidget* getInstance(Position); + +- ModularWidget(const char* = "<ModularWidget>") throw(); +- ModularWidget(const ModularWidget&) throw(); ++ ModularWidget(const char* = "<ModularWidget>"); ++ ModularWidget(const ModularWidget&); + ~ModularWidget() throw(); + +- virtual void destroy() throw(); +- virtual void clear() throw(); ++// virtual void destroy(); ++ virtual void clear(); + + static void registerWidget(ModularWidget*) throw(NullPointer); + // virtual void initializeWidget(MainControl&); + // virtual void finalizeWidget(MainControl&); + virtual void checkMenu(MainControl&) throw(); +-// virtual void initializePreferencesTab(Preferences&) throw(); ++// virtual void initializePreferencesTab(Preferences&); + // virtual void finalizePreferencesTab(Preferences&) throw(); + virtual void applyPreferences() throw(); + virtual void fetchPreferences(INIFile&) throw(); +-- +1.9.1 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch b/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch new file mode 100644 index 000000000000..f6b8ff45fa7f --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch @@ -0,0 +1,28 @@ +From e7cc50705bed20e160bd4b637b23f57270f580a8 Mon Sep 17 00:00:00 2001 +From: Daniel Stoeckel <dstoeckel@bioinf.uni-sb.de> +Date: Sat, 6 Apr 2013 01:06:55 +0200 +Subject: [PATCH] PDBFile:Fix compilation with gcc 4.8 + +Apparently the automatic conversion from boost::shared_ptr<CrystalInfo> +to boost::shared_ptr<PersistentObject> is no longer supported. +Just change the type of the pointer and work around this issue. +--- + source/FORMAT/PDBFileDetails.C | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/source/FORMAT/PDBFileDetails.C b/source/FORMAT/PDBFileDetails.C +index 97c2572..aedc5db 100644 +--- a/source/FORMAT/PDBFileDetails.C ++++ b/source/FORMAT/PDBFileDetails.C +@@ -901,7 +901,7 @@ namespace BALL + { + if (!(current_protein_->hasProperty("CRYSTALINFO"))) + { +- boost::shared_ptr<CrystalInfo> temp_ptr(new CrystalInfo()); ++ boost::shared_ptr<PersistentObject> temp_ptr(new CrystalInfo()); + current_protein_->setProperty(NamedProperty("CRYSTALINFO", temp_ptr)); + } + +-- +1.9.1 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch b/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch new file mode 100644 index 000000000000..615a92290805 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch @@ -0,0 +1,44 @@ +From 1e76c9cb1920e9176b725269985c7eb43126d188 Mon Sep 17 00:00:00 2001 +From: Luis de la Garza <delagarza@informatik.uni-tuebingen.de> +Date: Fri, 22 Nov 2013 15:18:55 +0100 +Subject: [PATCH] QT4_EXTRACT_OPTIONS CMake macro changed in CMake 2.8.12; + fixed BALLMacros.cmake + +--- + cmake/BALLMacros.cmake | 14 ++++++++++---- + 1 file changed, 10 insertions(+), 4 deletions(-) + +diff --git a/cmake/BALLMacros.cmake b/cmake/BALLMacros.cmake +index f81ab89..0ac1b87 100644 +--- a/cmake/BALLMacros.cmake ++++ b/cmake/BALLMacros.cmake +@@ -6,16 +6,22 @@ + ### minor modifications (marked with ## BALL ###) + ### + MACRO(QT4_WRAP_UI_BALL outfiles ) +- QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN}) +- +- ### BALL ### ++ # since 2.8.12 qt4_extract_options has an additional argument ++ # copied fix from OpenMS ++ IF(${CMAKE_VERSION} VERSION_LESS "2.8.12") ++ QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN}) ++ ELSE() ++ QT4_EXTRACT_OPTIONS(ui_files ui_options ui_target ${ARGN}) ++ ENDIF() ++ ++ ### BALL ### + # create output directory (will not exist for out-of-source builds) + FILE(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/) + + FOREACH (it ${ui_files}) + GET_FILENAME_COMPONENT(outfile ${it} NAME_WE) + GET_FILENAME_COMPONENT(infile ${it} ABSOLUTE) +- ### BALL ### ++ ### BALL ### + SET(outfile ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/ui_${outfile}.h) + ADD_CUSTOM_COMMAND(OUTPUT ${outfile} + COMMAND ${QT_UIC_EXECUTABLE} +-- +1.9.1 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch b/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch new file mode 100644 index 000000000000..825f41978c13 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch @@ -0,0 +1,16 @@ + source/APPLICATIONS/BALLVIEW/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt +index 6d16212..f94ce76 100644 +--- a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt ++++ b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt +@@ -85,7 +85,7 @@ IF (UNIX) + LIST(APPEND BALLVIEW_SUPPORT_LIBRARIES "pthread") + ENDIF () + +-TARGET_LINK_LIBRARIES(BALLView BALL VIEW ${BALLVIEW_SUPPORT_LIBRARIES}) ++TARGET_LINK_LIBRARIES(BALLView BALL VIEW ${BALLVIEW_SUPPORT_LIBRARIES} X11) + + #Setup the translations + INCLUDE(${CMAKE_SOURCE_DIR}/cmake/BALLViewTranslations.cmake) diff --git a/sci-chemistry/ball/metadata.xml b/sci-chemistry/ball/metadata.xml new file mode 100644 index 000000000000..066e13dd4a53 --- /dev/null +++ b/sci-chemistry/ball/metadata.xml @@ -0,0 +1,32 @@ +<?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> +Rapid Software Prototyping can significantly reduce development times in the +field of Computational Molecular Biology and Molecular Modeling. +BALL (Biochemical Algorithms Library) is an application framework in C++ that +has been specifically designed for this purpose. It provides an extensive set +of data structures as well as classes for Molecular Mechanics, advanced +solvation methods, comparison and analysis of protein structures, file +import/export, and visualization . + +BALL has been carefully designed to be robust, easy to use, and open to +extensions. Especially its extensibility which results from an object-oriented +and generic programming approach distinguishes it from other software packages. +BALL is well suited to serve as a public repository for reliable data +structures and algorithms. + +Based on BALL we have developed a stand-alone tool for molecular visualization, +BALLView . BALLView makes the broad functionality available through an +integrated user-friendly GUI. +</longdescription> + <use> + <flag name="sql">Include SQL database support</flag> + <flag name="cuda">Include cuda support</flag> + <flag name="webkit">Uses <pkg>dev-qt/qtwebkit</pkg> for drawing</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/bkchem/Manifest b/sci-chemistry/bkchem/Manifest new file mode 100644 index 000000000000..8073e9e6a720 --- /dev/null +++ b/sci-chemistry/bkchem/Manifest @@ -0,0 +1 @@ +DIST bkchem-0.14.0-pre2.tar.gz 998916 SHA256 65b93128932959b394eff8e5a8018a19b30d26ee1ae44345e8bb87167303ed26 SHA512 7fc3bbd7bfe27bc91cf69a98c347a3fb92f4ea25b45a13debd0646a6b02d7a40c5729ae1b2a9ac33c1049d6b90e38355c3cd80e06660a0a2fcc5dafb3514ef20 WHIRLPOOL 732bc45913248aa3df5929933f2072d09d90a46cdc3b3e22f1849adf391d7fd62704e71a98e24649bd74e1ebe96b30d7d398dadabffc0fcd114d8c13922241c6 diff --git a/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r1.ebuild b/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r1.ebuild new file mode 100644 index 000000000000..c5aa86e917a0 --- /dev/null +++ b/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +PYTHON_REQ_USE="tk" + +inherit distutils-r1 eutils versionator + +MY_P="${PN}-$(replace_version_separator 3 -)" + +DESCRIPTION="Chemical drawing program" +HOMEPAGE="http://bkchem.zirael.org/" +SRC_URI="http://bkchem.zirael.org/download/${MY_P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +LICENSE="GPL-2" +IUSE="cairo" + +DEPEND="cairo? ( dev-python/pycairo[svg,${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${MY_P} + +PATCHES=( + "${FILESDIR}"/${P}-nolauncher.patch +) + +python_install() { + distutils-r1_python_install "--strip=${ED}/_${EPYTHON}" +} + +python_install_all() { + distutils-r1_python_install_all + python_foreach_impl python_newscript ${PN}/${PN}.py ${PN} + make_desktop_entry bkchem BKChem "${EPREFIX}"/usr/share/${PN}/images/${PN}.png Science +} diff --git a/sci-chemistry/bkchem/files/0.14.0_pre1-piddle-Fix-assertions.patch b/sci-chemistry/bkchem/files/0.14.0_pre1-piddle-Fix-assertions.patch new file mode 100644 index 000000000000..6270e59d5320 --- /dev/null +++ b/sci-chemistry/bkchem/files/0.14.0_pre1-piddle-Fix-assertions.patch @@ -0,0 +1,48 @@ +diff --git a/bkchem/plugins/piddle/pdfgen.py b/bkchem/plugins/piddle/pdfgen.py +index 5213672..4c056c7 100644 +--- a/bkchem/plugins/piddle/pdfgen.py ++++ b/bkchem/plugins/piddle/pdfgen.py +@@ -639,7 +639,7 @@ class Canvas: + + #use a flate filter and Ascii Base 85 to compress + raw = myimage.tostring() +- assert(len(raw) == imgwidth * imgheight, "Wrong amount of data for image") ++ assert len(raw) == imgwidth * imgheight, "Wrong amount of data for image" + compressed = zlib.compress(raw) #this bit is very fast... + encoded = pdfutils._AsciiBase85Encode(compressed) #...sadly this isn't + +diff --git a/bkchem/plugins/piddle/pdfutils.py b/bkchem/plugins/piddle/pdfutils.py +index ebde677..4a7675d 100644 +--- a/bkchem/plugins/piddle/pdfutils.py ++++ b/bkchem/plugins/piddle/pdfutils.py +@@ -27,7 +27,7 @@ def cacheImageFile(filename): + code.append('ID') + #use a flate filter and Ascii Base 85 + raw = img.tostring() +- assert(len(raw) == imgwidth * imgheight, "Wrong amount of data for image") ++ assert len(raw) == imgwidth * imgheight, "Wrong amount of data for image" + compressed = zlib.compress(raw) #this bit is very fast... + encoded = _AsciiBase85Encode(compressed) #...sadly this isn't + +diff --git a/bkchem/plugins/piddle/piddlePS.py b/bkchem/plugins/piddle/piddlePS.py +index 4d3c327..3afa361 100644 +--- a/bkchem/plugins/piddle/piddlePS.py ++++ b/bkchem/plugins/piddle/piddlePS.py +@@ -866,7 +866,7 @@ translate + # piddlePDF again + + rawimage = myimage.tostring() +- assert(len(rawimage) == imgwidth*imgheight, 'Wrong amount of data for image') ++ assert len(rawimage) == imgwidth*imgheight, 'Wrong amount of data for image' + #compressed = zlib.compress(rawimage) # no zlib at moment + hex_encoded = self._AsciiHexEncode(rawimage) + +@@ -957,7 +957,7 @@ translate + 'image']) + # after image operator just need to dump image dat to file as hexstring + rawimage = myimage.tostring() +- assert(len(rawimage) == imwidth*imheight, 'Wrong amount of data for image') ++ assert len(rawimage) == imwidth*imheight, 'Wrong amount of data for image' + #compressed = zlib.compress(rawimage) # no zlib at moment + hex_encoded = self._AsciiHexEncode(rawimage) + diff --git a/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch b/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch new file mode 100644 index 000000000000..202c47a9c74f --- /dev/null +++ b/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch @@ -0,0 +1,106 @@ + bkchem/bkchem.py | 24 +++++++++++++----------- + setup.py | 23 ----------------------- + 2 files changed, 13 insertions(+), 34 deletions(-) + +diff --git a/bkchem/bkchem.py b/bkchem/bkchem.py +index b336b9c..bcb68b0 100644 +--- a/bkchem/bkchem.py ++++ b/bkchem/bkchem.py +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python2 + #-------------------------------------------------------------------------- + # This file is part of BKChem - a chemical drawing program + # Copyright (C) 2002-2009 Beda Kosata <beda@zirael.org> +@@ -18,18 +19,19 @@ + #-------------------------------------------------------------------------- + + +-"""this is just a starter of the application""" ++#"""this is just a starter of the application""" + + ## support for loading from outside of bkchem dir + +-import os_support, sys ++from bkchem import os_support ++import sys + sys.path.insert( 1, os_support.get_module_path()) + + + ### now starting for real + +-from singleton_store import Store +-import pref_manager ++from bkchem.singleton_store import Store ++from bkchem import pref_manager + + # at first preference manager + Store.pm = pref_manager.pref_manager( +@@ -78,13 +80,13 @@ else: + + + +-import config ++from bkchem import config + + if not config.debug: + # checking of important modules availability + # import modules +- import import_checker +- import messages ++ from bkchem import import_checker ++ from bkchem import messages + + # we need sets from the 2.3 version + if not import_checker.python_version_ok: +@@ -103,16 +105,16 @@ if not config.debug: + + + #import Tkinter +-from main import BKChem +-from splash import Splash +-from singleton_store import Store ++from bkchem.main import BKChem ++from bkchem.splash import Splash ++from bkchem.singleton_store import Store + + myapp = BKChem() + myapp.withdraw() + + if __name__ == '__main__': + +- import messages ++ from bkchem import messages + enc = sys.getfilesystemencoding() + if not enc: + enc = sys.getdefaultencoding() +diff --git a/setup.py b/setup.py +index d4b2a21..2319216 100755 +--- a/setup.py ++++ b/setup.py +@@ -91,26 +91,3 @@ if len( sys.argv) > 1 and sys.argv[1] == 'install' and '--help' not in sys.argv: + print "file %s created" % config_name + + +- # the executable +- if not os.path.isdir( bin_dir): +- try: +- os.mkdir( bin_dir) +- except: +- print "ERROR: could not create directory %s" % bin_dir +- sys.exit( 201) +- exec_name = os.path.join( bin_dir, 'bkchem') +- try: +- file = open( exec_name, 'w') +- except: +- print "ERROR: couldn't open the file %s for write" % exec_name +- sys.exit( 201) +- file.write( "#!/bin/sh\n") +- file.write( 'python %s "$@"\n' % strip_path( os.path.join( py_dir, "bkchem", "bkchem.py"))) +- file.close() +- print "file %s created" % exec_name +- try: +- os.chmod( os.path.join( bin_dir, 'bkchem'), 5+5*8+7*8*8) +- except: +- print "ERROR: failed to make %s executable" % exec_name +- sys.exit( 201) +- print "file %s made executable" % exec_name diff --git a/sci-chemistry/bkchem/metadata.xml b/sci-chemistry/bkchem/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/bkchem/metadata.xml @@ -0,0 +1,8 @@ +<?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> +</pkgmetadata> diff --git a/sci-chemistry/bodr/Manifest b/sci-chemistry/bodr/Manifest new file mode 100644 index 000000000000..53b218466c9e --- /dev/null +++ b/sci-chemistry/bodr/Manifest @@ -0,0 +1,2 @@ +DIST bodr-10.tar.bz2 225671 SHA256 738a0f0e263cdc088581d0a67a0ea16ec586ceb424704d0ff73bdb5da5d4ee81 SHA512 a3e0e7195914938d8824127aa4777c4054c302ef7811d82d1e012d9be5d7a13d7f2225d4216f4a30ae7dbf70eb3b0b38571c3ee0dbe1d97af15f04171dd51bec WHIRLPOOL e61db3427f6f994a1a628eec12c1a41cf8d9cdbd1a16814a267363ffe4fa320f3fb9b03f8188c746899774631dc5d0398830b8d779d225f3317158809c182c3e +DIST bodr-9.tar.bz2 210548 SHA256 a7ed30ecc385ff9fe9b2af84710574ac12febea081b5123db6d6337a4a7a4b60 SHA512 5bcdd682729e11a0bc48f9306262e03fa2a3ca3a805633c2b40d7f94608ce6e2e778cc89ed0c57ec3bf6105c2f759204e158ac6f29c9e6ee3aa37190f8f0d772 WHIRLPOOL 78061c24718a4ce5c5694e369d3c97eb90826b2c3b3f694ba9a0f405173ef0efdc565583373b26c96582c853e1606314ee2c5ab3e5cc8e889c0625358f87291b diff --git a/sci-chemistry/bodr/bodr-10.ebuild b/sci-chemistry/bodr/bodr-10.ebuild new file mode 100644 index 000000000000..7958b8c319da --- /dev/null +++ b/sci-chemistry/bodr/bodr-10.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="The Blue Obelisk Data Repository listing element and isotope properties" +HOMEPAGE="http://sourceforge.net/projects/bodr" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos" +IUSE="" + +DEPEND="dev-libs/libxslt" +RDEPEND="" + +DOCS=( "THANKS" "AUTHORS" "README" "ChangeLog" ) + +src_prepare(){ + sed -i -e "s/COPYING//g" Makefile.* || die +} + +src_configure() { + econf --docdir="${EPREFIX}"/usr/share/doc/${PF} +} diff --git a/sci-chemistry/bodr/bodr-9-r1.ebuild b/sci-chemistry/bodr/bodr-9-r1.ebuild new file mode 100644 index 000000000000..7958b8c319da --- /dev/null +++ b/sci-chemistry/bodr/bodr-9-r1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="The Blue Obelisk Data Repository listing element and isotope properties" +HOMEPAGE="http://sourceforge.net/projects/bodr" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos" +IUSE="" + +DEPEND="dev-libs/libxslt" +RDEPEND="" + +DOCS=( "THANKS" "AUTHORS" "README" "ChangeLog" ) + +src_prepare(){ + sed -i -e "s/COPYING//g" Makefile.* || die +} + +src_configure() { + econf --docdir="${EPREFIX}"/usr/share/doc/${PF} +} diff --git a/sci-chemistry/bodr/metadata.xml b/sci-chemistry/bodr/metadata.xml new file mode 100644 index 000000000000..a30a888d000f --- /dev/null +++ b/sci-chemistry/bodr/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> + Blue Obelisk Data Repository (BODR) is a shared data repository. It lists + many important chemoinformatics data such as elemental properties, atomic + radii, etc. including references to original literature. Software developers + can use this repository on online webpages or in chemistry software for + free. + </longdescription> + <upstream> + <remote-id type="sourceforge">bodr</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/burrow-owl/Manifest b/sci-chemistry/burrow-owl/Manifest new file mode 100644 index 000000000000..8b584ea4ad29 --- /dev/null +++ b/sci-chemistry/burrow-owl/Manifest @@ -0,0 +1,2 @@ +DIST burrow-demos.tar 80896000 SHA256 f93e957889adab0521c6e3234f117cf984b7bb18ba6641a3edbdd30202db4b96 SHA512 76948846b4bff2f5c0814e41ee1745122580d6e28f8de217edbf42c4530bc64fb093dc9c96e9c0c083098755c525300b563ee1368caa12be791b2bea7015ee6b WHIRLPOOL 88ca227d8e808814187630c9568e927620a0dc4fb0eba4131ab14cae842aa778fda6294b32e8ec0e23224fca3b5a2a65609ed7f97a34691267439a557bfa0c42 +DIST burrow-owl-1.5.1.tar.gz 1408249 SHA256 76a4ab0746b1b945e0177d441f7ced8042063d4ff2c9171343ea20ddc19a9bbb SHA512 38b428c8b40cdca6caabc7ed9d247118dbf67b537afaec3af14909353d6b138fdf98a33dee6241ce5224631e16c4dbce11b9aadcfe01fecf92f1aae692ce71e1 WHIRLPOOL e165b0508b28e03a47c77ee72ea0d2347ef9088fe33df9788935e3ec0906efd511f77eebe27d74ed79a913f420cde015a39faebdc3195edc1d279ac0d607d39b diff --git a/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild b/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild new file mode 100644 index 000000000000..76018815c9cd --- /dev/null +++ b/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit autotools-utils virtualx + +DESCRIPTION="Visualize multidimensional nuclear magnetic resonance (NMR) spectra" +HOMEPAGE="http://burrow-owl.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${P}.tar.gz + examples? ( mirror://sourceforge/${PN}/burrow-demos.tar )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples static-libs" + +RDEPEND=" + dev-libs/g-wrap + dev-libs/glib:2 + dev-scheme/guile[networking,regex] + dev-scheme/guile-cairo + dev-scheme/guile-gnome-platform + sci-libs/starparse + x11-libs/gtk+:2" +DEPEND="${RDEPEND} + dev-util/indent + virtual/pkgconfig + doc? ( app-doc/doxygen ) +" + +src_configure() { + local myeconfargs=( + $(use_with doc doxygen doxygen) + ) + autotools-utils_src_configure +} + +src_test () { + cd "${AUTOTOOLS_BUILD_DIR}" || die + virtualmake -C test-suite check +} + +src_install() { + use doc && HTML_DOCS=( "${AUTOTOOLS_BUILD_DIR}/doc/api/html/." ) + autotools-utils_src_install + + use examples && \ + insinto /usr/share/${PN} && \ + doins -r "${WORKDIR}"/burrow-demos/* +} diff --git a/sci-chemistry/burrow-owl/files/1.4-glibc-2.12.patch b/sci-chemistry/burrow-owl/files/1.4-glibc-2.12.patch new file mode 100644 index 000000000000..cca640a6347d --- /dev/null +++ b/sci-chemistry/burrow-owl/files/1.4-glibc-2.12.patch @@ -0,0 +1,38 @@ +Fix build with GLIBC-2.12 + +http://bugs.gentoo.org/show_bug.cgi?id=333843 + +--- src/Makefile.am ++++ src/Makefile.am +@@ -82,8 +82,8 @@ + painter.h \ + ticket.c \ + ticket.h \ +-endian.c \ +-endian.h \ ++bo_endian.c \ ++bo_endian.h \ + version.c \ + version.h + +--- src/hosbackingfile.c ++++ src/hosbackingfile.c +@@ -18,6 +18,7 @@ + */ + + #include "hosbackingfile.h" ++#include "bo_endian.h" + + #define DEFAULT_BUF_SIZE 512 + +--- src/nih.c ++++ src/nih.c +@@ -24,7 +24,7 @@ + #include "hosdimensionblock.h" + #include "hosbackingblock.h" + #include "hosbackingfile.h" +-#include "endian.h" ++#include "bo_endian.h" + + /* --- header contents ---- + * diff --git a/sci-chemistry/burrow-owl/files/1.4-include.patch b/sci-chemistry/burrow-owl/files/1.4-include.patch new file mode 100644 index 000000000000..3dc4cbdf8000 --- /dev/null +++ b/sci-chemistry/burrow-owl/files/1.4-include.patch @@ -0,0 +1,12 @@ +diff --git a/src/gw/spectrum-spec.scm b/src/gw/spectrum-spec.scm +index 253464c..605796c 100644 +--- a/src/gw/spectrum-spec.scm ++++ b/src/gw/spectrum-spec.scm +@@ -30,6 +30,7 @@ + "#include <painter_gdk.h>\n" + "#include <burrow/nih.h>\n" + "#include <hosbackingsim.h>\n" ++ "#include <guile-cairo/guile-cairo-smob-types.h>\n" + "\n")) + + ; couple of disabled sources diff --git a/sci-chemistry/burrow-owl/files/burrow-owl-1.5-prll.patch b/sci-chemistry/burrow-owl/files/burrow-owl-1.5-prll.patch new file mode 100644 index 000000000000..340ccd2366e5 --- /dev/null +++ b/sci-chemistry/burrow-owl/files/burrow-owl-1.5-prll.patch @@ -0,0 +1,20 @@ + burrow/canvas/gw/Makefile.am | 4 +++- + 1 files changed, 3 insertions(+), 1 deletions(-) + +diff --git a/burrow/canvas/gw/Makefile.am b/burrow/canvas/gw/Makefile.am +index da50ee3..2ed89bc 100644 +--- a/burrow/canvas/gw/Makefile.am ++++ b/burrow/canvas/gw/Makefile.am +@@ -31,9 +31,11 @@ H2DEF=@top_srcdir@/utils/h2def.py + canvas.defs: $(HEADERS_1) + $(H2DEF) --all $(HEADERS_1) > $@ + +-canvas-gw.c canvas-gw.h canvas-gw.scm: canvas.defs ++canvas-gw.c canvas-gw.h: canvas.defs + GUILE_LOAD_PATH=@srcdir@:@builddir@:@GUILE_GNOME_MODULE_DIR@:@G_WRAP_MODULE_DIR@:$$GUILE_LOAD_PATH $(GUILE) -s @srcdir@/run-g-wrap.scm + ++BUILT_SOURCES=canvas-gw.c canvas-gw.h canvas.defs ++ + INCLUDES=@GTK_CFLAGS@ @G_WRAP_CFLAGS@ @GUILE_GNOME_CFLAGS@ @GUILE_CAIRO_CFLAGS@ @GUILE_CFLAGS@ -I$(headers_dir) -I@top_srcdir@ + + moduledir=$(datadir)/guile/burrow diff --git a/sci-chemistry/burrow-owl/metadata.xml b/sci-chemistry/burrow-owl/metadata.xml new file mode 100644 index 000000000000..9849d77b1370 --- /dev/null +++ b/sci-chemistry/burrow-owl/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">burrow-owl</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/cara-bin/Manifest b/sci-chemistry/cara-bin/Manifest new file mode 100644 index 000000000000..12c0fa6dee54 --- /dev/null +++ b/sci-chemistry/cara-bin/Manifest @@ -0,0 +1,2 @@ +DIST Start1.2.cara.xz 43124 SHA256 c28321b051902bc020ea04a46b33ceb19b1b3d902264956474c90798f2d60d25 SHA512 26874d634491558dc593a0ec32e83d5cfceedc69bbf901f4d25d6b9515b84aebffbf495d1ac34b3664b8b5822954edf62c5b88dcca6bcfcb152715caa88f5f03 WHIRLPOOL 034e8b73354e7244e4fcc21c03da7b99c02019ebef1e0754dd9cb8249fe68b82be1e78db9848912fc48c8625b0f2acf0f41242d83949a117f0b8a648a930445e +DIST cara_1.8.4_linux.gz 6677463 SHA256 5ba34cc8b0782e1791186cde5a02ec036665769df7f5c559db27377b6f3cc6d6 SHA512 e264cfbef640f267132dfd48b940203a319c8f34de71c5b786c6bfc2ab561bdf3fbd79516d619ca52b2aca64a2887f770fabfabedb76433c5f78aa02c65f898f WHIRLPOOL 5619c70bc31dfb328a72233c8fc3e3d8dcfdccc3db4e5a67430f0ebe8a0a474f998abb2a0ec56f4a3c2e6e4b95e324ec3c667864c81cb3531a1e162439c780da diff --git a/sci-chemistry/cara-bin/cara-bin-1.8.4-r1.ebuild b/sci-chemistry/cara-bin/cara-bin-1.8.4-r1.ebuild new file mode 100644 index 000000000000..d17c035cd3bc --- /dev/null +++ b/sci-chemistry/cara-bin/cara-bin-1.8.4-r1.