# Removal in 30 days. Bug #697376.
app-text/scrollkeeper
-# Michał Górny <mgorny@gentoo.org> (2019-10-19)
-# sci-chemistry/ccpn is unfetchable and mirror-restricted.
-# sci-chemistry/aria is its reverse dependency which can't be installed
-# as a result.
-# sci-chemistry/cns is fetch-restricted and the package request form
-# is dead. Also, its only dependency is aria.
-# Removal in 30 days. Bug #695784.
-sci-chemistry/aria
-sci-chemistry/ccpn
-sci-libs/ccpn-data
-sci-chemistry/cns
-
# Michał Górny <mgorny@gentoo.org> (2019-10-19)
# The Linux installer/update is unfetchable, and can't be redistributed.
# Removal in 30 days. Bug #695778.
+++ /dev/null
-DIST aria2.3.2_08.26.2013.tar.gz 1878602 BLAKE2B 3044192853c0ed0653d20fea959d3b01321f559845c555289658f93b65e9148f8cd0f59619e8690887b2811d613e6cc2f67b67af7d84ade4b8fc18403367086c SHA512 a6d8c45218f5d494174587a5f8f1feec940ac8cc4cd7b707dac65b2378219ecf27967e70807e6cb7ae22a7d4aec7239af763f077ad7183c078b1991cac71bc3e
+++ /dev/null
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-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="
- ${PYTHON_DEPS}
- dev-tcltk/tix
- dev-lang/tk:0=
- >=dev-python/numpy-1.1[${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 ${A}"
- einfo "and place it into your DISTDIR directory."
-}
-
-pkg_setup() {
- python-single-r1_pkg_setup
-}
-
-src_test(){
- export CCPNMR_TOP_DIR=$(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)"
-}
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
-</pkgmetadata>
+++ /dev/null
-DIST analysis2.4.1.tar.gz 36088236 BLAKE2B 8aaf4ffe5a8dc7a6b805a7a66e163cb03b0fc8a45617ebf892268a2f3658e49c48e3c2de4ea654a840eef2c01cf3a3f28f45e053697e68bbc83ce22d19a29cf3 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1
-DIST analysis2.4.2.tar.gz 36390919 BLAKE2B 5e7fa44b2029d834ef634b2cd9f2c34d7e6dbfd3e257b9344cff92d13750a21325a2a2f82eb072ae385c528a7406796959c8201edbc1422bc54a17e176d7db33 SHA512 694faefd3c085b559b6bb4729141a9ab885334f578bfbb0ebf260366dbca38c31738d5f5af50b5c7ea16b304b27adf80411082859796a5afeec630c36d56bd8b
-DIST ccpn-update-2.4.1-150226.patch.xz 10732 BLAKE2B 9f31bd16e7a866b016c5db8b837e3ee926d2db7cd3b15e7cd32fe00f7723e511214d36221ba86651e79223f0a1d30e2402aa446eb063a078b989102032ae743b SHA512 60eb4acf6179f80207a72076ff5d5d733d3c3e804c1ce0a48701dd6e923146af49cd6759a529c8125f4b26eb3f8f83b35acc0c48b88a3e3034b25b5438a04feb
-DIST ccpn-update-2.4.2-150325.patch.xz 2096 BLAKE2B 589c8129d2e1df6231412cd1398823208cbdc7307f63f3a5480a65e428aeb0b6411b9110ddd380ad37addd2ea9118bc6156662c5fd80a7eee362f53fd417e724 SHA512 c544e0a4a93d0e3275a22d07d21bf3bb5ed90cf041f40bf08fbc687b431640ad5c56180eadd4b43e4023b08ef42afe5a874423becc6f9313a0b1f642a4b97873
-DIST ccpn-update-2.4.2-150413.patch.xz 3132 BLAKE2B f4d55e4b301df4500f29d281de2b274f7912d61d1ad54fedf992e76dd254e86dcb2e9d2a2f4d58ce028d4c9df6bedad847a9e72bef7627800c2d31cc7c43909e SHA512 99893ca009ff76b015017b29cfd97e0ae935ed2d62aa5a99d52dd9a5f22cf0d369e5019273fe3c3811c28b32568721fb64f71c5927eb57d0cc91dcea44b0288d
-DIST ccpn-update-2.4.2-150421.patch.xz 3788 BLAKE2B 125eed69e2593e0ab64e6d3cdcee026c4af067c3aa2e9742b033741cc65cc0391fb86c825b372c02dcd549ca260196fd4e8938516d218653d3db80f60ce9caf2 SHA512 0e8a10b6d9721b52574cd2fe0413dca0fac32a948eb31d3db6e2c4d4f7d85c341e8d53d70954341792ea598a37ec87e4392a615e1c2f6f8bbfc0e42a750be648
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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/v2-software/software"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
- && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${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 ${_file}
- done
- eend
- python_optimize
-}
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-#PATCHSET="${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/v2-software/software"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
- && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${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 ${_file}
- done
- eend
- python_optimize
-}
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-PATCHSET="${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/v2-software/software"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
- && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${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 ${_file}
- done
- eend
- python_optimize
-}
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-PATCHSET="${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/v2-software/software"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
- && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${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 ${_file}
- done
- eend
- python_optimize
-}
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-PATCHSET="${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/v2-software/software"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
- && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${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
-}
+++ /dev/null
-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
-+ $(MAKE) -C other/cambridge/bayes
-
- clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean
-
+++ /dev/null
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${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 $6
+++ /dev/null
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${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 $6
+++ /dev/null
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${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 $6
+++ /dev/null