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MY_PN="${PN%%-bin}" +MY_P="${MY_PN}_${PV}" + +DESCRIPTION="Analysis of NMR spectra and Computer Aided Resonance Assignment" +SRC_URI=" + http://www.cara.nmr-software.org/downloads/${MY_P}_linux.gz + http://dev.gentoo.org/~jlec/distfiles//Start1.2.cara.xz" +HOMEPAGE="http://www.nmr.ch" + +LICENSE="CARA" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="lua" + +RDEPEND=" + !prefix? ( + >=media-libs/fontconfig-2.10.92[abi_x86_32(-)] + >=media-libs/freetype-2.5.0.1[abi_x86_32(-)] + >=x11-libs/libICE-1.0.8-r1[abi_x86_32(-)] + >=x11-libs/libSM-1.2.1-r1[abi_x86_32(-)] + >=x11-libs/libX11-1.6.2[abi_x86_32(-)] + >=x11-libs/libXcursor-1.1.14[abi_x86_32(-)] + >=x11-libs/libXext-1.3.2[abi_x86_32(-)] + >=x11-libs/libXi-1.7.2[abi_x86_32(-)] + >=x11-libs/libXrandr-1.4.2[abi_x86_32(-)] + >=x11-libs/libXrender-0.9.8[abi_x86_32(-)] + ) + virtual/libstdc++ + lua? ( dev-lang/lua )" +DEPEND="" + +RESTRICT="mirror" + +QA_PREBUILT="opt/cara/*" + +S="${WORKDIR}" + +src_install() { + exeinto /opt/cara + doexe ${MY_P}_linux + dosym ../cara/${MY_P}_linux /opt/bin/cara + dodoc Start1.2.cara +} diff --git a/sci-chemistry/cara-bin/metadata.xml b/sci-chemistry/cara-bin/metadata.xml new file mode 100644 index 000000000000..4a00a64b40ae --- /dev/null +++ b/sci-chemistry/cara-bin/metadata.xml @@ -0,0 +1,7 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest new file mode 100644 index 000000000000..e56aec5512a2 --- /dev/null +++ b/sci-chemistry/ccp4-apps/Manifest @@ -0,0 +1,2 @@ +DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820 +DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild new file mode 100644 index 000000000000..854cc48db0cf --- /dev/null +++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild @@ -0,0 +1,395 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools eutils fortran-2 flag-o-matic gnuconfig python-single-r1 toolchain-funcs + +MY_P="${PN/-apps}-${PV}" + +#UPDATE="04_03_09" +#PATCHDATE="090511" + +PATCH_TOT="0" + +DESCRIPTION="Protein X-ray crystallography toolkit" +HOMEPAGE="http://www.ccp4.ac.uk/" +SRC="ftp://ftp.ccp4.ac.uk/ccp4" +SRC_URI=" + ${SRC}/${PV}/${MY_P}-core-src.tar.gz + http://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" +# patch tarball from upstream + [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" +# patches created by us + [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" + +for i in $(seq $PATCH_TOT); do + NAME="PATCH${i}[1]" + SRC_URI="${SRC_URI} + ${SRC}/${PV}/patches/${!NAME}" +done + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="examples X" + +X11DEPS=" + x11-libs/libX11 + x11-libs/libXaw + x11-libs/libXt + x11-libs/libxdl_view" + +TKDEPS=" + >=dev-lang/tk-8.3:0= + >=dev-tcltk/blt-2.4 + dev-tcltk/iwidgets + dev-tcltk/itcl + dev-tcltk/itk + >=dev-tcltk/tdom-0.8 + dev-tcltk/tktreectrl" + +SCILIBS=" + ~sci-libs/ccp4-libs-${PV} + >=sci-libs/ccp4-libs-${PV}-r7 + sci-libs/clipper + sci-libs/fftw:2.1 + sci-libs/mmdb:0 + sci-libs/ssm + virtual/blas + virtual/lapack" + +SCIAPPS=" + sci-chemistry/pdb-extract + sci-chemistry/pymol + sci-chemistry/rasmol + >=sci-chemistry/oasis-4.0-r1" + +RDEPEND=" + ${TKDEPS} + ${SCILIBS} + app-shells/tcsh + dev-python/pyxml + dev-libs/libxml2:2 + dev-libs/libjwc_c + dev-libs/libjwc_f + dev-libs/boehm-gc + !app-office/sc + !<sci-chemistry/ccp4-6.1.3 + X? ( ${X11DEPS} )" +DEPEND="${RDEPEND} + X? ( + x11-misc/imake + x11-proto/inputproto + x11-proto/xextproto + )" +PDEPEND="${SCIAPPS}" + +RESTRICT="mirror" + +S="${WORKDIR}/${MY_P}" + +pkg_setup() { + fortran-2_pkg_setup + python-single-r1_pkg_setup +} + +src_prepare() { + tc-export PKG_CONFIG + einfo "Applying upstream patches ..." + for patch in $(seq $PATCH_TOT); do + base="PATCH${patch}" + dir=$(eval echo \${${base}[0]}) + p=$(eval echo \${${base}[1]}) + pushd "${dir}" >& /dev/null + ccp_patch "${DISTDIR}/${p}" + popd >& /dev/null + done + einfo "Done." + echo + + [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch + + einfo "Applying Gentoo patches ..." + + # it tries to create libdir, bindir etc on live system in configure + ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch + + # We already have sci-chemistry/rasmol + # Also remember to create the bindir. + ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch + + # libraries come from sci-libs/ccp4-libs + ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch + + # We have seperate ebuilds for those + for bin in molref xia scala imosflm balbes; do + ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch + done + + # don't configure what is not build + ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-pisa.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch + + # Fix upstreams code + ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch + + # Not renaming, but unbundling libs + ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch + + # Use pkg-config to detect BLAS/LAPCK + ccp_patch "${FILESDIR}"/${PV}-lapack.patch + + # unbundle libs + ccp_patch "${FILESDIR}"/${PV}-unbundle.patch + + # tcl-8.6 + ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch + + # Update things for oasis 4 usage + epatch "${WORKDIR}"/${PV}-oasis4.0.patch + sed 's: oasis : :g' -i src/Makefile.in || die + + einfo "Done." # done applying Gentoo patches + echo + + find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete + + sed \ + -e "s:/usr:${EPREFIX}/usr:g" \ + -e 's:-Wl,-rpath,$CLIB::g' \ + -e 's: -rpath $CLIB::g' \ + -e 's: -I${srcdir}/include/cpp_c_headers::g' \ + -e 's:sleep 1:sleep .2:g' \ + -e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \ + -e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \ + -e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \ + -e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \ + -i configure || die + + sed \ + -e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \ + -i src/Makefile* || die + + find "${S}" -name "Makefile.*" \ + -exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \; + + # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version + sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die + + # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those. + pushd src/rapper 2>/dev/null + eautoreconf + popd 2>/dev/null + + gnuconfig_update + + python_fix_shebang -f . +} + +src_configure() { + # Build system is broken if we set LDFLAGS + export GENTOOLDFLAGS="${LDFLAGS}" + unset LDFLAGS + + # These are broken with ./src/procheck/ps.f + filter-flags "-floop-*" + + # GENTOO_OSNAME can be one of: + # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd + # linux_compaq_compilers linux_intel_compilers generic Darwin + # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers + if [[ "$(tc-getFC)" = "ifort" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + "${S}"/include/ccp4.setup + + # We agree to the license by emerging this, set in LICENSE + sed -i \ + -e "s~^\(^agreed=\).*~\1yes~g" \ + "${S}"/configure || die + + # Fix up variables -- need to reset CCP4_MASTER at install-time + sed -i \ + -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ + -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ + -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ + -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ + -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ + "${S}"/include/ccp4.setup* || die + + # Set up variables for build + source "${S}"/include/ccp4.setup-sh + + export CC=$(tc-getCC) + export CXX=$(tc-getCXX) + export COPTIM=${CFLAGS} + export CXXOPTIM=${CXXFLAGS} + # Default to -O2 if FFLAGS is unset + export FC=$(tc-getFC) + export FOPTIM=${FFLAGS:- -O2} + export BINSORT_SCR="${T}" + export CCP4_MASTER="${WORKDIR}" + export CCP4I_TCLTK="${EPREFIX}/usr/bin" + export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}" + + # Can't use econf, configure rejects unknown options like --prefix + ./configure \ + $(use_enable X x) \ + --with-shared-libs \ + --with-fftw="${EPREFIX}/usr" \ + --with-warnings \ + --disable-pdb_extract \ + --disable-cctbx \ + --disable-phaser \ + --disable-diffractionImg \ + --disable-clipper \ + --disable-ssm \ + --disable-mosflm \ + --disable-mrbump \ + --tmpdir="${TMPDIR}" \ + ${GENTOO_OSNAME} || die "configure failed" + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd src/clipper_progs 2>/dev/null + econf \ + --prefix="${S}" \ + --bindir="${ED}"/usr/libexec/ccp4/bin \ + --with-ccp4="${S}" \ + --with-clipper="${EPREFIX}/usr" \ + --with-fftw="${EPREFIX}/usr" \ + --with-mmdb="${EPREFIX}/usr" \ + CXX=$(tc-getCXX) + popd 2>/dev/null +} + +src_compile() { + # fsplit is required for the programs + pushd lib/src 2>/dev/null + emake fsplit -j1 || die + popd 2>/dev/null + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd src/clipper_progs 2>/dev/null + emake || die + popd 2>/dev/null + + emake -j1 || die "emake failed" +} + +src_install() { + # Set up variables for build + source "${S}"/include/ccp4.setup-sh + + # if we don't make this, a ton of programs fail to install + mkdir "${S}"/bin || die + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd "${S}"/src/clipper_progs 2>/dev/null + emake install || die + popd 2>/dev/null + + einstall || die "install failed" + + # Collision with sci-chemistry/mrbump + rm -f "${S}"/bin/{mrbump,pydbviewer} || die + + # Bins + exeinto /usr/libexec/ccp4/bin/ + doexe "${S}"/bin/* || die + + # Libs + for file in "${S}"/lib/*; do + if [[ -d ${file} ]]; then + continue + elif [[ -x ${file} ]]; then + dolib.so ${file} || die + else + insinto /usr/$(get_libdir) + doins ${file} || die + fi + done + + rm -f "${S}"/include/ccp4.setup* + + # smartie -- log parsing + insinto /usr/share/ccp4 + doins -r "${S}"/share/smartie || die + + # Install docs and examples + local _man + pushd "${S}"/man/cat1 > /dev/null + for _man in *; do + newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2} + done + popd > /dev/null + + mv "${S}"/manual/README "${S}"/manual/README-manual + dodoc manual/* README CHANGES doc/* examples/README || die + + rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.* + rm "${ED}"/usr/share/doc/${PF}/COPYING.* + + dohtml -r "${S}"/html/* + + if use examples; then + for i in data rnase toxd; do + docinto examples/${i} + dodoc "${S}"/examples/${i}/* + done + + docinto examples/tutorial + dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css + for i in data results; do + docinto examples/tutorial/${i} + dodoc "${S}"/examples/tutorial/${i}/* + done + + for i in non-runnable runnable; do + docinto examples/unix/${i} + dodoc "${S}"/examples/unix/${i}/* + done + fi + # Needed for ccp4i docs to work + dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die + + cat >> "${T}"/baubles <<- EOF + #!${EPREFIX}/bin/bash + exec "${EPYTHON}" "\${CCP4}/share/ccp4/smartie/baubles.py" + EOF + + exeinto /usr/libexec/ccp4/bin/ + doexe "${T}"/baubles || die +} + +# Epatch wrapper for bulk patching +ccp_patch() { + EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} +} diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch new file mode 100644 index 000000000000..433a78dbd23b --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch @@ -0,0 +1,70 @@ +--- src/clipper_progs/src/intensity_target.h.orig 2010-01-21 11:27:13.236795886 -0600 ++++ src/clipper_progs/src/intensity_target.h 2010-01-21 11:31:33.450686927 -0600 +@@ -70,9 +70,31 @@ + { + public: + //! constructor: takes the datalist against which to calc target +- TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ); ++ TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) ++ { ++ hkl_data1 = &hkl_data1_; ++ hkl_data2 = &hkl_data2_; ++ } + //! return the value and derivatives of the target function +- Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const; ++ Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const ++ { ++ Rderiv result; ++ result.r = result.dr = result.dr2 = 0.0; ++ const T1& it1 = (*hkl_data1)[ih]; ++ const T2& it2 = (*hkl_data2)[ih]; ++ if ( !it1.missing() && !it2.missing() ) ++ if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { ++ const ftype eps = ih.hkl_class().epsilon(); ++ const ftype i1 = it1.I() / eps; ++ const ftype i2 = it2.I() / eps; ++ const ftype w = sqrt( i1 * i2 ); ++ const ftype d = intensityh + log(i1) - log(i2); ++ result.r = w * d * d; ++ result.dr = 2.0 * w * d; ++ result.dr2 = 2.0 * w; ++ } ++ return result; ++ } + //! the type of the function: optionally used to improve convergence + FNtype type() const { return QUADRATIC; } + private: +@@ -109,33 +131,4 @@ + return result; + } + +- // Log I1-I2 scaling +- +- template<class T1, class T2> TargetFn_scaleLogI1I2<T1,T2>::TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) +- { +- hkl_data1 = &hkl_data1_; +- hkl_data2 = &hkl_data2_; +- } +- +- template<class T1, class T2> TargetFn_base::Rderiv TargetFn_scaleLogI1I2<T1,T2>::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const +- { +- Rderiv result; +- result.r = result.dr = result.dr2 = 0.0; +- const T1& it1 = (*hkl_data1)[ih]; +- const T2& it2 = (*hkl_data2)[ih]; +- if ( !it1.missing() && !it2.missing() ) +- if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { +- const ftype eps = ih.hkl_class().epsilon(); +- const ftype i1 = it1.I() / eps; +- const ftype i2 = it2.I() / eps; +- const ftype w = sqrt( i1 * i2 ); +- const ftype d = intensityh + log(i1) - log(i2); +- result.r = w * d * d; +- result.dr = 2.0 * w * d; +- result.dr2 = 2.0 * w; +- } +- return result; +- } +- +- + #endif diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch new file mode 100644 index 000000000000..f1df3e5e19f9 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch @@ -0,0 +1,14 @@ +diff --git a/share/Makefile.in b/share/Makefile.in +index 2d4f20b..4500993 100755 +--- a/share/Makefile.in ++++ b/share/Makefile.in +@@ -18,9 +18,6 @@ install : + for i in $(MRBUMP_TARGETS); do \ + test -s $(MRBUMP_BINDIR)/$$i && $(INSTALL_PROGRAM) $(MRBUMP_BINDIR)/$$i $(bindir)/$$i || true ;\ + done +- for i in $(BALBES_TARGETS); do \ +- test -s $(BALBES_BINDIR)/$$i && $(INSTALL_PROGRAM) $(BALBES_BINDIR)/$$i $(bindir)/$$i || true ;\ +- done + + clean : ; -rm -f core *.o *~ a.out + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch new file mode 100644 index 000000000000..e62ae12adfbe --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch @@ -0,0 +1,24 @@ +--- ccp4-6.1.1/x-windows/Makefile.in 2008-08-11 19:20:01.000000000 +0200 ++++ ccp4-6.1.1/x-windows/Makefile.in.new 2009-02-27 14:32:25.000000000 +0100 +@@ -35,7 +35,7 @@ + # + # all + # +-all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy rasmol2 ipmosflm ++all : rotgen_ hklview xjiffy + # + # xdl_view + # +@@ -157,11 +157,10 @@ + # + install_obj = hklview rotgen ipmosflm + install: all ++ mkdir -p $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) + cd $(srcdir)/XCCPJIFFY ; $(MAKE) bindir=$(bindir) libdir=$(libdir) install +- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install +- $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) + # + # clean + # diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch new file mode 100644 index 000000000000..f645643e1c67 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch @@ -0,0 +1,11 @@ +--- ccp4i/Makefile.in 2009-06-19 15:08:53.000000000 +0200 ++++ ccp4i/Makefile.in.new 2009-08-04 21:10:14.000000000 +0200 +@@ -9,7 +9,7 @@ + SHELL = /bin/sh + DESTDIR = $(prefix) + CCP4I_BINDIR = $(top_srcdir)/ccp4i/bin +-CCP4I_TARGETS = ccp4i imosflm loggraph crank mapslicer ++CCP4I_TARGETS = ccp4i loggraph crank mapslicer + + install : + for i in $(CCP4I_TARGETS); do \ diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch new file mode 100644 index 000000000000..1d1323005540 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch @@ -0,0 +1,35 @@ +--- Makefile.in 2009-06-19 15:13:29.000000000 +0200 ++++ Makefile.in.new 2009-08-02 23:06:41.000000000 +0200 +@@ -2,7 +2,7 @@ + # $Id$ + + SHELL = /bin/sh +-DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) ++DIRS = src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) + # this is for the benefit of makes that don't pass variable values in + # recursive invocations, so that you can override these values on the + # command line at the top level +@@ -69,19 +69,19 @@ + $(MAKE) -i $(MFLAGS) $(MVARS) install; else true; fi ; \ + $(MAKE) install + +-srcdir : FORCE libdir ++srcdir : FORCE + if test -d src; then cd src; $(MAKE) $(MFLAGS) $(MVARS); else true; fi + + supported : srcdir + +-unsupported : FORCE libdir ++unsupported : FORCE + if test -d unsupported/src; then cd unsupported/src; \ + $(MAKE) $(MFLAGS) $(MVARS); else true; fi + +-datadir : FORCE libdir ++datadir : FORCE + cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) + +-xwindir : FORCE libdir ++xwindir : FORCE + if test -f x-windows/Makefile; then cd x-windows; \ + $(MAKE) -i $(MFLAGS) ; else true; fi + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch new file mode 100644 index 000000000000..f16b0ecb938c --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch @@ -0,0 +1,19 @@ +--- src/pisa/Makefile.am 2007-07-10 10:56:05.000000000 +0200 ++++ src/pisa/Makefile.am.new 2009-06-11 21:16:51.000000000 +0200 +@@ -1,4 +1,4 @@ +-SUBDIRS = molref pisastore sbase ++SUBDIRS = pisastore sbase + + pkgdatadir = $(datadir)/pisa + +--- src/pisa/Makefile.in 2009-06-12 21:12:08.000000000 +0200 ++++ src/pisa/Makefile.in.new 2009-06-12 21:41:52.000000000 +0200 +@@ -82,7 +82,7 @@ + am__quote = @am__quote@ + install_sh = @install_sh@ + pisa_LDFLAGS = @pisa_LDFLAGS@ +-SUBDIRS = molref pisastore sbase ++SUBDIRS = pisastore sbase + + dist_pkgdata_DATA = pisa.cfg + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch new file mode 100644 index 000000000000..af4fd8219c4f --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch @@ -0,0 +1,42 @@ +--- ./src/Makefile.in 2009-03-20 15:06:41.000000000 +0100 ++++ ./src/Makefile.in.new 2009-07-31 23:46:13.000000000 +0200 +@@ -50,7 +50,7 @@ + + # these live in subdirectories and have more than one dependency: + OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ +- scala dm dmmulti stereo mapmask maprot ncsmask \ ++ dm dmmulti stereo mapmask maprot ncsmask \ + sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ + anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat + +@@ -637,7 +637,7 @@ + + ### scala, mapmask, maprot, ncsmask, combat + +-scala mapmask maprot ncsmask combat sc dyndom: # dependencies below ++mapmask maprot ncsmask combat sc dyndom: # dependencies below + @$(SETFLAGS) pwd=`pwd` ; rm -f $@; \ + cd $(srcdir)/$@_; \ + echo $(FC) $${$@_FLAGS-"$(FFLAGS)"} -c -o $$pwd/$@.o `pwd`/$@.f ;\ +@@ -1002,21 +1002,6 @@ + proclean: $(srcdir)/procheck/clean.f $(srcdir)/procheck/brkcln.par + rmsdev: $(srcdir)/procheck/rmsdev.f $(srcdir)/procheck/rmsdev.inc + +-scaladir = $(srcdir)/scala_ +-scala : $(scaladir)/scala.f $(scaladir)/column.fh $(scaladir)/orient.fh \ +- $(scaladir)/params.fh $(scaladir)/rfile.fh $(scaladir)/scales.fh \ +- $(scaladir)/nbtchc.fh $(scaladir)/parameter.fh $(scaladir)/refcon.fh \ +- $(scaladir)/rundef.fh $(scaladir)/sdfacc.fh $(scaladir)/flags.fh \ +- $(scaladir)/inout.fh $(scaladir)/dump.fh $(scaladir)/tie.fh \ +- $(scaladir)/outcon.fh $(scaladir)/version.fh $(scaladir)/anomtc.fh \ +- $(scaladir)/axes.fh $(scaladir)/bigarg.fh \ +- $(scaladir)/errors.fh $(scaladir)/flow.fh $(scaladir)/glocon.fh \ +- $(scaladir)/means.fh $(scaladir)/refflg.fh $(scaladir)/stats.fh \ +- $(scaladir)/symmty.fh $(scaladir)/sharvest.fh $(scaladir)/chtml.fh \ +- $(scaladir)/htmbuf.fh $(scaladir)/sphhrm.fh $(scaladir)/crlncf.fh \ +- $(scaladir)/datasets.fh $(scaladir)/dts_storage.fh \ +- $(scaladir)/sclinimeans.fh $(scaladir)/timecor.fh +- + freemask.o: $(dmdir)/freemask.f $(dmdir)/crystal.fh $(dmdir)/cycl.fh \ + $(dmdir)/dmheader.fh $(dmdir)/io.fh $(dmdir)/output.fh \ + $(dmdir)/params.fh $(dmdir)/uvwdata.fh diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch new file mode 100644 index 000000000000..3af4af503fa6 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch @@ -0,0 +1,14 @@ +--- src/Makefile.in 2009-07-05 16:50:25.000000000 +0200 ++++ src/Makefile.in.new 2009-07-05 19:38:06.000000000 +0200 +@@ -50,9 +50,9 @@ + + # these live in subdirectories and have more than one dependency: + OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ +- scala dm dmmulti stereo mapmask maprot ncsmask chef \ ++ scala dm dmmulti stereo mapmask maprot ncsmask \ + sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ +- anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat ++ anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf + + # targets built from .c sources: + CSIMPLE = pltdev binsort diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch new file mode 100644 index 000000000000..1e59578473ff --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch @@ -0,0 +1,111 @@ +--- configure 2009-08-07 12:11:28.000000000 +0200 ++++ configure.new.nolib 2009-08-17 22:30:39.000000000 +0200 +@@ -3113,41 +3113,6 @@ + RX_L="$configdir/lib/rxdispencer/rx" + export RX_H RX_L + fi +- echo +- echo "Running separate configure for CCIF library." +- echo +- cd lib/ccif +- echo "Updating modification times for configuration files" +- echo "Please wait..." +- for i in configure.in aclocal.m4 configure Makefile.in; do +- touch $i && sleep 1 +- done +- echo "...done." +- +- if [ "X$LIBFOPTIM" != "X" ]; then +- FOPTIM_save=$FOPTIM +- FOPTIM=$LIBFOPTIM +- FFLAGS="${FOPTIM} ${XFFLAGS}" +- fi +- if [ "X$LIBCOPTIM" != "X" ]; then +- COPTIM_save=$COPTIM +- COPTIM=$LIBCOPTIM +- CFLAGS="${COPTIM} ${XCFLAGS}" +- fi +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif +- rm -f /tmp/$$.cache_file +- if [ "X$LIBFOPTIM" != "X" ]; then +- FOPTIM=$FOPTIM_save +- FFLAGS="${FOPTIM} ${XFFLAGS}" +- fi +- if [ "X$LIBCOPTIM" != "X" ]; then +- COPTIM=$COPTIM_save +- CFLAGS="${COPTIM} ${XCFLAGS}" +- fi +- cd ../.. + echo + echo "Returning to main configure." + echo +@@ -5094,53 +5059,6 @@ + echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" + ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} + echo +- echo "CCP4 configure: Running separate configure for libjwc_c library." +- echo +- cd ${srcdir}/${xwindir}/libjwc/libjwc_c +- echo "Updating modification times for configuration files in libjwc_c" +- echo "Please wait..." +- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do +- touch $i && sleep 1 +- done +- echo "...done." +- echo +- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- rm -f /tmp/$$.cache_file +- echo +- echo "CCP4 configure: Running separate configure for libjwc_f library." +- echo +- cd ${srcdir}/${xwindir}/libjwc/libjwc_f +- # for g77 3.1 some builds do not have no-common for system libs, +- # so disable for now +- echo "Updating modification times for configuration files in libjwc_f" +- echo "Please wait..." +- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do +- touch $i && sleep 1 +- done +- echo "...done." +- echo +- # for g77 3.1 some builds do not have no-common for system libs, +- # so disable for now +- case $system in +- Darwin* ) +- echo "configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- ;; +- * ) +- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- esac +- rm -f /tmp/$$.cache_file + + if test "$non_shared" = yes; then + #this is a bit of a cheat/fudge but that's life! +@@ -5210,12 +5128,6 @@ + fi + + echo +- echo "CCP4 configure: Running separate configure for Mosflm" +- echo +- cd ${srcdir}/${mosflmdir} +- echo "configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ./configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- echo + cd ../.. + echo "Returning to main configure." + echo diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch new file mode 100644 index 000000000000..583697cea0a1 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-6.0.99e.orig/configure 2008-07-31 10:37:22.000000000 -0700 ++++ ccp4-6.0.99e/configure 2008-07-31 10:39:18.000000000 -0700 +@@ -643,45 +643,45 @@ + # echo "! Beware -- the $system installation isn't properly tested." ; } + syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' + +-if test -z "$onlylibs" ; then +- for i in CCP4_SCR BINSORT_SCR; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the value of $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir includedir; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the argument of --$i." +- badvar=1 +- fi +- done +- +- for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do +- if test -d $i || mkdir $i; then : +- else +- eval echo "! No directory $i and can\'t create it." +- badvar=1 +- fi +- done +-else +- # Kludge to fool the "Makefile" target in the top-level CCP4 +- # Makefile into not trying to remake src/Makefile.in +- for i in $srcdir/src $srcdir/lib/src ; do +- if test -d $i || mkdir $i; then +- if ! test -f $i/Makefile.in ; then +- echo +- echo "onlylibs: making dummy file $i/Makefile.in" +- touch $i/Makefile.in +- fi +- fi +- done +-fi ++#if test -z "$onlylibs" ; then ++# for i in CCP4_SCR BINSORT_SCR; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the value of $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir includedir; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the argument of --$i." ++# badvar=1 ++# fi ++# done ++# ++# for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do ++# if test -d $i || mkdir $i; then : ++# else ++# eval echo "! No directory $i and can\'t create it." ++# badvar=1 ++# fi ++# done ++#else ++# # Kludge to fool the "Makefile" target in the top-level CCP4 ++# # Makefile into not trying to remake src/Makefile.in ++# for i in $srcdir/src $srcdir/lib/src ; do ++# if test -d $i || mkdir $i; then ++# if ! test -f $i/Makefile.in ; then ++# echo ++# echo "onlylibs: making dummy file $i/Makefile.in" ++# touch $i/Makefile.in ++# fi ++# fi ++# done ++#fi + + ### sanity checks + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch new file mode 100644 index 000000000000..db8236063043 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch @@ -0,0 +1,152 @@ +diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c +index bfda882..f821e04 100755 +--- a/lib/DiffractionImage/Bruker/FRM_LIB.c ++++ b/lib/DiffractionImage/Bruker/FRM_LIB.c +@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files. + #include "sys/types.h" /* _open, etc. */ + #include "sys/stat.h" /* _open, etc. */ + ++#include <unistd.h> ++ + #ifndef _MSC_VER + int min(int a, int b) + { +diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c +index 1a933de..1c40c32 100755 +--- a/lib/DiffractionImage/MAR/mar300_header.c ++++ b/lib/DiffractionImage/MAR/mar300_header.c +@@ -23,6 +23,9 @@ + */ + #include "mar300_header.h" + ++#include <sys/types.h> ++#include <unistd.h> ++ + /* + * Local functions + */ +diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c +index a8351ea..16d0f7b 100755 +--- a/lib/DiffractionImage/MAR/mar345_header.c ++++ b/lib/DiffractionImage/MAR/mar345_header.c +@@ -32,6 +32,9 @@ + */ + #include "mar345_header.h" + ++#include <sys/types.h> ++#include <unistd.h> ++ + /* + * Definitions + */ +diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c +index 07f2741..6364ca4 100755 +--- a/lib/DiffractionImage/MAR/nb_header.c ++++ b/lib/DiffractionImage/MAR/nb_header.c +@@ -20,6 +20,8 @@ + #include <io.h> + #endif + ++#include <sys/types.h> ++#include <unistd.h> + /* + * mar software include files + */ +diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c +index 443bb8c..0d96b3f 100755 +--- a/lib/DiffractionImage/MAR/swap.c ++++ b/lib/DiffractionImage/MAR/swap.c +@@ -10,6 +10,9 @@ + * + **********************************************************************/ + ++#define _XOPEN_SOURCE ++#include <unistd.h> ++ + void swaplong(); + void swapshort(); + +diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c +index 0f6a6b7..a09dc48 100755 +--- a/lib/ccif/f_interface.c ++++ b/lib/ccif/f_interface.c +@@ -25,6 +25,7 @@ + ********************************************************************/ + + #include "stdpccts.h" ++#include <sys/mman.h> + + /* This file is terribly organised, and badly needs re-doing. There is probably + * scope for splitting this into three modules: +diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c +index 8b5d04f..74ee3f7 100755 +--- a/lib/src/ccp4_general_f.c ++++ b/lib/src/ccp4_general_f.c +@@ -26,6 +26,7 @@ + #include <string.h> + #include <stdlib.h> + #include <math.h> ++#include <time.h> + #include "ccp4_errno.h" + #include "ccp4_fortran.h" + #include "ccp4_parser.h" +diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c +index 3e83d4d..bb3e975 100755 +--- a/lib/src/ccp4_program.c ++++ b/lib/src/ccp4_program.c +@@ -25,6 +25,7 @@ + #include <stdio.h> + #include <stdlib.h> + #include <string.h> ++#include <time.h> + #include "ccp4_program.h" + #include "ccp4_parser.h" + #include "ccp4_utils.h" +diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c +index ee8af24..c6fb3cd 100755 +--- a/lib/src/fsplit.c ++++ b/lib/src/fsplit.c +@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c 5.5 (Berkeley) 3/12/91"; + #include <string.h> + #include <sys/types.h> + #include <sys/stat.h> ++#include <unistd.h> + + /* + * usage: fsplit [-e efile] ... [file] +diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c +index ea52e96..30dbd56 100755 +--- a/src/clipper_progs/src/pirate/compress42.c ++++ b/src/clipper_progs/src/pirate/compress42.c +@@ -142,6 +142,7 @@ + #include <sys/types.h> + #include <sys/stat.h> + #include <errno.h> ++#include <unistd.h> + + #ifdef DIRENT + # include <dirent.h> +diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c +index e224430..c7b82f4 100755 +--- a/src/mtz2cif_/mtz2cif.c ++++ b/src/mtz2cif_/mtz2cif.c +@@ -28,6 +28,7 @@ + #include "cmtzlib.h" + #include "ccp4_parser.h" + #include "ccp4_general.h" ++#include "ccp4_program.h" + #include "csymlib.h" + #include "mtz2cif_lib.h" + +diff --git a/x-windows/XCCPJIFFY/xplot84driver.c b/x-windows/XCCPJIFFY/xplot84driver.c +index 67e0bf1..76526ab 100755 +--- a/x-windows/XCCPJIFFY/xplot84driver.c ++++ b/x-windows/XCCPJIFFY/xplot84driver.c +@@ -11,6 +11,7 @@ + + #include <stdio.h> + #include <sys/types.h> ++#include <stdlib.h> + + #include <X11/StringDefs.h> + #include <X11/Intrinsic.h> diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch new file mode 100644 index 000000000000..62892db01147 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch @@ -0,0 +1,597 @@ +diff --git a/configure b/configure +index 833f483..bcfa62d 100755 +--- a/configure ++++ b/configure +@@ -3226,574 +3226,14 @@ else + echo + echo "Warning: this option has not been extensively tested!" + echo "Please report problems to ccp4@ccp4.ac.uk" +- # Search for vendor LAPACK/BLAS first +- if test ! "$with_netlib_lapack" ; then +- # Initialise variables to blank +- lapackdir= +- XLAPACK_LIB= +- # Possible directories to check for vendor or pre-existing LAPACK or +- # BLAS - add to these if you want to test others +- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib" +- # Possible library names +- # These are the names like xxxx where the library will be libxxxx.a +- # or libxxxx.so +- echo +- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries" +- echo "on this system" +- case $system in +- linux | linux64 | linux32 ) +- # linux users will usually have them in /usr/lib but don't call it +- trylapack="lapack" +- tryblas="blas" +- # if code is non_shared then this can lead to problems. both blas and lapack +- # need to be resolved even if they are not called! +- if test "$non_shared" = yes; then +- echo "You are compiling linux non_shared. This sometimes causes problems " +- echo " so checking for requirements." +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +- PROGRAM TESTLINK +-C A bit of scala code to test the linking +- real bf(3), bnorm +-c +- integer maxbmt +- parameter (maxbmt = 2) +- double precision B(maxbmt,maxbmt), eigval(maxbmt), +- $ eigvec(maxbmt,maxbmt), w(5*maxbmt) +- integer m, ia, ix, istat +-c +- B(1,1) = 1.00 +- B(1,2) = 1.00 +- B(2,1) = 1.00 +- B(2,2) = 1.00 +-c +- m = maxbmt +- ia = maxbmt +- ix = maxbmt +- call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat) +- end +-EOF +- #firstly test without -lblas +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" +- echo $test_compile +- if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... only -llapack needed" +- XLAPACK_LIB="-llapack" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="lapack" +- noblas=yes +- trylapack= +- tryblas= +- else +- echo "more than just -llapack needed...." +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "...-llapack and -lblas were needed" +- XLAPACK_LIB="-llapack -lblas" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="lapack blas" +- noblas=no +- trylapack= +- tryblas= +- else +- echo "....could not find either lapack or blas." +- fi +- fi +- fi +- # add 64 bit libs +- case $system in +- linux64 ) trydirs="/usr/lib64 ${trydirs}" ;; +- esac +- +- ;; +- osf1) +- # OSF1 has dxml (old version) and cxml +- # which should have both lapack and blas +- trylapack="dxml cxml" +- tryblas= +- trydirs="${trydirs} /usr/shlib" +- ;; +- irix) +- # Additional search paths for IRIX +- trydirs="${trydirs} /usr/lib32" +- # SCSL should have both LAPACK and BLAS +- trylapack="scs" +- tryblas="blas" +- ;; +- irix64) +- # Additional search paths for IRIX64 +- trydirs="${trydirs} /usr/lib64" +- # SCSL should have both LAPACK and BLAS +- trylapack="scs" +- tryblas="blas" +- # Extra compiler flags? +- #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON" +- ;; +- aix) +- # Additional search paths for AIX +- trydirs="${trydirs}" +- # AIX might have ESSL library - blas only I think +- trylapack= +- tryblas="essl" +- ;; +- hpux) +- # Additional search paths for HPUX +- trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0" +- # HPUX should have both LAPACK (part of mlib) and BLAS +- trylapack="lapack" +- tryblas="blas" +- # Extra compiler flags? +- # +U77 required for ETIME function - this is already in XFFLAGS +- #XLAPACKFLAGS="+U77" +- ;; +- +- sunos | sunos64) +- # Sun has libraries with BLAS and LAPACK invoked using +- # -xlic_lib=sunperf +- trylapack= +- tryblas= +- echo "SunOs can use the Sun Performance Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- echo "Looking for a valid library to use..." +- echo +- # Loop over the possible library names +- try_libs="sunperf" +- for testlib in $try_libs +- do +- if test ! "$XLAPACK_LIB" ; then +- # Try running a test compile to see if this a valid library +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -xlic_lib=$testlib is okay" +- XLAPACK_LIB="-dalign -xlic_lib=$testlib" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="$testlib" +- noblas=yes +- else +- # Compilation failed +- echo "... cannot use -xlic_lib=$testlib" +- fi +- # End of test for testlib +- fi +- # End of loop over possible lib names +- done +- # Report if no suitable library was found +- if test ! "$XLAPACK_LIB" ; then +- echo +- echo "No suitable LAPACK library was found." +- echo "This may be because the Sun Performance Library is not" +- echo "installed on your system" +- echo "Contact your system administrator or Sun vendor" +- fi +- ;; +- Darwin | Darwin32 | Darwin64 ) +- # Darwin has libraries with BLAS and LAPACK invoked using +- # -framework vecLib +- echo "Darwin can use the vecLib Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- # This is a special case so try running a test compile +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -framework vecLib is okay" +- XLAPACK_LIB="-framework vecLib" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="vecLib" +- noblas=yes +- else +-#alternative linking for vecLib libraries +- case `uname -sr` in +- *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;; +- * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;; +- esac +- +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -framework vecLib is okay" +- XLAPACK_LIB="-Wl,-framework -Wl,vecLib" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="-Wl,-framework -Wl,vecLib" +- noblas=yes +- else +- # Compilation failed +- echo "... cannot use -framework vecLib" +- echo +- fi +- fi +- trylapack= +- tryblas= +-# try the fink installation +- trydirs="${trydirs} /sw" +- ;; +- Darwin_ibm_compilers ) +- # Darwin has libraries with BLAS and LAPACK invoked using +- # -framework vecLib +- echo "Darwin can use the vecLib Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- # This is a special case so try running a test compile +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- case `uname -sr` in +- Darwin\ 8* ) +- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" +- ;; +- Darwin\ 7* ) +- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB" +- ;; +- *) +- XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib" +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" +- esac +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -framework vecLib is okay" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="vecLib" +- noblas=yes +- else +- # Compilation failed +- XLAPACK_LIB="" +- echo "... cannot use -framework vecLib" +- echo +- fi +- trylapack= +- tryblas= +-# try the fink installation +- trydirs="${trydirs} /sw" +- ;; +- +- Darwin_intel_compilers) +- # Darwin has libraries with BLAS and LAPACK invoked using +- # -F vecLib +- echo "Darwin can use the vecLib Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- # This is a special case so try running a test compile +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- # doesn't try to build netlib libraries +- XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib" +- LAPACKLIB="vecLib" +- noblas=yes +- else +- # Compilation failed +- echo "... cannot use -framework vecLib" +- echo +- fi +- trylapack= +- tryblas= +-# try the fink installation +- trydirs="${trydirs} /sw" +- ;; +- +-# linux_ia64_sgi_altix) +-# SGI Japan +- ia64_linux_intel) +- # Additional search paths for Linux/IA64 +- trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib" +- # SCSL and MKL should have both LAPACK and BLAS +- trylapack="mkl_lapack scs lapack" +- tryblas="mkl scs blas" +- ;; +- linux_ibm_compilers ) +- trylapack="lapack" +- tryblas="blas" +- ;; +- linux64_ibm_compilers ) +- trydirs="/usr/lib64 ${trydirs}" +- trylapack="lapack" +- tryblas="blas" +- ;; +- linux_intel_compilers ) +- trydirs="/usr/lib64 ${trydirs}" +- trylapack="mkl_lapack lapack" +- tryblas="mkl blas" +- ;; +- *) +- echo "The guesses for this system may not be correct - please" +- echo "e-mail ccp4@ccp4.ac.uk if you have any extra information" +- echo +- # Default guess is just libblas +- trylapack="lapack" +- tryblas="blas" +- ;; +- esac +- # +- # Search for LAPACK libraries +- # +- # Write out what the guesses are +- if test "$trylapack" ; then +- echo "Possible LAPACK library names for this system:" +- for libname in $trylapack +- do +- echo " lib$libname" +- done +- # Possible library name extensions +- tryexts="a so dylib" +- # Now loop over all the possibilities and see if anything +- # turns up +- echo +- echo "Searching for libraries with LAPACK and BLAS:" +- for testdir in $trydirs +- do +- for testlib in $trylapack +- do +- for ext in $tryexts +- do +- if test ! "$LAPACKLIB"; then +- if test -s "$testdir/lib$testlib.