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${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 $@
+++ /dev/null
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${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 $*
+++ /dev/null
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${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 $@
+++ /dev/null
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${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 $6
+++ /dev/null
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${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 $6
+++ /dev/null
-#!/bin/bash
-
-export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${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 $6
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
-</pkgmetadata>
+++ /dev/null
-DIST aria2.3.1.tar.gz 1833973 BLAKE2B 4bf51626a4283452e75a834d0160a4204efd5a35ee8b07329f2a4f933ceea23e53177e6ed19bc9cc158b2a00491d20c75d443bdc04e7feb2d7eda3dc006818e1 SHA512 79a2cd89e2120acecb04f286a153dbf52c16500e8956c9dad49b1e1ed94a7b2449c7b044bae6f87e0d2b452a1467a2c02de74f0fa85b0eae66042386e2f5e2d5
-DIST aria2.3.2.tar.gz 1836270 BLAKE2B 725b0db2b5de36d1b132c5073b8a91f26fa19b48549f4c899041a2b140127524f660c4faeb8c35e94d3d19c24b0252f379de0e85c8fb08b86fc7834252239fb9 SHA512 009a1d0079f5cc162dc732749ddd2b33297268f0d988b2f37bda4ed50c7764ceef7ae5b56b322c7ac79427a4a2a92d1239199891445cb5e2b3d0908ed670e2aa
-DIST cns_solve_1.21_all-mp.tar.gz 32748040 BLAKE2B 7c82fd9cddc56a00d791d6d5525491b91525962f000c2fdfb02a3ab81305c0c026c115c2328dac99ac7b30146ca591620f4f42019938fb49e7ce52235b281121 SHA512 383324d771570b501e388fba9bf20789f483a3a4044eb3334c7a7e7835e0c345b784e0d344b22d20a10fe1c33ed21c9013adb1af5912808af480b96abe275857
-DIST cns_solve_1.3_all.tar.gz 64167735 BLAKE2B 3901a597eb0deac7f2fad173e15d78bfcd753c4019739e22c8851194c9446305cd92bcff73f7f06dc21b6d055852863993412296e1e555ef0b3b730052934cbd SHA512 4fe73820e96999bb33a59ff6da979794628552f49bc03cdebcb9439b57e6042b92190e04bb7e4079157adf06a6facc5c16b8ae91621bd24a4b35ee382e53ae37
+++ /dev/null
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic
-
-MY_PN="${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 "into your DISTDIR directory."
-}
-
-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
-}
+++ /dev/null
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-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 "into your DISTDIR directory."
-}
-
-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 "${D}"/usr/bin/dos2unix || die
-}
-
-pkg_postinst() {
- if use openmp; then
- elog "Set OMP_NUM_THREADS to the number of threads you want."
- elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
- elog "variable if using gcc (16384 should be good)."
- fi
-}
+++ /dev/null
---- source/xfft.f.orig 2008-08-03 00:36:52.000000000 -0700
-+++ source/xfft.f 2008-08-03 00:37:06.000000000 -0700
-@@ -514,7 +514,7 @@
- LOGICAL QHERM
- DOUBLE PRECISION XRCELL(9), MAPR
- C local
--!$ 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!
+++ /dev/null
-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)')
+++ /dev/null
---- 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`
+++ /dev/null
-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.')
+++ /dev/null
-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):
+++ /dev/null
-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) {
+++ /dev/null
-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 $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile`
+++ /dev/null
-#!/bin/sh
-#
-# This file sets up the appropriate environmental variables and paths
-# for CNSsolve. In the case of the same machines with different versions
-# of the OS, backward compatibility is assumed - ie. a later version will
-# be setup for a previous version of the OS if nothing else is available.
-#
-# written by: Paul Adams
-#
-# copyright Yale University
-#
-# ==========================================================================
-#
-# >>>>>> Important: define the location of the CNSsolve directory <<<<<<
-#
-# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY
-
- CNS_SOLVE=_CNSsolve_location_
-
-#
-# ==========================================================================
-#
-# full expansion of the CNS_SOLVE variable prior to use.
-#
-export CNS_SOLVE; CNS_SOLVE=$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
- done
- fi
-#
-# now look for a backwards compatible match (with os version major/minor)
-#
- if [ $cns_found -eq 0 ]; then
- for cns_dir in $cns_dirs ; do
- if [ $cns_found -eq 0 ]; then
- cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'`
- if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
- if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then
- osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'`
- if [ $osv_test -eq 1 ]; then
- cns_archenv=$cns_dir
- cns_found=1
- fi
- fi
- fi
- fi
- done
- fi
-#
-# now look for a wildcard match on cpu
-#
- if [ $cns_found -eq 0 ]; then
- cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'`
- cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'`
- for cns_dir in $cns_dirs ; do
- if [ $cns_found -eq 0 ]; then
- cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'`
- cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'`
- if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
- if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \
- $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then
- cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'`
- if [ $cpu_test -eq 1 ]; then
- cns_archenv=$cns_dir
- cns_found=1
- fi
- fi
- fi