$ext" ; then +- echo "...found LAPACK library: $testdir/lib$testlib.$ext" +- # Now try and link to a test program +- # This is really for IRIX where libraries can be +- # o32 or n32 +- echo " Testing: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- have_lapack=yes +- else +-# cover clapack option +- echo $test_ccompile +- if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then +- have_lapack=yes +- fi +- fi +- if test x$have_lapack = xyes ; then +- # This one is okay +- LAPACKLIB="$testlib" +- LAPACKDIR="$testdir" +- echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" +- # +- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" +- # +- # Test to see if we need BLAS too +- # Do this by trying to compile a test program +- # Use the LSAME test for now +- echo +- echo " * Checking whether we need a separate BLAS library *" +- echo " Testing: try linking library against test program" +- cd lib/lapack/test +- if test -f testlsame ; then +- rm -f testsame testlsame.o +- fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" +- echo $test_compile +- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then +- have_blas=yes +- else +-#cblas route +- echo $test_ccompile +- if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then +- have_blas=yes +- fi +- fi +- if test x$have_blas = xyes ; then +- echo "Test program okay - additional separate BLAS not required" +- noblas=yes +- else +- echo "Test program failed - need a separate BLAS library" +- fi +- cd ../../.. +- else +- # Keep looking +- echo " link failed - cannot use lib$testlib" +- fi +- fi +- fi +- done +- done +- if test ! "$LAPACKLIB"; then +- echo "...nothing in $testdir" +- fi +- done +- fi +- +- # If LAPACKLIB hasn't been set at this point then no LAPACK library +- # was found +- if test ! "$LAPACKLIB" ; then +- echo +- echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead" +- make_lapack=lapacklib +- fi +- # Look for possible BLAS +- if test ! "$noblas" ; then +- if test "$tryblas" ; then +- echo +- echo "Possible BLAS library names for this system:" +- for libname in $tryblas +- do +- echo " lib$libname" +- done +- # Possible library name extensions +- tryexts="a so" +- # Now loop over all the possibilities and see if anything +- # turns up +- echo +- echo "Searching for libraries with BLAS:" +- for testdir in $trydirs +- do +- for testlib in $tryblas +- do +- for ext in $tryexts +- do +- if test ! "$BLASLIB"; then +- if test -s "$testdir/lib$testlib.$ext" ; then +- echo "...found BLAS library: $testdir/lib$testlib.$ext" +- # Now try and link to a test program +- # This is really for IRIX where libraries can be +- # o32 or n32 +- echo " Testing: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" +- echo $test_compile +- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then +- have_blas=yes +- else +- echo $test_ccompile +- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then +- have_blas=yes +- fi +- fi +- if test x$have_blas = xyes ; then +- # This one is okay +- BLASLIB="$testlib" +- BLASDIR="$testdir" +- BLASEXT="$ext" +- echo "Link ok - using lib$BLASLIB from $BLASDIR" +- XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB" +- else +- # Keep looking +- echo " link failed - cannot use lib$testlib" +- fi +- fi +- fi +- done +- done +- if test ! "$BLASLIB"; then +- echo "...nothing in $testdir" +- fi +- done +- fi +- # Do we need to build BLAS too? +- if test ! "$BLASLIB" ; then +- echo +- echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead" +- echo "This may result in poorer performance of the LAPACK routines" +- make_blas=blaslib +- BLASLIB=blas +- BLASDIR="$srcdir/lib/lapack" +- BLASEXT="a" +- fi +- fi ++ # gentoo is clever ++ make_blas= ++ make_lapack= ++ BLASLIB=$(${PKG_CONFIG} --libs blas) ++ LAPACKLIB=$(${PKG_CONFIG} --libs lapack) ++ XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}" ++ XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)" + # Otherwise force building of NetLib BLAS and LAPACK libs +- else +- echo +- echo "! Force building of NetLib BLAS and LAPACK..." +- make_blas=blaslib +- make_lapack=lapacklib +- BLASLIB=blas +- BLASDIR="$srcdir/lib/lapack" +- BLASEXT="a" +- fi + # need to know if we the lapack library was linked using the C or + # fortran linker + if test -f testlink.f || test -f testlink || test -f testlink.c ; then +@@ -3916,8 +3356,8 @@ RANLIB = ${RANLIB} + INSTALL_DATA = ${INSTALL_DATA} + libdir = $libdir + # +-BLASLIB = lib${BLASLIB}.${BLASEXT} +-LAPACKLIB = liblapack.a ++BLASLIB = ${BLASLIB} ++LAPACKLIB = ${LAPACKLIB} + # + # These variables define targets in the main Makefile + blaslib = ${make_blas} diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch new file mode 100644 index 000000000000..9d8fefe965e5 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch @@ -0,0 +1,23 @@ +diff --git a/src/pisa/sbase/Makefile.am b/src/pisa/sbase/Makefile.am +index 053e83a..4ff3394 100755 +--- a/src/pisa/sbase/Makefile.am ++++ b/src/pisa/sbase/Makefile.am +@@ -1,4 +1,4 @@ +-pkgdatadir = $(datadir)/sbase ++pkgdatadir = $(datadir)/pisa/sbase + dist_pkgdata_DATA = \ + graph.sbase index.sbase struct.sbase + +diff --git a/src/pisa/sbase/Makefile.in b/src/pisa/sbase/Makefile.in +index faa3f7f..8630bd7 100755 +--- a/src/pisa/sbase/Makefile.in ++++ b/src/pisa/sbase/Makefile.in +@@ -62,7 +62,7 @@ POST_UNINSTALL = : + EXEEXT = @EXEEXT@ + OBJEXT = @OBJEXT@ + PATH_SEPARATOR = @PATH_SEPARATOR@ +-pkgdatadir = $(datadir)/sbase ++pkgdatadir = $(datadir)/pisa/sbase + AMTAR = @AMTAR@ + AR_FLAGS = @AR_FLAGS@ + AWK = @AWK@ diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch new file mode 100644 index 000000000000..7a012be6ef02 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch @@ -0,0 +1,65 @@ +diff --git a/ccp4-6.1.2/include/ccp4.setup-bash b/ccp4-6.1.2/include/ccp4.setup-bash +index 9848101..cea8ae6 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-bash ++++ b/ccp4-6.1.2/include/ccp4.setup-bash +@@ -188,9 +188,9 @@ fi + #Python path for the subprocess fixed module + + if [ $ccp4_first_in_path -eq 1 ]; then +- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} ++ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python ++ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + fi + + ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### +diff --git a/ccp4-6.1.2/include/ccp4.setup-csh b/ccp4-6.1.2/include/ccp4.setup-csh +index 42f0820..93c2cf3 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-csh ++++ b/ccp4-6.1.2/include/ccp4.setup-csh +@@ -180,9 +180,9 @@ endif + #Python path for the subprocess fixed module + if (${?PYTHONPATH}) then + if ($ccp4_first_in_path) then +- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} ++ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python ++ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + endif + else + setenv PYTHONPATH ${CCP4}/share/python +diff --git a/ccp4-6.1.2/include/ccp4.setup-sh b/ccp4-6.1.2/include/ccp4.setup-sh +index 4396ebf..a0455bd 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-sh ++++ b/ccp4-6.1.2/include/ccp4.setup-sh +@@ -228,9 +228,9 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg + #Python path for the subprocess fixed module + + if test $ccp4_first_in_path -eq 1; then +- export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} ++ export PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python ++ export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + fi + + ################### THE REST SHOULDN'T NEED EDITING ##################### +diff --git a/ccp4-6.1.2/include/ccp4.setup-zsh b/ccp4-6.1.2/include/ccp4.setup-zsh +index 0e5c2ce..53523f3 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-zsh ++++ b/ccp4-6.1.2/include/ccp4.setup-zsh +@@ -157,10 +157,10 @@ export CLASSPATH + #Python path for the subprocess fixed module + + if ($ccp4_first_in_path) then +- PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} ++ PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + export PYTHONPATH + else +- PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python ++ PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + export PYTHONPATH + fi + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch new file mode 100644 index 000000000000..a5144cfa5d33 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch @@ -0,0 +1,60 @@ +diff --git a/src/Makefile.in b/src/Makefile.in +index 70781f3..b2dcc25 100755 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o + pdbcur : $(pdbcurobjs) + @$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS) + ncont : $(ncontobjs) +- @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) ++ @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb + coord_format : $(coord_formatobjs) + @$(SETFLAGS) xxx=1 ; \ + rm -f coord_format; \ +diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am +index 85f212e..2608c6d 100755 +--- a/src/rapper/LOOP/Makefile.am ++++ b/src/rapper/LOOP/Makefile.am +@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains. + hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \ + residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp + +-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la ++rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@ + + pkgdatadir = $(datadir)/rapper + dist_pkgdata_DATA = params.xml + +-INCLUDES = -I. -I../gc7.0/include -I../libxml2/include ++INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@ + #SUBDIRS = \ + #@PYTHON_USE_TRUE@ python + +diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am +index e78b10d..486b931 100755 +--- a/src/rapper/Makefile.am ++++ b/src/rapper/Makefile.am +@@ -1,3 +1,3 @@ +-SUBDIRS = libxml2 gc7.0 LOOP data ++SUBDIRS = LOOP data + + EXTRA_DIST = +diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac +index 5e4ef69..268a579 100755 +--- a/src/rapper/configure.ac ++++ b/src/rapper/configure.ac +@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) + + AC_SUBST(rapper_LDFLAGS) + +-AC_CONFIG_SUBDIRS([gc7.0 libxml2]) ++PKG_CHECK_MODULES([LIBXML],[libxml-2.0]) ++AC_SUBST([LIBXML_CFLAGS]) ++AC_SUBST([LIBXML_LIBS]) ++ ++PKG_CHECK_MODULES([GC],[bdw-gc]) ++AC_SUBST([GC_CFLAGS]) ++AC_SUBST([GC_LIBS]) ++ + #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) + AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch new file mode 100644 index 000000000000..107cfd740238 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch @@ -0,0 +1,131 @@ + src/Makefile.in | 14 +++++----- + src/pisa/configure.ac | 67 +++++++++---------------------------------------- + 2 files changed, 19 insertions(+), 62 deletions(-) + +diff --git a/src/Makefile.in b/src/Makefile.in +index 70781f3..b11db04 100755 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -778,8 +778,8 @@ chainsaw : $(chainsawobjs) + eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o chainsaw $(chainsawobjs) $(LDCXXFLAGS) + pdbcur.o pcur_funcs.o ncont.o coord_format.o pdb_merge.o chainsaw.o: # dependencies at end + @$(SETFLAGS) xxx=1 ; \ +- echo $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; +- eval $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ++ echo $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; ++ eval $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp + + ### bp3, afro, gcx + +@@ -813,8 +813,8 @@ gcx : libbp3 $(gcxobjs) + + $(libbp3objs) $(bp3objs) $(afroobjs) $(gcxobjs) : # dependencies at end + @$(SETFLAGS) xxx=1 ; \ +- echo $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ +- eval $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ++ echo $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ ++ eval $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C + + ### crunch2 pmf + +@@ -853,7 +853,7 @@ cif2xml : $(cif2xmlobjs) + cross_validate : $(cross_validateobjs) + @$(SETFLAGS); rm -f cross_validate; eval $(CXX) $${harvest_app_FLAGS-"$(CXXFLAGS)"} -o cross_validate $(cross_validateobjs) $(LDCXXFLAGS) + cif2xml.o cross_validate.o : # dependencies at end +- @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) -I$(incdir)/mmdb $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp ++ @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp + + pdb_extractdir = $(srcdir)/harvest_app_/pdb_extract + pdb_extract_suite : +@@ -873,8 +873,8 @@ $(dev_tools_ctargets) : + $(dev_tools_cxxtargets) : + @$(SETFLAGS) xxx=1; \ + rm -f $@; \ +- echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ;\ +- eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ++ echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) ;\ ++ eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) + + ### mlphare + mlphare: +diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac +index 81afdda..044b6f8 100755 +--- a/src/pisa/configure.ac ++++ b/src/pisa/configure.ac +@@ -31,64 +31,21 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) + # test for function in m + AC_CHECK_LIB([m], [sqrt]) + +-dnl Optional: Check for MMDB. +-AM_PATH_MMDB(, +- [ if test "x$mmdb_prefix" != x ; then +- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then +- case "$ac_MMDB_CXXFLAGS" in +- *src/mmdb ) +- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` +- ;; +- *include/mmdb ) +- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` +- ;; +- *) +- esac +- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" +- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` +- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) +- else +- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" +- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" +- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) +- fi +- else +- AC_MSG_ERROR([mmdb not found]) +- fi +- ] +-) ++PKG_CHECK_MODULES([MMDB],[mmdb]) ++PKG_CHECK_MODULES([SSM],[ssm]) ++ ++MMDB_CXXFLAGS=${MMDB_CFLAGS} ++ ++AC_SUBST([MMDB_CFLAGS]) ++AC_SUBST([MMDB_CXXFLAGS]) ++AC_SUBST([SSM_CFLAGS]) ++ ++AC_SUBST([MMDB_LIBS]) ++AC_SUBST([SSM_LIBS]) + +-ac_saved_CXXFLAGS=$CXXFLAGS +-ac_saved_LIBS=$LIBS + CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" + LIBS="$MMDB_LIBS $LIBS" +-AM_PATH_SSM(, +- [ if test "x$ssm_prefix" != x ; then +- if test "x$ac_SSM_CXXFLAGS" != x && test "x$ac_SSM_LDOPTS" = x ; then +- case "$ac_SSM_CXXFLAGS" in +- *lib/ssm ) +- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#lib/ssm#lib#g` +- ;; +- *include/ssm ) +- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#include/ssm#lib#g` +- ;; +- *) +- esac +- SSM_CXXFLAGS="$ac_SSM_CXXFLAGS" +- SSM_LIBS=`echo "$ac_SSM_LDOPTS -lssm" | sed s#-I#-L#` +- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) +- else +- SSM_CXXFLAGS="-I$ssm_prefix/include/ssm -I$ssm_prefix/lib/ssm" +- SSM_LIBS="-L$ssm_prefix/lib -L$ssm_prefix/lib/ssm -lssm" +- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) +- fi +- else +- AC_MSG_ERROR([ssm not found]) +- fi +- ] +-) +-CXXFLAGS=$ac_saved_CXXFLAGS +-LIBS=$ac_saved_LIBS ++ + + # Checks for typedefs, structures, and compiler characteristics. + # diff --git a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch new file mode 100644 index 000000000000..4b98545eec83 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch @@ -0,0 +1,130 @@ + src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c | 34 ++++++++++++++--------------- + 1 file changed, 17 insertions(+), 17 deletions(-) + +diff --git a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c +index 2c9f02f..98d814a 100755 +--- a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c ++++ b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c +@@ -297,7 +297,7 @@ int canvas_draw_line(char *canvas, int npts, float *x, float *y, char *tags, + puts("canvas_draw_line: about to evaluate the command..."); + } + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_draw_line: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_draw_line: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + return 0; + } + if (CCP4MAPWISH_CANVAS_DIAG) +@@ -432,7 +432,7 @@ int canvas_draw_rectangle(char *canvas, int npts, float *x, float *y, + puts("canvas_draw_rectangle: about to evaluate the command..."); + } + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_draw_rectangle: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_draw_rectangle: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + printf("canvas_draw_rectangle:\ncanvas = \"%s\"\ntags = \"%s\"\ncolor = \"%s\"\nunits = \"%c\"\n",canvas,tags,color,units); + return 0; + } +@@ -536,7 +536,7 @@ int canvas_draw_label(char *canvas, char *text, float x, float y, + /* Execute the command which draws the label */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_draw_label: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_draw_label: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_draw_label: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -617,7 +617,7 @@ int canvas_scale_canvas(char *canvas, char *tag, float scale) + /* Execute the command which scales the canvas */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_scale_canvas: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -706,7 +706,7 @@ int canvas_shift_canvas(char *canvas) + /* Execute the command which resizes the canvas */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -789,7 +789,7 @@ int canvas_shift_element(char *canvas, char *tag, int shiftx, int shifty) + /* Execute the command which resizes the canvas */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_shift_element: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_shift_element: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -861,7 +861,7 @@ int canvas_delete(char *canvas, char *tag) + /* Execute the command which deletes the tagged items */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_delete: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -892,15 +892,15 @@ int canvas_exists(char *canvas) + + sprintf(tmpstr,"winfo exists %s",canvas); + if (Tcl_Eval(interp,tmpstr) != TCL_OK) { +- printf("canvas_exists: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_exists: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + return 0; + } + /* Extract a long int using strtol + If no conversion takes place then "endptr" will be equal + to "result" */ +- istatus = (int) strtol(interp->result,&endptr,10); +- if (strcmp(interp->result,endptr) == 0) { +- printf("canvas_exists: bad return status from winfo command \"%s\"\n",interp->result); ++ istatus = (int) strtol(Tcl_GetStringResult(interp),&endptr,10); ++ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) { ++ printf("canvas_exists: bad return status from winfo command \"%s\"\n",Tcl_GetStringResult(interp)); + return 0; + } + if (!istatus) { +@@ -930,13 +930,13 @@ float canvas_get_tk_scaling(char *canvas, char units) + + /* Execute the tk scaling command */ + if (Tcl_Eval(interp,"tk scaling") != TCL_OK) { +- printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + return (float) 0.0; + } + + /* Extract a float from the result */ +- tkscale = ((float) strtod(interp->result,&endptr)); +- if (strcmp(interp->result,endptr) == 0) { ++ tkscale = ((float) strtod(Tcl_GetStringResult(interp),&endptr)); ++ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) { + printf("canvas_get_tk_scaling: couldn't extract scale factor\n"); + return (float) 0.0; + } +@@ -1021,19 +1021,19 @@ int canvas_get_limits(char *canvas, int limits[4]) + + /* Evaluate the command */ + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_get_limits: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_get_limits: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + + /* Process the result - it should consist of 4 integers */ + /* Use strtok which can split the string based on tokens + set by the programmer - in this case a space */ +- if (!interp->result) { ++ if (!Tcl_GetStringResult(interp)) { + puts("canvas_get_limits: failed to fetch canvas limits"); + return TCL_ERROR; + } + i = 0; +- p = strtok(interp->result," "); ++ p = strtok(Tcl_GetStringResult(interp)," "); + if (p == NULL) { + return 0; + } diff --git a/sci-chemistry/ccp4-apps/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/ccp4-apps/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild b/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild new file mode 100644 index 000000000000..eea4a408b472 --- /dev/null +++ b/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit fortran-2 + +DESCRIPTION="Protein X-ray crystallography toolkit -- meta package" +HOMEPAGE="http://www.ccp4.ac.uk/" +SRC_URI="" + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="X arpwarp +balbes" + +RDEPEND=" + ~sci-chemistry/ccp4-apps-${PV}[X?] + !<=sci-chemistry/ccp4-apps-${PV}-r2 + >=sci-chemistry/molrep-11.0.00-r1 + >=sci-chemistry/mosflm-7.0.6-r2 + sci-chemistry/mrbump[X?] + >=sci-chemistry/oasis-4.0-r1 + >=sci-chemistry/pdb-extract-3.004-r2 + >=sci-chemistry/refmac-5.5.0110-r1 + >=sci-chemistry/scala-3.3.18-r1 + >=sci-chemistry/sfcheck-7.03.18-r1 + sci-chemistry/xia2 + arpwarp? ( sci-chemistry/arp-warp-bin ) + balbes? ( sci-chemistry/balbes ) + X? ( + ~sci-chemistry/ccp4i-${PV} + sci-chemistry/imosflm + sci-chemistry/pymol + sci-chemistry/rasmol + )" +DEPEND="" diff --git a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch new file mode 100644 index 000000000000..1420419ffab0 --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-6.0.1.orig/configure 2006-06-10 17:30:02.000000000 -0700 ++++ ccp4-6.0.1/configure 2006-06-10 17:45:43.000000000 -0700 +@@ -623,45 +623,45 @@ + # echo "! Beware -- the $system installation isn't properly tested." ; } + syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' + +-if test -z "$onlylibs" ; then +- for i in CCP4_SCR BINSORT_SCR; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the value of $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the argument of --$i." +- badvar=1 +- fi +- done +- +- for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do +- if test -d $i || mkdir $i; then : +- else +- eval echo "! No directory $i and can\'t create it." +- badvar=1 +- fi +- done +-else +- # Kludge to fool the "Makefile" target in the top-level CCP4 +- # Makefile into not trying to remake src/Makefile.in +- for i in $srcdir/src $srcdir/lib/src ; do +- if test -d $i || mkdir $i; then +- if ! test -f $i/Makefile.in ; then +- echo +- echo "onlylibs: making dummy file $i/Makefile.in" +- touch $i/Makefile.in +- fi +- fi +- done +-fi ++#if test -z "$onlylibs" ; then ++# for i in CCP4_SCR BINSORT_SCR; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the value of $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the argument of --$i." ++# badvar=1 ++# fi ++# done ++# ++# for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do ++# if test -d $i || mkdir $i; then : ++# else ++# eval echo "! No directory $i and can\'t create it." ++# badvar=1 ++# fi ++# done ++#else ++# # Kludge to fool the "Makefile" target in the top-level CCP4 ++# # Makefile into not trying to remake src/Makefile.in ++# for i in $srcdir/src $srcdir/lib/src ; do ++# if test -d $i || mkdir $i; then ++# if ! test -f $i/Makefile.in ; then ++# echo ++# echo "onlylibs: making dummy file $i/Makefile.in" ++# touch $i/Makefile.in ++# fi ++# fi ++# done ++#fi + + ### sanity checks + diff --git a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch new file mode 100644 index 000000000000..a77d9494a05c --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch @@ -0,0 +1,11 @@ +--- ccp4-6.0.1.orig/lib/src/library_f.c 2006-06-12 07:06:22.000000000 -0700 ++++ ccp4-6.0.1/lib/src/library_f.c 2006-06-12 07:21:56.000000000 -0700 +@@ -716,7 +716,7 @@ + + #endif /* end of apple xlf support */ + +-#if ( defined (__linux__) && defined (_CALL_SYSV) ) ++#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) ) + /* linuxppc xlf support */ + void gerror_ (str, Lstr) + char *str; diff --git a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch new file mode 100644 index 000000000000..1420419ffab0 --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-6.0.1.orig/configure 2006-06-10 17:30:02.000000000 -0700 ++++ ccp4-6.0.1/configure 2006-06-10 17:45:43.000000000 -0700 +@@ -623,45 +623,45 @@ + # echo "! Beware -- the $system installation isn't properly tested." ; } + syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' + +-if test -z "$onlylibs" ; then +- for i in CCP4_SCR BINSORT_SCR; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the value of $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the argument of --$i." +- badvar=1 +- fi +- done +- +- for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do +- if test -d $i || mkdir $i; then : +- else +- eval echo "! No directory $i and can\'t create it." +- badvar=1 +- fi +- done +-else +- # Kludge to fool the "Makefile" target in the top-level CCP4 +- # Makefile into not trying to remake src/Makefile.in +- for i in $srcdir/src $srcdir/lib/src ; do +- if test -d $i || mkdir $i; then +- if ! test -f $i/Makefile.in ; then +- echo +- echo "onlylibs: making dummy file $i/Makefile.in" +- touch $i/Makefile.in +- fi +- fi +- done +-fi ++#if test -z "$onlylibs" ; then ++# for i in CCP4_SCR BINSORT_SCR; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the value of $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the argument of --$i." ++# badvar=1 ++# fi ++# done ++# ++# for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do ++# if test -d $i || mkdir $i; then : ++# else ++# eval echo "! No directory $i and can\'t create it." ++# badvar=1 ++# fi ++# done ++#else ++# # Kludge to fool the "Makefile" target in the top-level CCP4 ++# # Makefile into not trying to remake src/Makefile.in ++# for i in $srcdir/src $srcdir/lib/src ; do ++# if test -d $i || mkdir $i; then ++# if ! test -f $i/Makefile.in ; then ++# echo ++# echo "onlylibs: making dummy file $i/Makefile.in" ++# touch $i/Makefile.in ++# fi ++# fi ++# done ++#fi + + ### sanity checks + diff --git a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch b/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch new file mode 100644 index 000000000000..c118cc53baff --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch @@ -0,0 +1,14 @@ +https://bugs.gentoo.org/show_bug.cgi?id=175630 +JTRiley + +--- ccp4-6.0.2.orig/src/refmac5_/make_unix_ccp4.f 2005-09-06 07:29:56.000000000 -0400 ++++ ccp4-6.0.2.new/src/refmac5_/make_unix_ccp4.f 2007-05-02 20:03:46.000000000 -0400 +@@ -97,7 +97,7 @@ + + READ(CID,'(I2,1X,I2,1X,I2,2X)') IH(4),IH(3),IH(2) + +- CALL IDATE(IMON,IDAY,IYR) ++ CALL UIDATE(IMON,IDAY,IYR) + IF(IYR.GE.99) THEN + IYR=IYR+1900 + ELSE diff --git a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch new file mode 100644 index 000000000000..a77d9494a05c --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch @@ -0,0 +1,11 @@ +--- ccp4-6.0.1.orig/lib/src/library_f.c 2006-06-12 07:06:22.000000000 -0700 ++++ ccp4-6.0.1/lib/src/library_f.c 2006-06-12 07:21:56.000000000 -0700 +@@ -716,7 +716,7 @@ + + #endif /* end of apple xlf support */ + +-#if ( defined (__linux__) && defined (_CALL_SYSV) ) ++#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) ) + /* linuxppc xlf support */ + void gerror_ (str, Lstr) + char *str; diff --git a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch new file mode 100644 index 000000000000..106db895b775 --- /dev/null +++ b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch @@ -0,0 +1,13 @@ +--- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist 2006-01-06 17:54:17.000000000 -0800 ++++ ccp4-5.99.5/ccp4i/etc/configure.def.dist 2006-01-06 17:54:47.000000000 -0800 +@@ -54,8 +54,8 @@ + MESSAGE _text "" + BLT_LIBRARY _text "" + MENU_LENGTH _positiveint 25 +-HYPERTEXT_VIEWER _text netscape +-START_NETSCAPE _text netscape ++HYPERTEXT_VIEWER _text firefox ++START_NETSCAPE _text firefox + O_MAPMAN _text mapman + MAPMAN_MAXSIZE _positiveint 4194304 + QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch new file mode 100644 index 000000000000..02a2aa6d8877 --- /dev/null +++ b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch @@ -0,0 +1,103 @@ +--- ccp4-5.99.5.orig/configure 2006-01-17 00:35:36.000000000 -0800 ++++ ccp4-5.99.5/configure 2006-01-17 10:44:39.000000000 -0800 +@@ -2410,12 +2410,12 @@ + end + EOF + #firslty test without -lblas +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread" + echo $test_compile + if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then + # Compilation was okay +- echo "... only -llapack needed" +- XLAPACK_LIB="-llapack" ++ echo "... only -llapack -lpthread needed" ++ XLAPACK_LIB="-llapack -lpthread" + # Set the next two variables so that configure + # doesn't try to build netlib libraries + LAPACKLIB="lapack" +@@ -2424,12 +2424,12 @@ + tryblas= + else + echo "more than just -llapack needed...." +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread" + echo $test_compile + if { (eval $test_compile ) 2>&1; } && test -s testlink ; then + # Compilation was okay +- echo "...-llapack and -lblas were needed" +- XLAPACK_LIB="-llapack -lblas" ++ echo "...-llapack, -lpthread and -lblas were needed" ++ XLAPACK_LIB="-llapack -lpthread -lblas" + # Set the next two variables so that configure + # doesn't try to build netlib libraries + LAPACKLIB="lapack blas" +@@ -2720,8 +2720,8 @@ + STOP + END + EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" + echo $test_compile + if { (eval $test_compile ) 2>&1; } && test -s testlink ; then + have_lapack=yes +@@ -2738,7 +2738,7 @@ + LAPACKDIR="$testdir" + echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" + # +- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" ++ XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread" + # + # Test to see if we need BLAS too + # Do this by trying to compile a test program +@@ -2750,8 +2750,8 @@ + if test -f testlsame ; then + rm -f testsame testlsame.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then + have_blas=yes +@@ -2830,8 +2830,8 @@ + STOP + END + EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlink ; then + have_blas=yes +@@ -3033,7 +3033,7 @@ + if test -f testlsame ; then + rm -f testsame testlsame.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then + echo "Found LSAME in lib$BLASLIB" +@@ -3046,7 +3046,7 @@ + if test -f testxerbla ; then + rm -f testxerbla testxerbla.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then + # Found lsame +@@ -3080,7 +3080,7 @@ + cd ../.. + # + lapackdir=lib/lapack +- XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB" ++ XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread" + # netlib lapack is in fortran, so we may need the fortran libraries when + # we are linking using the C or C++ compilers + case $system in diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch new file mode 100644 index 000000000000..3bf5a0652247 --- /dev/null +++ b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5/lib/clipper/configure.orig 2006-01-07 16:54:13.000000000 -0800 ++++ ccp4-5.99.5/lib/clipper/configure 2006-01-07 16:54:31.000000000 -0800 +@@ -21751,7 +21751,7 @@ + + if test "x$mccp4_prefix" != x; then + # ie. mccp4=thing was given (thing is what we're checking for) +- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include" ++ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4" + ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4" + else + # treat as standard lib/include diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch new file mode 100644 index 000000000000..34d6197572fc --- /dev/null +++ b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2006-01-06 12:31:02.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Makefile.in 2006-01-06 12:31:30.000000000 -0800 +@@ -158,6 +158,7 @@ + install_obj = ipdisp.exe hklview xdldataman xdlmapman \ + rotgen ipmosflm + install: all ++ mkdir -p $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch new file mode 100644 index 000000000000..8da54fd26de8 --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-build-rasmol.patch @@ -0,0 +1,19 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 03:06:57.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Makefile.in 2005-12-05 03:07:23.000000000 -0800 +@@ -35,7 +35,7 @@ + # + # all + # +-all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm ++all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm + # + # xdl_view + # +@@ -161,7 +161,6 @@ + $(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir) + cd $(srcdir)/XCCPJIFFY ; $(MAKE) install +- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install + $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) + cd $(xdlview_dir); $(MAKE) install diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch new file mode 100644 index 000000000000..7813141b2ec2 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:12.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:41.000000000 -0800 +@@ -37,6 +37,7 @@ + ${F77} ${FFLAGS} -o $@ $< + + ipmosflm: ${OBJS} ++ mkdir -p ${DPSBIN} + ${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \ + -o ${DPSBIN}/ipmosflm ${LDFLAGS} + diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch new file mode 100644 index 000000000000..ae4b7633b105 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:42:19.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:43:35.000000000 -0800 +@@ -132,7 +132,7 @@ + # + # CBF library + # +-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) ++$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB) + $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) + $(AR) cr $@ *.o + $(RANLIB) $@ diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch new file mode 100644 index 000000000000..97607b689672 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:09.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:30.000000000 -0800 +@@ -76,6 +76,7 @@ + + # local version of libdps_index.a + ${LIB}/dps_index.a: ${IOBJS} ${HOBJS} ++ mkdir -p ${LIB} + ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS} + + ${LIB}/libpeak.a: diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch new file mode 100644 index 000000000000..eac1b9f1721e --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:48:47.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:49:02.000000000 -0800 +@@ -42,6 +42,7 @@ + $(LOCALLIBS) $(LIBS) + + index: $(IOBJS) ++ mkdir -p $(LIBDIR) + ${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS) + chmod 644 $(LIBDIR)/libdps_index.a + diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch new file mode 100644 index 000000000000..3e1a8b0e6be8 --- /dev/null +++ b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5.orig/configure 2006-01-06 11:45:43.000000000 -0800 ++++ ccp4-5.99.5/configure 2006-01-06 11:46:53.000000000 -0800 +@@ -3210,7 +3210,7 @@ + #ccp4 setup + xopts="${xopts} --with-ccp4=${srcdir}" + #interface setup +- xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol" ++ xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr" + echo + echo "********* CLIPPER CONFIGURATION ***********" + echo diff --git a/sci-chemistry/ccp4/metadata.xml b/sci-chemistry/ccp4/metadata.xml new file mode 100644 index 000000000000..d37774eb9ada --- /dev/null +++ b/sci-chemistry/ccp4/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <use> + <flag name="balbes">Install sci-chemistry/balbes</flag> + <flag name="arpwarp">Add binary arp-warp for molecular replacement</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest new file mode 100644 index 000000000000..e082cb44f7fb --- /dev/null +++ b/sci-chemistry/ccp4i/Manifest @@ -0,0 +1,3 @@ +DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820 +DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c +DIST ccp4i-6.1.3-arpwarp.patch.bz2 58498 SHA256 297e6f75354f3a1932302f7039bf449484c95eb41b8634ae96d93c754b47c687 SHA512 0bf18d9768b722c553e79eed04de316f6b0b4695f7678e1d850d5e22735ecc79cdb961ea76b6482457fff232892b81ce191cd48fa588ded8058184a871dffb65 WHIRLPOOL f24625941e31e951f13c94cf31e2ca061840b016aa3fd038d29710d9ca400d364467dc3fa1e42a55944d63ac7e42a0a6baa39a596c55b18610eeb552d232d1b8 diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild new file mode 100644 index 000000000000..f5ac55ef17fa --- /dev/null +++ b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild @@ -0,0 +1,99 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-single-r1 virtualx + +MY_PN="${PN%i}" +MY_P="${MY_PN}-${PV}" + +#UPDATE="04_03_09" +#PATCHDATE="090511" + +SRC="ftp://ftp.ccp4.ac.uk/ccp4" + +DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface" +HOMEPAGE="http://www.ccp4.ac.uk/" +SRC_URI=" + ${SRC}/${PV}/${MY_P}-core-src.tar.gz + mirror://gentoo/${P}-arpwarp.patch.bz2 + http://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" +[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" +[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" + +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +LICENSE="ccp4" +IUSE="" + +RDEPEND=" + app-shells/tcsh + media-gfx/graphviz + >=dev-lang/tk-8.3:0 + >=dev-tcltk/blt-2.4 + sci-libs/ccp4-libs" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}"/${PV}-fix-baubles.patch + "${WORKDIR}"/${P}-arpwarp.patch + ) + +src_prepare() { + epatch ${PATCHES[@]} + + [[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch + + epatch "${WORKDIR}"/${PV}-oasis4.0.patch + python_fix_shebang ccp4i/ share/dbccp4i/ +} + +src_configure() { + : +} + +src_compile() { + : +} + +src_install() { + # rm imosflm stuff + rm -rf "${S}"/ccp4i/{bin/imosflm,imosflm} || die + + rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS || die + + # This is installed by mrbump + rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} || die + + # CCP4Interface - GUI + insinto /usr/$(get_libdir)/ccp4 + doins -r "${S}"/ccp4i + exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin + doexe "${S}"/ccp4i/bin/* + dosym ../$(get_libdir)/ccp4/ccp4i/bin/ccp4i /usr/bin/ccp4i + + dodir /usr/$(get_libdir)/ccp4/ccp4i/unix + + # dbccp4i + insinto /usr/share/ccp4 + doins -r "${S}"/share/dbccp4i +} + +pkg_postinst() { + _ccp4-setup() { + source "${EPREFIX}/etc/profile" + export USER=root + bash "${EPREFIX}"/usr/$(get_libdir)/ccp4/ccp4i/bin/ccp4i -h > /dev/null + } + VIRTUALX_COMMAND="_ccp4-setup" virtualmake + echo "" + elog "ccp4i needs some enviromental settings. So please" + elog "\t source ${EPREFIX}/etc/profile" + echo "" +} diff --git a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch new file mode 100644 index 000000000000..2c5f659b8018 --- /dev/null +++ b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch @@ -0,0 +1,22 @@ +--- ccp4i/etc/configure.def.dist 2009-01-09 16:45:08.000000000 +0100 ++++ ccp4i/etc/configure.def.dist.new 2009-07-07 23:17:26.000000000 +0200 +@@ -53,8 +53,8 @@ + RUN_IMOSFLM _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]" + RUN_CCP4MG _text "ccp4mg" + RUN_COOT _text "coot" +-RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share smartie baubles.py]" +-RUN_DBVIEWER _text "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]" ++RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]" ++RUN_DBVIEWER _text "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]" + ENABLE_BUBBLE_HELP _logical 1 + DISABLE_TASKS _logical 1 + CCP4_SETUP_COMMAND _text setup_ccp4 +@@ -62,7 +62,7 @@ + BLT_LIBRARY _text "" + MENU_LENGTH _positiveint 25 + HYPERTEXT_VIEWER _text firefox +-START_NETSCAPE _text netscape ++START_NETSCAPE _text firefox + O_MAPMAN _text mapman + MAPMAN_MAXSIZE _positiveint 4194304 + QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch new file mode 100644 index 000000000000..9f5cfb4b635f --- /dev/null +++ b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch @@ -0,0 +1,61 @@ +diff --git a/ccp4i/scripts/check.script b/ccp4i/scripts/check.script +index def44bc..dd4bb7e 100755 +--- a/ccp4i/scripts/check.script ++++ b/ccp4i/scripts/check.script +@@ -24,7 +24,7 @@ + if $RUN_RAMPAGE { + + # Generate command line +- set cmd "[BinPath rapper]" ++ set cmd "[BinPath rappermc]" + + set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] + set paramsfile [FileJoin $rapperdatadir params.xml] +diff --git a/ccp4i/scripts/rapper.script b/ccp4i/scripts/rapper.script +index cdae1e2..faae226 100755 +--- a/ccp4i/scripts/rapper.script ++++ b/ccp4i/scripts/rapper.script +@@ -17,7 +17,7 @@ + + #set up command line + +-set cmd "[BinPath rapper]" ++set cmd "[BinPath rappermc]" + + set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] + set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml] +@@ -180,7 +180,7 @@ append outfiles " $XYZOUT PROJECT" + + # Run RAPPER to join loop back to framework and out put to defined pdb file + # Also need to sort out multimodel files join - FIX ME +-set cmd2 "[BinPath rapper]" ++set cmd2 "[BinPath rappermc]" + append cmd2 " $paramsfile joinpdb " + append cmd2 " --pdb2 \"$root\-loop.pdb\" " + append cmd2 " --pdb \"$root\-framework.pdb\" " +diff --git a/ccp4i/tasks/check.tcl b/ccp4i/tasks/check.tcl +index ae88ff2..ee3307b 100755 +--- a/ccp4i/tasks/check.tcl ++++ b/ccp4i/tasks/check.tcl +@@ -46,7 +46,7 @@ proc check_run { arrayname } { + # Check for Rampage program. If it is not found, we switch off the option. + # If it was the only option, script will fail with next check. + if { $array(RUN_RAMPAGE) == 1 } { +- if { [FindExecutable "rapper"] == "" } { ++ if { [FindExecutable "rappermc"] == "" } { + WarningMessage "Input Error: Rapper_Rampage program not found in system path." + set array(RUN_RAMPAGE) 0 + } +diff --git a/ccp4i/tasks/rapper.tcl b/ccp4i/tasks/rapper.tcl +index e299057..8843a3f 100755 +--- a/ccp4i/tasks/rapper.tcl ++++ b/ccp4i/tasks/rapper.tcl +@@ -28,7 +28,7 @@ proc rapper_run { arrayname } { + # Check for RAPPER program. If it is not found, we switch off the option. + # If it was the only option, script will fail with next check. + if { [regexp MODEL $build_type ] && $prog_type == "RAPPER"} { +- if { [FindExecutable "rapper"] == "" } { ++ if { [FindExecutable "rappermc"] == "" } { + WarningMessage "Input Error: RAPPER program not found in system path." + set build_type 0 + } diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch new file mode 100644 index 000000000000..74cd2b946601 --- /dev/null +++ b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch @@ -0,0 +1,26 @@ +diff --git a/ccp4i/scripts/superpose.script b/ccp4i/scripts/superpose.script +index 3483c97..5027536 100755 +--- a/ccp4i/scripts/superpose.script ++++ b/ccp4i/scripts/superpose.script +@@ -21,7 +21,7 @@ + + if { [regexp SSM $SUPERPOSE_MODE ] } { + +- set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" ++ set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" + set status [Execute $cmd "" program_status report ] + + } elseif { [regexp TOP $SUPERPOSE_MODE ] } { +diff --git a/ccp4i/tasks/superpose.tcl b/ccp4i/tasks/superpose.tcl +index 748bf6e..c92122a 100755 +--- a/ccp4i/tasks/superpose.tcl ++++ b/ccp4i/tasks/superpose.tcl +@@ -100,7 +100,7 @@ proc superpose_run { arrayname } { + # If user is match equivalent named residues/atoms then fit in the match fields + switch [GetValue $arrayname SUPERPOSE_MODE] \ + SSM { +- if { ![file exists [FindExecutable superpose]] } { ++ if { ![file exists [FindExecutable superpose-ccp4]] } { + WarningMessage "The program \"superpose\" is not on your path. + Check your installation for \"superpose\" program and \"ssm\" library." + return 0 diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch new file mode 100644 index 000000000000..9af60b7c5152 --- /dev/null +++ b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch @@ -0,0 +1,91 @@ +diff --git a/ccp4i/crank/plugins/prep/crank_prep.tcl b/ccp4i/crank/plugins/prep/crank_prep.tcl +index 7d05905..d01f1dc 100755 +--- a/ccp4i/crank/plugins/prep/crank_prep.tcl ++++ b/ccp4i/crank/plugins/prep/crank_prep.tcl +@@ -226,7 +226,7 @@ proc run_truncate { i j } { + set script "$script\n$labout" + set script "$script\nEND\n" + +- set run_command "truncate $command << \"$script\"" ++ set run_command "ftruncate $command << \"$script\"" + puts $run_command + catch {eval exec $run_command } output + puts $output +diff --git a/ccp4i/scripts/dtrek2mtz.script b/ccp4i/scripts/dtrek2mtz.script +index e74aa0d..a2a1adb 100755 +--- a/ccp4i/scripts/dtrek2mtz.script ++++ b/ccp4i/scripts/dtrek2mtz.script +@@ -36,7 +36,7 @@ + set HKL_TRUNCATE [GetTmpFileName -ext mtz] + + CreateComScript truncate truncate_script +- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" + set status [Execute $cmd $truncate_script program_status report] + + HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate +diff --git a/ccp4i/scripts/import.script b/ccp4i/scripts/import.script +index 90cba83..1c90c33 100755 +--- a/ccp4i/scripts/import.script ++++ b/ccp4i/scripts/import.script +@@ -144,7 +144,7 @@ if { $FORMAT == "MTZ" } { + + set truncatemtz [GetTmpFileName -ext mtz ] + CreateComScript truncate truncate_script +- set cmd "[BinPath truncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\"" + set status [Execute $cmd $truncate_script program_status report] + + +diff --git a/ccp4i/scripts/import_scaled.script b/ccp4i/scripts/import_scaled.script +index dcc619b..7250513 100755 +--- a/ccp4i/scripts/import_scaled.script ++++ b/ccp4i/scripts/import_scaled.script +@@ -62,7 +62,7 @@ + + } else { + CreateComScript truncate truncate_script +- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" + set status [Execute $cmd $truncate_script program_status report] + + HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate +diff --git a/ccp4i/scripts/scala.script b/ccp4i/scripts/scala.script +index 6940ccd..bde10d6 100755 +--- a/ccp4i/scripts/scala.script ++++ b/ccp4i/scripts/scala.script +@@ -275,7 +275,7 @@ END" + + } else { + CreateComScript truncate truncate_script +- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" + set status [Execute $cmd $truncate_script $LOG_FILE program_status report ] + } + +diff --git a/ccp4i/scripts/scalepack2mtz.script b/ccp4i/scripts/scalepack2mtz.script +index 986e06c..a1947a6 100755 +--- a/ccp4i/scripts/scalepack2mtz.script ++++ b/ccp4i/scripts/scalepack2mtz.script +@@ -35,7 +35,7 @@ + + set HKL_TRUNCATE [GetTmpFileName -ext mtz] + CreateComScript truncate truncate_script +- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" + set status [Execute $cmd $truncate_script program_status report] + + HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate +diff --git a/ccp4i/scripts/truncate.script b/ccp4i/scripts/truncate.script +index e0e09ce..2d448a2 100755 +--- a/ccp4i/scripts/truncate.script ++++ b/ccp4i/scripts/truncate.script +@@ -45,7 +45,7 @@ + + CreateComScript truncate truncate_script + +- set cmd "[BinPath truncate] HKLIN \"$HKLIN\"" ++ set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\"" + if { ![StringSame $INPUT_DATA AMPLITUDES] } { + append cmd " HKLOUT \"$HKL_TRUNCATE\"" + } diff --git a/sci-chemistry/ccp4i/metadata.xml b/sci-chemistry/ccp4i/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/ccp4i/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest new file mode 100644 index 000000000000..73f83f19c7b2 --- /dev/null +++ b/sci-chemistry/ccpn/Manifest @@ -0,0 +1,6 @@ +DIST analysis2.4.1.tar.gz 36088236 SHA256 1cb089dcc739e8536d938a68536f556094f5d728907b251fe337758ba5bef106 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1 WHIRLPOOL b53fc0438a878a8f8ce0244f5c1ce9edb616665149a699364e3bcd38c5db548c22b80ef67b4183ad5321b71b69a3b85aecc7d912893bba947700003a411651ac +DIST analysis2.4.2.tar.gz 36390919 SHA256 14941131033cbd4b0b13d6d4fe3f9253360a7c2ace8ece9194be00c1fe4b2903 SHA512 694faefd3c085b559b6bb4729141a9ab885334f578bfbb0ebf260366dbca38c31738d5f5af50b5c7ea16b304b27adf80411082859796a5afeec630c36d56bd8b WHIRLPOOL 4499dcb074d445bfc972f9dea43e6f3e3c28722d513dce0fec4e1b2b5dab8be098f53f82565d86a4e7935f0595ef303465668230aa61021cf88e13cce8606214 +DIST ccpn-update-2.4.1-150226.patch.xz 10732 SHA256 74e8723d310d336cd4215ed4e9a1a1c0b2c0efdb4c03aaacba7ecd0575b38287 SHA512 60eb4acf6179f80207a72076ff5d5d733d3c3e804c1ce0a48701dd6e923146af49cd6759a529c8125f4b26eb3f8f83b35acc0c48b88a3e3034b25b5438a04feb WHIRLPOOL 3a2357d4fcb086206d45edd5b9cc807313b5f62be2f2a70e8f011f5521cf8729371b8c7149837c4ea1f6f059e26a49c1d20492f338a844e15f38ccf543faf6e1 +DIST ccpn-update-2.4.2-150325.patch.xz 2096 SHA256 d33676fd93aaa5814aa43179f221df69f4bae9b8ec98ce5b6cc57ce6aacab732 SHA512 c544e0a4a93d0e3275a22d07d21bf3bb5ed90cf041f40bf08fbc687b431640ad5c56180eadd4b43e4023b08ef42afe5a874423becc6f9313a0b1f642a4b97873 WHIRLPOOL f2e9780eb3216185cc6b89ca490e14c2de1130393eda4308fc71e6a2eb0460fc97f83ab3c92fb6a488a1926ba2f3099c7ae5f0a4bd216f8ffa24bfd87e360838 +DIST ccpn-update-2.4.2-150413.patch.xz 3132 SHA256 c0796e1f739f799003304c8b8d23ea0ee42b2e0a6dd59b292cb2a1167b5725f5 SHA512 99893ca009ff76b015017b29cfd97e0ae935ed2d62aa5a99d52dd9a5f22cf0d369e5019273fe3c3811c28b32568721fb64f71c5927eb57d0cc91dcea44b0288d WHIRLPOOL 48a355ef4824d41517d618178be4cd4efc42a6f5e190bac88348041504da0807aa1b34bafbc3937d7f6fc3b5b52fe469431fb6ce9df40bb1c56d7faad88cfe51 +DIST ccpn-update-2.4.2-150421.patch.xz 3788 SHA256 df8f7dd81281f3f7ddd266b8bd90a089f61a9e8f0cda3bcba8b495a6f4be6238 SHA512 0e8a10b6d9721b52574cd2fe0413dca0fac32a948eb31d3db6e2c4d4f7d85c341e8d53d70954341792ea598a37ec87e4392a615e1c2f6f8bbfc0e42a750be648 WHIRLPOOL 2673ac33b2eca1a3fb873567784f1d77937e7ec6aec3ab7eef6065f9322513326993786bd3865a50c50c58e05bf874ba25df02d15083f50aef9acb404ca4e1ef diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild new file mode 100644 index 000000000000..6768d790f140 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild new file mode 100644 index 000000000000..b97807a88f38 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +#PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild new file mode 100644 index 000000000000..6768d790f140 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild new file mode 100644 index 000000000000..6768d790f140 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild new file mode 100644 index 000000000000..6768d790f140 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/files/2.3.1-parallel.patch b/sci-chemistry/ccpn/files/2.3.1-parallel.patch new file mode 100644 index 000000000000..fcf44707e082 --- /dev/null +++ b/sci-chemistry/ccpn/files/2.3.1-parallel.patch @@ -0,0 +1,38 @@ +diff --git a/ccpnmr2.3/c/Makefile b/ccpnmr2.3/c/Makefile +index 01fb25a..8e8e1fe 100644 +--- a/ccpnmr2.3/c/Makefile ++++ b/ccpnmr2.3/c/Makefile +@@ -5,22 +5,22 @@ all: compile + compile: global structure analysis clouds dynamics bayes + + global: +- cd memops/global && $(MAKE) ++ $(MAKE) -C memops/global + +-structure: +- cd ccp/structure && $(MAKE) ++structure: global ++ $(MAKE) -C ccp/structure + +-analysis: +- cd ccpnmr/analysis && $(MAKE) ++analysis: global ++ $(MAKE) -C ccpnmr/analysis + +-clouds: +- cd ccpnmr/clouds && $(MAKE) ++clouds: global ++ $(MAKE) -C ccpnmr/clouds + +-dynamics: +- cd ccpnmr/dynamics && $(MAKE) ++dynamics: global ++ $(MAKE) -C ccpnmr/dynamics + +-bayes: +- cd other/cambridge/bayes && $(MAKE) ++bayes: global ++ $(MAKE) -C other/cambridge/bayes + + clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean + diff --git a/sci-chemistry/ccpn/files/analysis b/sci-chemistry/ccpn/files/analysis new file mode 100644 index 000000000000..828ed4e64ae9 --- /dev/null +++ b/sci-chemistry/ccpn/files/analysis @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -i -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/analysis/AnalysisGui.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/dangle b/sci-chemistry/ccpn/files/dangle new file mode 100644 index 000000000000..6d8a42e615de --- /dev/null +++ b/sci-chemistry/ccpn/files/dangle @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/cambridge/dangle/DangleGui.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/dataShifter b/sci-chemistry/ccpn/files/dataShifter new file mode 100644 index 000000000000..c083960f2f60 --- /dev/null +++ b/sci-chemistry/ccpn/files/dataShifter @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/DataShifter.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/depositionFileImporter b/sci-chemistry/ccpn/files/depositionFileImporter new file mode 100644 index 000000000000..09505ccc4925 --- /dev/null +++ b/sci-chemistry/ccpn/files/depositionFileImporter @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/pdbe/deposition/dataFileImport/dataFileImportGui.py $@ diff --git a/sci-chemistry/ccpn/files/eci b/sci-chemistry/ccpn/files/eci new file mode 100644 index 000000000000..54d913348718 --- /dev/null +++ b/sci-chemistry/ccpn/files/eci @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/eci/EntryCompletionGui.py $* diff --git a/sci-chemistry/ccpn/files/extendNmr b/sci-chemistry/ccpn/files/extendNmr new file mode 100644 index 000000000000..a2fe4c997c7c --- /dev/null +++ b/sci-chemistry/ccpn/files/extendNmr @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O -i -O ${CCPNMR_TOP_DIR}/ccpn/python/extendNmr/ExtendNmrGui.py $@ diff --git a/sci-chemistry/ccpn/files/formatConverter b/sci-chemistry/ccpn/files/formatConverter new file mode 100644 index 000000000000..6cb273612352 --- /dev/null +++ b/sci-chemistry/ccpn/files/formatConverter @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/FormatConverter.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/pipe2azara b/sci-chemistry/ccpn/files/pipe2azara new file mode 100644 index 000000000000..5a3710a134a7 --- /dev/null +++ b/sci-chemistry/ccpn/files/pipe2azara @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/NmrPipeData.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/talosn.patch b/sci-chemistry/ccpn/files/talosn.patch new file mode 100644 index 000000000000..e19a0ab19783 --- /dev/null +++ b/sci-chemistry/ccpn/files/talosn.patch @@ -0,0 +1,16 @@ + ccpnmr2.3/python/ccpnmr/format/general/Constants.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/ccpnmr2.3/python/ccpnmr/format/general/Constants.py b/ccpnmr2.3/python/ccpnmr/format/general/Constants.py +index d10553e..fb732db 100644 +--- a/ccpnmr2.3/python/ccpnmr/format/general/Constants.py ++++ b/ccpnmr2.3/python/ccpnmr/format/general/Constants.py +@@ -865,7 +865,7 @@ IoSetupList = [ + 'cyana': ['dihedrals.aco',1,1, [['SelectionList','version','Cyana version:',['2.0','2.1'],None]], + [['SelectionList','version','Cyana version:',['2.0','2.1'],None]]], + 'nmrStar': ['nmrStar.str',1,0, [],[]], +- 'talos': ['dihedral.tab',1,0, [['MultiSelectionList','validClasses','Classes for valid constraint:',['Good','New','Warn','None'],None], ++ 'talos': ['dihedral.tab',1,0, [['MultiSelectionList','validClasses','Classes for valid constraint:',['Good','New','Warn','Dyn', 'Strong', 'Generous', 'None'],None], + ['IntEntry','validCount','Count variable lower limit for valid constraint:',0,None], + ['FloatEntry','multiplyDeviation','Multiplication factor to convert deviation in constraint range:',2.0,None]], + []]}, diff --git a/sci-chemistry/ccpn/files/xeasy2azara b/sci-chemistry/ccpn/files/xeasy2azara new file mode 100644 index 000000000000..7b73714c2fa5 --- /dev/null +++ b/sci-chemistry/ccpn/files/xeasy2azara @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/XeasyData.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/metadata.xml b/sci-chemistry/ccpn/metadata.xml new file mode 100644 index 000000000000..ae9ec7c5f6a4 --- /dev/null +++ b/sci-chemistry/ccpn/metadata.xml @@ -0,0 +1,8 @@ +<?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> +</pkgmetadata> diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest new file mode 100644 index 000000000000..d8db80c30926 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/Manifest @@ -0,0 +1 @@ +DIST chemical-mime-data-0.1.94.tar.bz2 146077 SHA256 4907cdf60e9edca0a453f6f24e9179ae9da085b67168e932ba44a4280316bff1 SHA512 7f3d967149f27ab1de53c948dc055959e661e1be9d778e3d56d06bea95769da7770ab5fb66afab6607747ef91ffb1dbbcf921e5f06e3303351781968594b5f00 WHIRLPOOL 2e601b37ca22cc1d2b77b5d82713e756dea380fcb0a01c517513be0271162df6e19e7cc7dbc0af8f25e579bb809e0768cc2ee394124c91c296ed0d4c38cfa213 diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r1.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r1.ebuild new file mode 100644 index 000000000000..c63c806baa7c --- /dev/null +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils fdo-mime + +DESCRIPTION="A collection of data files to add support for chemical MIME types" +HOMEPAGE="http://chemical-mime.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="virtual/pkgconfig + x11-misc/shared-mime-info + dev-util/intltool + dev-util/desktop-file-utils + dev-libs/libxslt + media-gfx/imagemagick[xml] + gnome-base/gnome-mime-data" + +RDEPEND="" + +src_configure() { + econf --disable-update-database --htmldir=/usr/share/doc/${PF}/html +} + +src_install() { + emake DESTDIR="${D}" install || die "emake install failed" +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + ewarn "You can ignore any 'Unknown media type in type' warnings." +} diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild new file mode 100644 index 000000000000..851bd6b2bec4 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils fdo-mime + +DESCRIPTION="A collection of data files to add support for chemical MIME types" +HOMEPAGE="http://chemical-mime.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + gnome-base/gnome-mime-data + x11-misc/shared-mime-info" +DEPEND="${RDEPEND} + dev-util/intltool + dev-util/desktop-file-utils + dev-libs/libxslt + media-gfx/imagemagick[xml] + media-gfx/inkscape + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}"/${P}-turbomole.patch + "${FILESDIR}"/${P}-pigz.patch + "${FILESDIR}"/${P}-namespace-svg.patch + ) + +src_prepare() { + # needed for convert/inkscape #464782 + export XDG_CONFIG_HOME=$HOME/.config + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-update-database + --htmldir=/usr/share/doc/${PF}/html + ) + autotools-utils_src_configure +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + ewarn "You can ignore any 'Unknown media type in type' warnings." +} + +pkg_postrm() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + ewarn "You can ignore any 'Unknown media type in type' warnings." +} diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94.ebuild new file mode 100644 index 000000000000..c965d2f88027 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils fdo-mime + +DESCRIPTION="A collection of data files to add support for chemical MIME types" +HOMEPAGE="http://chemical-mime.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND="virtual/pkgconfig + x11-misc/shared-mime-info + dev-util/intltool + dev-util/desktop-file-utils + dev-libs/libxslt + media-gfx/imagemagick[xml] + gnome-base/gnome-mime-data" + +RDEPEND="" + +src_configure() { + econf --disable-update-database --htmldir=/usr/share/doc/${PN}/html +} + +src_install() { + emake DESTDIR="${D}" install || die "emake install failed" +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + ewarn "You can ignore any 'Unknown media type in type' warnings." +} diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch new file mode 100644 index 000000000000..9860261af403 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch @@ -0,0 +1,16 @@ + icons/hicolor/gnome-mime-chemical.svg | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/icons/hicolor/gnome-mime-chemical.svg b/icons/hicolor/gnome-mime-chemical.svg +index 1a8d428..804514c 100644 +--- a/icons/hicolor/gnome-mime-chemical.svg ++++ b/icons/hicolor/gnome-mime-chemical.svg +@@ -5,7 +5,7 @@ + <!ENTITY ns_svg "http://www.w3.org/2000/svg"> + <!ENTITY ns_xlink "http://www.w3.org/1999/xlink"> + ]> +-<svg xmlns="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/" ++<svg xmlns:svg="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/" + width="128" height="128" viewBox="0 0 128 128" overflow="visible" enable-background="new 0 0 128 128" xml:space="preserve"> + <g id="Layer_1"> + <g> diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch new file mode 100644 index 000000000000..8b5ccfbc3fd9 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch @@ -0,0 +1,16 @@ + Makefile.am | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Makefile.am b/Makefile.am +index 96e03ab..ba0847a 100644 +--- a/icons/hicolor/Makefile.am ++++ b/icons/hicolor/Makefile.am +@@ -21,7 +21,7 @@ icon_sizes = 16 22 24 32 36 48 64 72 96 128 192 + if BOOL_HICOLOR_THEME + + .svg.svgz: +- gzip $< -c > $@ ++ gzip -c $< > $@ + for size in $(icon_sizes) ; do \ + if test "x$(RSVG)" != "x" ; then \ + $(RSVG) -w $${size} -h $${size} -f png $< $*_$${size}.png ; \ diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch new file mode 100644 index 000000000000..852d6b0605be --- /dev/null +++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch @@ -0,0 +1,57 @@ +diff -up chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in +--- chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole 2009-08-10 09:37:06.000000000 +0200 ++++ chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in 2009-08-10 09:40:57.000000000 +0200 +@@ -1290,7 +1290,7 @@ + <specification url="http://ca.expasy.org/sprot/userman.html"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-basis" support="no"> ++ <mime-type type="chemical/x-turbomole-basis" support="yes"> + <_comment>Turbomole Basis Set File</_comment> + <glob pattern="basis"/> + <sub-class-of type="text/plain"/> +@@ -1304,7 +1304,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-control" support="no"> ++ <mime-type type="chemical/x-turbomole-control" support="yes"> + <_comment>Turbomole Control File</_comment> + <glob pattern="control"/> + <sub-class-of type="text/plain"/> +@@ -1320,7 +1320,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/node230.html"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-coord" support="no"> ++ <mime-type type="chemical/x-turbomole-coord" support="yes"> + <_comment>Turbomole Coordinate File</_comment> + <glob pattern="coord"/> + <glob pattern="*.tmol"/> +@@ -1335,7 +1335,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-grad" support="no"> ++ <mime-type type="chemical/x-turbomole-grad" support="yes"> + <_comment>Turbomole Gradient File</_comment> + <glob pattern="gradient"/> + <sub-class-of type="text/plain"/> +@@ -1383,7 +1383,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-scfmo" support="no"> ++ <mime-type type="chemical/x-turbomole-scfmo" support="yes"> + <_comment>Turbomole SCF Molecular Orbital File</_comment> + <acronym>MO</acronym> + <expanded-acronym>Molecular Orbital</expanded-acronym> +@@ -1401,7 +1401,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-vibrational" support="no"> ++ <mime-type type="chemical/x-turbomole-vibrational" support="yes"> + <_comment>Turbomole Vibrational Data File</_comment> + <glob pattern="???"/> + <sub-class-of type="text/plain"/> diff --git a/sci-chemistry/chemical-mime-data/metadata.xml b/sci-chemistry/chemical-mime-data/metadata.xml new file mode 100644 index 000000000000..941ce487e86e --- /dev/null +++ b/sci-chemistry/chemical-mime-data/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <longdescription lang="en"> +A collection of data files to add support for chemical MIME types. +</longdescription> + <upstream> + <remote-id type="sourceforge">chemical-mime</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/chemtool/Manifest b/sci-chemistry/chemtool/Manifest new file mode 100644 index 000000000000..a364d0afdaea --- /dev/null +++ b/sci-chemistry/chemtool/Manifest @@ -0,0 +1,2 @@ +DIST chemtool-1.6.13.tar.gz 838868 SHA256 31a07683f55305c3e0c4d7af3bc3d1d3a9a2eff4d836455fe1e382962f0aa0c8 SHA512 6c248321f73b6eab4ad21e810639a1f0b14cc30db9c9fdc8fe66ee218bd88ead5e74f1f047f5badcb91b515827c2eddc64b28ead380d9b14ab5b76777e7134dd WHIRLPOOL c7158a75480e9b98eb2ed5c16d73c4d5e5fa05375009ac1778b7e9bf0e9a2ef9092032557d46ea506a6503c0799676998a6fcb80063ed56a7ae8d360c1f273bc +DIST chemtool-1.6.14.tar.gz 817735 SHA256 86161a0461386b334a5ffb17cdf094a491941884678272f45749813514ddafcb SHA512 066c83c61aced3134b081767e788143a047889a2fee4b6535c2b0a3166bccc73d75981e1cf35b7bcaa5b8fe2e0227b28693b659decd82f7783cb4082ac6ed2bd WHIRLPOOL 41a2bd4662c06307a94281e6a54d4e129b407bc597c7d08c8a9f976332cb727f3e195d1d85429716ac22a34ea1dae03b724167bbb5444c03dcb24131cc20ae1d diff --git a/sci-chemistry/chemtool/chemtool-1.6.13.ebuild b/sci-chemistry/chemtool/chemtool-1.6.13.ebuild new file mode 100644 index 000000000000..2ab2dc197a0b --- /dev/null +++ b/sci-chemistry/chemtool/chemtool-1.6.13.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils eutils + +DESCRIPTION="A GTK program for drawing organic molecules" +HOMEPAGE="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/" +SRC_URI="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="emf gnome nls" + +RDEPEND=" + dev-libs/glib:2 + media-gfx/transfig + x11-libs/gtk+:2 + x11-libs/libX11 + x11-libs/pango + emf? ( media-libs/libemf )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +PATCHES=( + "${FILESDIR}"/${PV}-no-underlinking.patch + ) + +src_configure() { + local myeconfargs=( + --without-kdedir + $(use_with gnome gnomedir /usr) + $(use_enable emf) + --enable-undo + --enable-menu + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + + insinto /usr/share/${PN}/examples + doins "${S}"/examples/* + if ! use nls; then rm -rf "${ED}"/usr/share/locale || die; fi + + insinto /usr/share/pixmaps + doins chemtool.xpm + make_desktop_entry ${PN} Chemtool ${PN} "Education;Science;Chemistry" +} diff --git a/sci-chemistry/chemtool/chemtool-1.6.14.ebuild b/sci-chemistry/chemtool/chemtool-1.6.14.ebuild new file mode 100644 index 000000000000..b77cb79569e4 --- /dev/null +++ b/sci-chemistry/chemtool/chemtool-1.6.14.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils eutils + +DESCRIPTION="A GTK program for drawing organic molecules" +HOMEPAGE="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/" +SRC_URI="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="emf gnome nls" + +RDEPEND=" + dev-libs/glib:2 + media-gfx/transfig + x11-libs/gtk+:2 + x11-libs/libX11 + x11-libs/pango + emf? ( media-libs/libemf )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +PATCHES=( + "${FILESDIR}"/1.6.13-no-underlinking.patch +) + +src_configure() { + local myeconfargs=( + --without-kdedir + $(use_with gnome gnomedir /usr) + $(use_enable emf) + --enable-undo + --enable-menu + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + + insinto /usr/share/${PN}/examples + doins "${S}"/examples/* + if ! use nls; then rm -rf "${ED}"/usr/share/locale || die; fi + + insinto /usr/share/pixmaps + doins chemtool.xpm + make_desktop_entry ${PN} Chemtool ${PN} "Education;Science;Chemistry" +} diff --git a/sci-chemistry/chemtool/files/1.6.13-no-underlinking.patch b/sci-chemistry/chemtool/files/1.6.13-no-underlinking.patch new file mode 100644 index 000000000000..5d2fe36d6bf1 --- /dev/null +++ b/sci-chemistry/chemtool/files/1.6.13-no-underlinking.patch @@ -0,0 +1,78 @@ + Makefile.am | 6 ++++-- + configure.ac | 24 ++++-------------------- + 2 files changed, 8 insertions(+), 22 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 99dbf8c..931ba16 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -22,10 +22,12 @@ localedir = $(datadir)/locale + DEFS = -DLOCALEDIR=\"$(localedir)\" @DEFS@ + + # Make sure the gettext.h include file is found. +-AM_CPPFLAGS = -I. -I$(srcdir) @GTK_CFLAGS@ ++AM_CPPFLAGS = -I. -I$(srcdir) @GTK_CFLAGS@ @EMFINCL@ + + # Link time dependencies. +-LDADD = @LIBINTL@ @GTK_LIBS@ @EMFLIBS@ ++LDADD = @LIBINTL@ @GTK_LIBS@ @EMFLIBS@ -lX11 ++ ++AM_CFLAGS = -DGTK2 + + # Additional files to be distributed. + EXTRA_DIST = autogen.sh autoclean.sh +diff --git a/configure.ac b/configure.ac +index 6d8c45a..c5fab42 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -32,32 +32,14 @@ AC_PATH_PROG(PKG_CONFIG, pkg-config, no) + + AC_MSG_CHECKING([for GTK version and compile options ]) + +-if test x$PKG_CONFIG = xno -o x$enable_gtk1 = xyes ; then +-AM_PATH_GTK(1.0.2, , exit 1) +-else +-if $PKG_CONFIG gtk+-2.0 --cflags ; then +- GTK_CFLAGS="-DGTK2 `$PKG_CONFIG gtk+-2.0 --cflags` " +- GTK_LIBS=`$PKG_CONFIG gtk+-2.0 --libs` +-dnl use_gtk2=yes +- AC_DEFINE([GTK2], [1], [the GTK2 library]) +- enable_stockgtk=yes +-else +-if $PKG_CONFIG --cflags gtk+ ; then +- GTK_CFLAGS=`$PKG_CONFIG gtk+ --cflags` +- GTK_LIBS=`$PKG_CONFIG gtk+ --libs` +-dnl use_gtk2=no +-fi +-fi +-fi +- +-dnl AC_MSG_RESULT using GTK2 : $use_gtk2 ++PKG_CHECK_MODULES([GTK],[gtk+-2.0]) + + dnl Checks for header files. + AC_PATH_XTRA + AC_HEADER_DIRENT + AC_HEADER_STDC + +-LDFLAGS="$X_LIBS" ++LDFLAGS+="$X_LIBS" + AC_CHECK_LIB([X11],[XOpenDisplay]) + dnl just an ugly hack to work around the more aggressive header checks + dnl in recent autoconf. Not sure if we should really rely on include +@@ -184,6 +166,7 @@ if test x$enable_emf = xyes; then + AC_MSG_RESULT(yes) + AC_DEFINE([EMF], [1], [use optional libEMF instead of fig2dev for EMF output]) + EMFLIBS="-lEMF -lstdc++" ++ EMFINCL="-I${includedir}libEMF" + else + AC_MSG_RESULT(no) + EMFLIBS="" +@@ -221,6 +204,7 @@ AC_SUBST(localedir) + AC_SUBST(kdemimedir) + AC_SUBST(gnomemimedir) + AC_SUBST(EMFLIBS) ++AC_SUBST(EMFINCL) + AC_SUBST(MYGTKSRCS) + AC_SUBST(MYGTKOBJS) + AC_SUBST(GTK_CFLAGS) diff --git a/sci-chemistry/chemtool/metadata.xml b/sci-chemistry/chemtool/metadata.xml new file mode 100644 index 000000000000..26c258873424 --- /dev/null +++ b/sci-chemistry/chemtool/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <use> + <flag name="emf">EMF export support</flag> + </use> +</pkgmetadata> 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 >= 0.4 A. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/cluster/Manifest b/sci-chemistry/cluster/Manifest new file mode 100644 index 000000000000..1a7bcd779934 --- /dev/null +++ b/sci-chemistry/cluster/Manifest @@ -0,0 +1 @@ +DIST cluster.1.3.081231.src.tgz 8860 SHA256 4e0986d5ff124936b5fff4b6f8989dd04be11180d6552fddc34b2c10dfcc870f SHA512 af5851ef467458d45ee5f2309c6344ae16145ac371a1b9d0a3d8b5769a18b98877cf7cb65b85f71108d927b0e6c363e06b85a67e7cb2e5e0b41af375cb2db7ac WHIRLPOOL 2f02de20b323792360b28d5a42d233d06be529414e29796a39a439651fee9e8ba73bdd05033907ac7434890bfa2a31aaf57ab98bbe59964d06a2d63646833f5f diff --git a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild new file mode 100644 index 000000000000..801d4209627a --- /dev/null +++ b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Build lists of collections of interacting items" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}"/${PN}1.3src + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-ldflags.patch \ + "${FILESDIR}"/${PV}-includes.patch + tc-export CXX +} + +src_install() { + newbin ${PN} molprobity-${PN} + dodoc README.cluster +} diff --git a/sci-chemistry/cluster/cluster-1.3.081231.ebuild b/sci-chemistry/cluster/cluster-1.3.081231.ebuild new file mode 100644 index 000000000000..abb875d7f2d0 --- /dev/null +++ b/sci-chemistry/cluster/cluster-1.3.081231.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Build lists of collections of interacting items" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}"/${PN}1.3src + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-ldflags.patch \ + "${FILESDIR}"/${PV}-includes.patch + tc-export CXX +} + +src_install() { + dobin ${PN} + dodoc README.cluster +} diff --git a/sci-chemistry/cluster/files/1.3.081231-includes.patch b/sci-chemistry/cluster/files/1.3.081231-includes.patch new file mode 100644 index 000000000000..a5586a540a4f --- /dev/null +++ b/sci-chemistry/cluster/files/1.3.081231-includes.patch @@ -0,0 +1,12 @@ +diff --git a/cluster.cpp b/cluster.cpp +index 0a8c3c1..1384949 100644 +--- a/cluster.cpp ++++ b/cluster.cpp +@@ -24,6 +24,7 @@ + #include <iostream> + #include <vector> + #include <string> ++#include <cstring> + + #include <iostream> + #include <fstream> diff --git a/sci-chemistry/cluster/files/1.3.081231-ldflags.patch b/sci-chemistry/cluster/files/1.3.081231-ldflags.patch new file mode 100644 index 000000000000..1b99f6d662f2 --- /dev/null +++ b/sci-chemistry/cluster/files/1.3.081231-ldflags.patch @@ -0,0 +1,41 @@ + Makefile | 12 ++++++------ + 1 files changed, 6 insertions(+), 6 deletions(-) + +diff --git a/Makefile b/Makefile +index 7892054..929564b 100644 +--- a/Makefile ++++ b/Makefile +@@ -3,27 +3,27 @@ PROG_FLGS = -D BOOLPREDEFINED + + SRCS = cluster.cpp DisjointSets.cpp utility.cpp + +-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) ++CXXFLAGS += $(OPT) $(DEBUG) $(PROG_FLGS) + + LFLAGS = + + OBJLIST = cluster.o DisjointSets.o utility.o + +-CXX = g++ ++CXX ?= g++ + + .cpp.o: +- $(CXX) -c $*.cpp $(CFLAGS) ++ $(CXX) $(CXXFLAGS) -c $*.cpp + +-OPT = -O3 ++OPT = + DEBUG = $(CXXDEBUGFLAGS) + + all: cluster + + cluster: $(OBJLIST) +- $(CXX) -o $@ $(OBJLIST) $(LFLAGS) ++ $(CXX) $(LDFLAGS) -o $@ $(OBJLIST) + + depend: +- makedepend -- $(CFLAGS) -- $(SRCS) ++ makedepend -- $(CXXFLAGS) -- $(SRCS) + + clean: + @rm -rf *.o *.ckp ii_files diff --git a/sci-chemistry/cluster/metadata.xml b/sci-chemistry/cluster/metadata.xml new file mode 100644 index 000000000000..76f6a5d9e463 --- /dev/null +++ b/sci-chemistry/cluster/metadata.xml @@ -0,0 +1,18 @@ +<?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> +Cluster is a simple UNIX C++ program to build lists of collections +of interacting items from records containing interacting pairs +and larger fragments. + +It reads in lines consisting of two or more names and output +connected clusters of names. Each line of output is +prefixed with a cluster number, the size of the cluster +and an optional name string. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest new file mode 100644 index 000000000000..d0d2b7b0dc55 --- /dev/null +++ b/sci-chemistry/cns/Manifest @@ -0,0 +1,4 @@ +DIST aria2.3.1.tar.gz 1833973 SHA256 cc45ed2d66182cf0ee197a7cf3bc7edd8d5043d95cdcd19e1cec9aeb82c2fdbc SHA512 79a2cd89e2120acecb04f286a153dbf52c16500e8956c9dad49b1e1ed94a7b2449c7b044bae6f87e0d2b452a1467a2c02de74f0fa85b0eae66042386e2f5e2d5 WHIRLPOOL 2ff003322601b42bec0d2431e2f1f85819b3982f8da612ff778bb404e51f0fcbca3faa6998e9c0635f9e73899609bb1e273420cac182952aa744364c20299723 +DIST aria2.3.2.tar.gz 1836270 SHA256 30727ea8bdc2e3b44e5970545008fcfa07fa59aa28b76824956a2aa71daa9615 SHA512 009a1d0079f5cc162dc732749ddd2b33297268f0d988b2f37bda4ed50c7764ceef7ae5b56b322c7ac79427a4a2a92d1239199891445cb5e2b3d0908ed670e2aa WHIRLPOOL f18af5b751e79c92e04f4dc12b6b806a1c505b269559a2342bdd6280b790f9f0df9bb4afe366af03beaf09af0128c6b68c39bc66603d51ad24914c78b2579cf3 +DIST cns_solve_1.21_all-mp.tar.gz 32748040 SHA256 7ab464e20932eb024ba6378738da77a4a03642d63b0ca9772b612a7cf27baec1 SHA512 383324d771570b501e388fba9bf20789f483a3a4044eb3334c7a7e7835e0c345b784e0d344b22d20a10fe1c33ed21c9013adb1af5912808af480b96abe275857 WHIRLPOOL fecd0b2dfba43e5525a9fcc8543a55867602b376744848ddafd4c132bcdfc32225780f543742fa225b5e0f0ce658c1029a9ca8b80d5ee3f2491b6d63e8ad91b0 +DIST cns_solve_1.3_all.tar.gz 64167735 SHA256 2ee368022c5ecabf66ce7d32059d93cd7d885ad2d684a094b87c64f6b3dfea0d SHA512 4fe73820e96999bb33a59ff6da979794628552f49bc03cdebcb9439b57e6042b92190e04bb7e4079157adf06a6facc5c16b8ae91621bd24a4b35ee382e53ae37 WHIRLPOOL b3cd14ab7a8a29a44f6e6c3cbc22ee2c665eb8c8565969337b24deffb2a1fd007fae11c5eb73ac38ddf9a38e850948e3b2df2548931722a2a383d5e8c72607a1 diff --git a/sci-chemistry/cns/cns-1.2.1-r8.ebuild b/sci-chemistry/cns/cns-1.2.1-r8.ebuild new file mode 100644 index 000000000000..d9cc723f98b3 --- /dev/null +++ b/sci-chemistry/cns/cns-1.2.1-r8.ebuild @@ -0,0 +1,233 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic + +MY_PN="${PN}_solve" +MY_PV="$(delete_version_separator 2)" +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Crystallography and NMR System" +HOMEPAGE="http://cns.csb.yale.edu/" +SRC_URI=" + ${MY_P}_all-mp.tar.gz + aria? ( aria2.3.2.tar.gz )" + +SLOT="0" +LICENSE="cns" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="aria openmp" + +RDEPEND="app-shells/tcsh" +DEPEND="${RDEPEND}" + +FORTRAN_NEED_OPENMP=1 + +S="${WORKDIR}/${MY_P}" + +RESTRICT="fetch test" + +pkg_nofetch() { + elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" + use aria && elog "and http://aria.pasteur.fr/" + elog "and place these files:" + elog ${A} + elog "in ${DISTDIR}." +} + +get_fcomp() { + case $(tc-getFC) in + *gfortran* ) + FCOMP="gfortran" ;; + ifort ) + FCOMP="ifc" ;; + * ) + FCOMP=$(tc-getFC) ;; + esac +} + +pkg_setup() { + fortran-2_pkg_setup + get_fcomp +} + +get_bitness() { + echo > "${T}"/test.c + $(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o + case $(file "${T}"/test.o) in + *64-bit*|*ppc64*|*x86_64*) export _bitness="64";; + *32-bit*|*ppc*|*i386*) export _bitness="32";; + *) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";; + esac +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-gentoo.patch \ + "${FILESDIR}"/${PV}-parallel.patch + + get_bitness + + if use aria; then + pushd "${WORKDIR}"/aria* >& /dev/null + # Update the cns sources in aria for version 1.2.1 + epatch "${FILESDIR}"/1.2.1-aria2.3.patch + + # Update the code with aria specific things + cp -rf cns/src/* "${S}"/source/ || die + popd >& /dev/null + fi + + # the code uses Intel-compiler-specific directives + if [[ $(tc-getFC) =~ gfortran ]]; then + epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch + use openmp && \ + append-flags -fopenmp && append-ldflags -fopenmp + COMP="gfortran" + [[ ${_bitness} == 64 ]] && \ + append-fflags -fdefault-integer-8 + elif [[ $(tc-getFC) == if* ]]; then + epatch "${FILESDIR}"/${PV}-ifort.patch + use openmp && \ + append-flags -openmp && append-ldflags -openmp + COMP="ifort" + [[ ${_bitness} == 64 ]] && append-fflags -i8 + fi + + [[ ${_bitness} == 64 ]] && \ + append-cflags "-DINTEGER='long long int'" + + # Set up location for the build directory + # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION + cp "${FILESDIR}"/cns_solve_env_sh "${T}"/ || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ + -i "${S}"/cns_solve_env || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ + -i "${T}"/cns_solve_env_sh || die + + einfo "Fixing shebangs..." + find "${S}" -type f \ + -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die +} + +src_compile() { + local GLOBALS + local MALIGN + if [[ $(tc-getFC) =~ g77 ]]; then + GLOBALS="-fno-globals" + MALIGN='\$(CNS_MALIGN_I86)' + fi + + # Set up the compiler to use + ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die + + # make install really means build, since it's expected to be used in-place + # -j1 doesn't mean we do no respect MAKEOPTS! + emake -j1 \ + CC="$(tc-getCC)" \ + F77=$(tc-getFC) \ + LD=$(tc-getFC) \ + CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + LDFLAGS="${LDFLAGS}" \ + F77OPT="${FCFLAGS} ${MALIGN}" \ + F77STD="${GLOBALS}" \ + OMPLIB="${OMPLIB}" \ + compiler="${COMP}" \ + install +} + +src_test() { + # We need to force on g77 manually, because we can't get aliases working + # when we source in a -c + einfo "Running tests ..." + csh -c \ + "export CNS_G77=ON; source ${S}/cns_solve_env; make run_tests" \ + || die "tests failed" + einfo "Displaying test results ..." + cat "${S}"/*_g77/test/*.diff-test +} + +src_install() { + # Install to locations resembling FHS + sed \ + -e "s:${S}:usr:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \ + -e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \ + -e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \ + -e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \ + -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ + -e "/^g77on/d" \ + -i "${S}"/cns_solve_env || die + # I don't entirely understand why the sh version requires a leading / + # for CNS_SOLVE and CNS_ROOT, but it does + sed \ + -e "s:${S}:/usr:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \ + -e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \ + -e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \ + -e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \ + -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ + -e "/^g77on/d" \ + -e "/^g77off/d" \ + -i "${T}"/cns_solve_env_sh || die + + # Get rid of setup stuff we don't need in the installed script + sed \ + -e "83,$ d" \ + -e "37,46 d" \ + -i "${S}"/cns_solve_env || die + sed \ + -e "84,$ d" \ + -e "39,50 d" \ + -i "${T}"/cns_solve_env_sh || die + + newbin "${S}"/*linux*/bin/cns_solve* cns_solve + + # Can be run by either cns_solve or cns + dosym cns_solve /usr/bin/cns + + # Don't want to install this + rm -f "${S}"/*linux*/utils/Makefile || die + + dobin "${S}"/*linux*/utils/* + + sed \ + -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ + -i "${S}"/bin/cns_web || die + + dobin "${S}"/bin/cns_{edit,header,transfer,web} + + insinto /usr/share/cns + doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib + doins "${S}"/bin/cns_info + + insinto /etc/profile.d + newins "${S}"/cns_solve_env cns_solve_env.csh + newins "${T}"/cns_solve_env_sh cns_solve_env.sh + + dohtml \ + -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ + -f all_cns_info_template,omac,def \ + -r doc/html/* + # Conflits with app-text/dos2unix + rm -f "${D}"/usr/bin/dos2unix || die +} + +pkg_postinst() { + if use openmp; then + elog "Set OMP_NUM_THREADS to the number of threads you want." + elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" + elog "variable if using gcc (16384 should be good)." + fi +} diff --git a/sci-chemistry/cns/cns-1.3_p7-r1.ebuild b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild new file mode 100644 index 000000000000..724c62f7e98c --- /dev/null +++ b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild @@ -0,0 +1,216 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic + +MY_PN="${PN}_solve" +MY_PV="$(delete_version_separator 2)" +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Crystallography and NMR System" +HOMEPAGE="http://cns.csb.yale.edu/" +SRC_URI=" + ${MY_P/p7}_all.tar.gz + aria? ( aria2.3.1.tar.gz )" + +SLOT="0" +LICENSE="cns" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="aria openmp" + +RDEPEND="app-shells/tcsh" +DEPEND="${RDEPEND}" + +FORTRAN_NEED_OPENMP=1 + +S="${WORKDIR}/${MY_P/p7}" + +RESTRICT="fetch" + +pkg_nofetch() { + elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" + use aria && elog "and http://aria.pasteur.fr/" + elog "and place these files:" + elog ${A} + elog "in ${DISTDIR}." +} + +get_fcomp() { + case $(tc-getFC) in + *gfortran* ) + FCOMP="gfortran" ;; + ifort ) + FCOMP="ifc" ;; + * ) + FCOMP=$(tc-getFC) ;; + esac +} + +pkg_setup() { + fortran-2_pkg_setup + get_fcomp +} + +get_bitness() { + echo > "${T}"/test.c + $(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o + case $(file "${T}"/test.o) in + *64-bit*|*ppc64*|*x86_64*) export _bitness="64";; + *32-bit*|*ppc*|*i386*) export _bitness="32";; + *) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";; + esac +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-gentoo.patch \ + "${FILESDIR}"/${PV}-delete.patch + + get_bitness + + if use aria; then + pushd "${WORKDIR}"/aria* >& /dev/null + # Update the cns sources in aria for version 1.2.1 + epatch "${FILESDIR}"/1.2.1-aria2.3.patch + + # Update the code with aria specific things + cp -rf cns/src/* "${S}"/source/ || die + popd >& /dev/null + fi + + # the code uses Intel-compiler-specific directives + if [[ $(tc-getFC) =~ gfortran ]]; then + use openmp && \ + append-flags -fopenmp && append-ldflags -fopenmp + COMP="gfortran" + [[ ${_bitness} == 64 ]] && \ + append-fflags -fdefault-integer-8 + elif [[ $(tc-getFC) == if* ]]; then + use openmp && \ + append-flags -openmp && append-ldflags -openmp + COMP="ifort" + [[ ${_bitness} == 64 ]] && append-fflags -i8 + fi + + [[ ${_bitness} == 64 ]] && \ + append-cflags "-DINTEGER='long long int'" + + # Set up location for the build directory + # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION + cp "${FILESDIR}"/cns_solve_env_sh-${PV} "${T}"/cns_solve_env_sh || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ + -i "${S}"/cns_solve_env || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ + -e "s:setenv OMP_STACKSIZE 256m:export OMP_STACKSIZE=256m:g" \ + -e "s:^limit:^ulimit:g" \ + -i "${T}"/cns_solve_env_sh || die + + ebegin "Fixing shebangs..." + find "${S}" -type f \ + -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die + find . -name "Makefile*" \ + -exec \ + sed \ + -e "s:^SHELL=/bin/sh:SHELL=${EPREFIX}/bin/sh:g" \ + -e "s:/bin/ls:ls:g" \ + -e "s:/bin/rm:rm:g" \ + -i '{}' + || die + eend +} + +src_compile() { + local GLOBALS + local MALIGN + + # Set up the compiler to use + ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die + + # make install really means build, since it's expected to be used in-place + # -j1 doesn't mean we do no respect MAKEOPTS! + emake -j1 \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + F77=$(tc-getFC) \ + LD=$(tc-getFC) \ + CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + CXXFLAGS="${CXXFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + LDFLAGS="${LDFLAGS}" \ + F77OPT="${FCFLAGS} ${MALIGN}" \ + F77STD="${GLOBALS}" \ + OMPLIB="${OMPLIB}" \ + compiler="${COMP}" \ + install +} + +src_test() { + # We need to force on g77 manually, because we can't get aliases working + # when we source in a -c + einfo "Running tests ..." + sh -c \ + "export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \ + || die "tests failed" + einfo "Displaying test results ..." + cat "${S}"/*_g77/test/*.diff-test +} + +src_install() { + cat >> "${T}"/66cns <<- EOF + CNS_SOLVE="${EPREFIX}/usr" + CNS_ROOT="${EPREFIX}/usr" + CNS_DATA="${EPREFIX}/usr/share/cns" + CNS_DOC="${EPREFIX}/usr/share/doc/cns-1.3" + CNS_LIB="${EPREFIX}/usr/share/cns/libraries" + CNS_MODULE="${EPREFIX}/usr/share/cns/modules" + CNS_TOPPAR="${EPREFIX}/usr/share/cns/libraries/toppar" + CNS_CONFDB="${EPREFIX}/usr/share/cns/libraries/confdb" + CNS_XTALLIB="${EPREFIX}/usr/share/cns/libraries/xtal" + CNS_NMRLIB="${EPREFIX}/usr/share/cns/libraries/nmr" + CNS_XRAYLIB="${EPREFIX}/usr/share/cns/libraries/xray" + CNS_XTALMODULE="${EPREFIX}/usr/share/cns/modules/xtal" + CNS_NMRMODULE="${EPREFIX}/usr/share/cns/modules/nmr" + CNS_HELPLIB="${EPREFIX}/usr/share/cns/helplib" + EOF + + doenvd "${T}"/66cns || die + + # Don't want to install this + rm -f "${S}"/*linux*/utils/Makefile || die + + sed \ + -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ + -i "${S}"/bin/cns_web || die + + newbin "${S}"/*linux*/bin/cns_solve* cns_solve + + # Can be run by either cns_solve or cns + dosym cns_solve /usr/bin/cns + + dobin \ + "${S}"/*linux*/utils/* \ + "${S}"/bin/cns_{edit,header,import_cif,transfer,web} + + insinto /usr/share/cns + doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib "${S}"/bin/cns_info + + dohtml \ + -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ + -f all_cns_info_template,omac,def \ + -r doc/html/* + # Conflits with app-text/dos2unix + rm -f "${D}"/usr/bin/dos2unix || die +} + +pkg_postinst() { + if use openmp; then + elog "Set OMP_NUM_THREADS to the number of threads you want." + elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" + elog "variable if using gcc (16384 should be good)." + fi +} diff --git a/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch new file mode 100644 index 000000000000..42b9b0572231 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch @@ -0,0 +1,20 @@ +--- source/xfft.f.orig 2008-08-03 00:36:52.000000000 -0700 ++++ source/xfft.f 2008-08-03 00:37:06.000000000 -0700 +@@ -514,7 +514,7 @@ + LOGICAL QHERM + DOUBLE PRECISION XRCELL(9), MAPR + C local +-!$ integer omp_get_max_threads, kmp_get_stacksize ++!$ integer omp_get_max_threads + LOGICAL DONE + DOUBLE PRECISION ZERO + PARAMETER (ZERO=0.0D0) +@@ -537,7 +537,7 @@ + NBPP=1 + ! The following command is only relevant for the ifort compiler (if -openmp option is used). + ! If your compiler is not ifort, and gives an error, just comment the next line out: +-!$ if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23) ++! if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23) + ! Explanation: the default KMP_STACKSIZE of ifort is 2**21 bytes (2Mb) for 32bit, + ! and 2**22 bytes (4Mb) for 64bit. + ! This may be low for big structures, which leads to segmentation faults! diff --git a/sci-chemistry/cns/files/1.2.1-aria2.3.patch b/sci-chemistry/cns/files/1.2.1-aria2.3.patch new file mode 100644 index 000000000000..8c6939d8eb92 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-aria2.3.patch @@ -0,0 +1,22 @@ +diff --git a/cns/src/cns.f b/cns/src/cns.f +index a3c2cbe..51a34f8 100644 +--- a/cns/src/cns.f ++++ b/cns/src/cns.f +@@ -470,6 +470,7 @@ C local + INTEGER HNLEN, TMP, PTRSZ, STLEN + CHARACTER*(1) CNSPTMP + CHARACTER*(4) ST ++!$ integer omp_get_max_threads + C + C write header + WRITE(6,'(10X,A)') +@@ -526,6 +527,9 @@ C + WRITE(6,'(10X,7A)') + & ' Running on machine: ',HOSTNM(1:HNLEN), + & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)' ++!$ write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(), ++!$ & ' threads' ++!$C (to change use setenv OMP_NUM_THREADS x) + C + CALL GETNAM(USERNM,12,TMP) + WRITE(6,'(10X,2A)') diff --git a/sci-chemistry/cns/files/1.2.1-gentoo.patch b/sci-chemistry/cns/files/1.2.1-gentoo.patch new file mode 100644 index 000000000000..2b47bfcc7d86 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-gentoo.patch @@ -0,0 +1,63 @@ +--- cns_solve_1.21/instlib/source/Makefile.proto 2000-09-07 20:35:33.000000000 +0200 ++++ cns_solve_1.21/instlib/source/Makefile.proto.new 2009-07-14 09:18:37.000000000 +0200 +@@ -11,6 +11,8 @@ + + SHELL=/bin/sh + ++cns_string=`date "+%y%m%d%H%M"` ++ + # commands + RM = /bin/rm + +@@ -25,26 +27,20 @@ + + # rule for the fortran routines + $(OBJS): +- @ echo "compiling: $(@:.o=.f)"; \ +- $(F77) -c $(F77FLAGS) $(@:.o=.f) ++ $(F77) -c $(F77FLAGS) $(@:.o=.f) + + # rule for the dynamic memory allocation C routines + dmemory.o: dmemory.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the machine specific C routines + machine_c.o: machine_c.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the executable itself + ../bin/cns_solve: $(DEPENDS) +- @ echo ; echo "linking: cns_solve"; echo +- @ cns_string=`date "+%y%m%d%H%M"`; \ +- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ +- $(LDFLAGS) \ +- $(CNS_FFTDIR) $(CNS_FFTLIB); \ ++ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ ++ $(CNS_FFTDIR) $(CNS_FFTLIB); \ + if [ -x cns_solve-$$cns_string.exe ]; \ + then echo "created executable file cns_solve-$$cns_string.exe"; \ + echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ +--- cns_solve_1.21/instlib/utils/Makefile 2004-08-30 00:40:35.000000000 +0200 ++++ cns_solve_1.21/instlib/utils/Makefile.new 2009-07-14 09:50:27.000000000 +0200 +@@ -22,14 +22,14 @@ + make clean + + .f: +- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) ++ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) + + .c: +- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) ++ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) + + .l: + lex $(@).l +- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) ++ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) + + relink: + @ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` diff --git a/sci-chemistry/cns/files/1.2.1-ifort.patch b/sci-chemistry/cns/files/1.2.1-ifort.patch new file mode 100644 index 000000000000..ba44bebd1b68 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-ifort.patch @@ -0,0 +1,126 @@ +diff --git a/source/angledb.f b/source/angledb.f +index 28ad657..eaa847d 100644 +--- a/source/angledb.f ++++ b/source/angledb.f +@@ -1416,10 +1416,10 @@ C include files + C local variables + INTEGER COUNT, SPTR, OLDCLASS, OLDMAXANGLEDBS + INTEGER THETYPE, CURPSIS, CURPHIS +- INTEGER CLASSINDEX ++ INTEGER CLASINDEX + DOUBLE PRECISION K1, CUTOFF + CHARACTER*4 THENAME +- CHARACTER*20 CLASSNAME ++ CHARACTER*20 CLASNAME + C begin + C + IF (ANGLEDBFLAG) THEN +@@ -1450,10 +1450,10 @@ C + ELSE IF (WD(1:4).EQ.'CLAS') THEN + OLDCLASS = CURANGLEDBCLASS + CALL NEXTWD('class name =') +- CLASSNAME = WD(1:20) ++ CLASNAME = WD(1:20) + ANGLEDBMODE = NEW + DO COUNT = 1, NANGLEDBCLASSES +- IF (ANGDBCLASSNAMES(COUNT).EQ.CLASSNAME) THEN ++ IF (ANGDBCLASSNAMES(COUNT).EQ.CLASNAME) THEN + ANGLEDBMODE = UPDATE + CURANGLEDBCLASS = COUNT + END IF +@@ -1472,7 +1472,7 @@ C + END IF + NANGLEDBCLASSES = NANGLEDBCLASSES + 1 + CURANGLEDBCLASS = NANGLEDBCLASSES +- ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASSNAME ++ ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASNAME + ANGLEDBASSNDX(CURANGLEDBCLASS) = NANGLEDBS + END IF + C +@@ -1733,16 +1733,16 @@ C + & HEAP(ANGLEDBTPTR)) + ELSE IF (WD(1:4).EQ.'CLAS') THEN + CALL NEXTWD('Class name>') +- CLASSNAME = WD(1:20) +- CLASSINDEX = 0 ++ CLASNAME = WD(1:20) ++ CLASINDEX = 0 + DO COUNT = 1, NANGLEDBCLASSES + IF (ANGDBCLASSNAMES(COUNT).EQ. +- & CLASSNAME) THEN ++ & CLASNAME) THEN + PRINTTHISCLASS(COUNT) = .TRUE. +- CLASSINDEX = COUNT ++ CLASINDEX = COUNT + END IF + END DO +- IF (CLASSINDEX.EQ.0) THEN ++ IF (CLASINDEX.EQ.0) THEN + CALL DSPERR('ANGLEDB', + & 'unknown class. Using first.') + PRINTTHISCLASS(1) = .TRUE. +diff --git a/source/rama.f b/source/rama.f +index c5d14f2..3063e7b 100644 +--- a/source/rama.f ++++ b/source/rama.f +@@ -1468,11 +1468,11 @@ C include files + C local variables + INTEGER COUNT, SPTR, OLDCLASS, OLDMAXRAMAS, + & THETYPE, CURPSIS, CURPHIS, +- & CURCHIS, CURTHTS, CLASSINDEX ++ & CURCHIS, CURTHTS, CLASINDEX + INTEGER CLEN + DOUBLE PRECISION K1, CUTOFF + CHARACTER*4 THENAME +- CHARACTER*50 CLASSNAME ++ CHARACTER*50 CLASNAME + C begin + C + C this is used by READRAMA2 to hold the selection +@@ -1503,10 +1503,10 @@ C + ELSE IF (WD(1:4).EQ.'CLAS') THEN + OLDCLASS = CURRAMACLASS + CALL NEXTWD('class name =') +- CLASSNAME = WD(1:50) ++ CLASNAME = WD(1:50) + RAMAMODE = NEW + DO COUNT = 1, NRAMACLASSES +- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) THEN ++ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) THEN + RAMAMODE = UPDATE + CURRAMACLASS = COUNT + END IF +@@ -1525,7 +1525,7 @@ C + END IF + NRAMACLASSES = NRAMACLASSES + 1 + CURRAMACLASS = NRAMACLASSES +- RAMACLASSNAMES(CURRAMACLASS) = CLASSNAME ++ RAMACLASSNAMES(CURRAMACLASS) = CLASNAME + END IF + C + C set force constant for current class, +@@ -1954,18 +1954,18 @@ C + & HEAP(RAMAATOMPTR), 0) + ELSE IF (WD(1:4).EQ.'CLAS') THEN + CALL NEXTWD('Class name>') +- CLASSINDEX = 0 ++ CLASINDEX = 0 + DO COUNT = 1, NRAMACLASSES +- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) +- & CLASSINDEX = COUNT ++ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) ++ & CLASINDEX = COUNT + END DO +- IF (CLASSINDEX.EQ.0) THEN ++ IF (CLASINDEX.EQ.0) THEN + CALL DSPERR('RAMA', + & 'unknown class. Using first.') +- CLASSINDEX = 1 ++ CLASINDEX = 1 + END IF + CALL PRINTRAMAS(CUTOFF, HEAP(CALCRAMAPTR), +- & HEAP(RAMAATOMPTR), CLASSINDEX) ++ & HEAP(RAMAATOMPTR), CLASINDEX) + ELSE + CALL DSPERR('RAMA', + & 'Expected ALL or CLASs.') diff --git a/sci-chemistry/cns/files/1.2.1-parallel.patch b/sci-chemistry/cns/files/1.2.1-parallel.patch new file mode 100644 index 000000000000..dfaa40021d66 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-parallel.patch @@ -0,0 +1,17 @@ +diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto +index 0d0dd3e..ae9e422 100644 +--- a/instlib/source/Makefile.proto ++++ b/instlib/source/Makefile.proto +@@ -19,9 +19,9 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o + + # the default is to make the cns executable + cns_solve: +- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k exepurge ++ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make exepurge + + # rule for the fortran routines + $(OBJS): diff --git a/sci-chemistry/cns/files/1.3_p7-delete.patch b/sci-chemistry/cns/files/1.3_p7-delete.patch new file mode 100644 index 000000000000..cbddf4289158 --- /dev/null +++ b/sci-chemistry/cns/files/1.3_p7-delete.patch @@ -0,0 +1,13 @@ +diff --git a/utils/cluster_struc.cpp b/utils/cluster_struc.cpp +index b64467a..5f727db 100644 +--- a/utils/cluster_struc.cpp ++++ b/utils/cluster_struc.cpp +@@ -173,7 +173,7 @@ int main(int argc, char *argv[]) { + for (int i = 0; i < nrstruc; i++) { + delete[] neighbor[i]; + } +- delete[] neighbor, neighborcount; ++ delete[] neighbor, delete[] neighborcount; + return 5; + } + if (rmsd < cutoff) { diff --git a/sci-chemistry/cns/files/1.3_p7-gentoo.patch b/sci-chemistry/cns/files/1.3_p7-gentoo.patch new file mode 100644 index 000000000000..7942c55abfb9 --- /dev/null +++ b/sci-chemistry/cns/files/1.3_p7-gentoo.patch @@ -0,0 +1,80 @@ +diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto +index 0d0dd3e..dd4b680 100644 +--- a/instlib/source/Makefile.proto ++++ b/instlib/source/Makefile.proto +@@ -11,6 +11,8 @@ + + SHELL=/bin/sh + ++cns_string=`date "+%y%m%d%H%M"` ++ + # commands + RM = /bin/rm + +@@ -19,32 +21,26 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o + + # the default is to make the cns executable + cns_solve: +- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k exepurge ++ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make exepurge + + # rule for the fortran routines + $(OBJS): +- @ echo "compiling: $(@:.o=.f)"; \ +- $(F77) -c $(F77FLAGS) $(@:.o=.f) ++ $(F77) -c $(F77FLAGS) $(@:.o=.f) + + # rule for the dynamic memory allocation C routines + dmemory.o: dmemory.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the machine specific C routines + machine_c.o: machine_c.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the executable itself + ../bin/cns_solve: $(DEPENDS) +- @ echo ; echo "linking: cns_solve"; echo +- @ cns_string=`date "+%y%m%d%H%M"`; \ +- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ +- $(LDFLAGS) \ +- $(CNS_FFTDIR) $(CNS_FFTLIB); \ ++ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ ++ $(CNS_FFTDIR) $(CNS_FFTLIB); \ + if [ -x cns_solve-$$cns_string.exe ]; \ + then echo "created executable file cns_solve-$$cns_string.exe"; \ + echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ +diff --git a/instlib/utils/Makefile b/instlib/utils/Makefile +index 98de84f..4f32b34 100644 +--- a/instlib/utils/Makefile ++++ b/instlib/utils/Makefile +@@ -22,17 +22,17 @@ utils: + make clean + + .f: +- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) ++ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) + + .c: +- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) ++ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) + + .cpp: +- $(CPP) -o $@ $(CCFLAGS) $(@).cpp $(CCLINK) ++ $(CXX) $(LDFLAGS) -o $@ $(CXXFLAGS) $(@).cpp $(CCLINK) + + .l: + lex $(@).l +- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) ++ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) + + relink: + @ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` diff --git a/sci-chemistry/cns/files/cns_solve_env_sh b/sci-chemistry/cns/files/cns_solve_env_sh new file mode 100644 index 000000000000..34e1a2b635cf --- /dev/null +++ b/sci-chemistry/cns/files/cns_solve_env_sh @@ -0,0 +1,221 @@ +#!/bin/sh +# +# This file sets up the appropriate environmental variables and paths +# for CNSsolve. In the case of the same machines with different versions +# of the OS, backward compatibility is assumed - ie. a later version will +# be setup for a previous version of the OS if nothing else is available. +# +# written by: Paul Adams +# +# copyright Yale University +# +# ========================================================================== +# +# >>>>>> Important: define the location of the CNSsolve directory <<<<<< +# +# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY + + CNS_SOLVE=_CNSsolve_location_ + +# +# ========================================================================== +# +# full expansion of the CNS_SOLVE variable prior to use. +# +export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE +# +# ========================================================================== +# +# set the number of threads for SGI multiprocessors +# if this causes a problem on other systems it can be commented out +# +export MP_SET_NUMTHREADS; MP_SET_NUMTHREADS=1 +# +# ========================================================================== +# +# get the machine architecture +# +if [ -d $CNS_SOLVE ]; then + if [ ! "$CNS_ARCH" ]; then + export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch` + fi +else + export CNS_ARCH; CNS_ARCH='unknown' +fi +# +# system variables (this is needed for openmp) +# +ulimit -s unlimited +# ========================================================================== +# +# general environmental variables +# +export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries +export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules +export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar +export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb +export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal +export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr +export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray +export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal +export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr +export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib +# +# general user aliases +# +cns_web () { $CNS_SOLVE/bin/cns_web; } +cns_header () { $CNS_SOLVE/bin/cns_header; } +cns_info () { cat $CNS_SOLVE/bin/cns_info; } +cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } +if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then + cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } +else + cns_edit () { $CNS_SOLVE/bin/cns_edit; } +fi +run_tutorial () { "csh -f tutorial.csh"; } +# +# g77 compilation and use +# +g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; } +g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; } +# +# developer aliases +# +run_tests () { $CNS_SOLVE/bin/run_tests; } +run_diffs () { $CNS_SOLVE/bin/run_diffs; } +maketar () { $CNS_SOLVE/bin/maketar; } +create_patch () { $CNS_SOLVE/bin/create_patch; } +# +# +# ========================================================================== +# +# to do expansions - unset noglob just in case user has it otherwise +# +set +f +# +# try to set up appropriate path +# +# first strip off any trailing information (eg. _g77) +# +CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'` +# +cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'` +cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'` +cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'` +cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'` +cns_minor=`echo $cns_major | sed -e 's/\./ /g'` +# +# if we are looking for a specific type of setup then limit search +# +cns_dirs="" +if [ ! "$CNS_G77" ]; then + if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then + cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" + fi +else + CNS_ARCH="${CNS_ARCH}_g77" + if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then + cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" + fi +fi +# +# first look for an exact match (with os version) +# +# +cns_found=0 +if [ -n "$cns_dirs" ]; then + for cns_dir in $cns_dirs ; do + cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \ + $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + done +# +# +# now look for an exact match (without os version) +# + if [ $cns_found -eq 0 ]; then + for cns_dir in $cns_dirs ; do + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \ + $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi < |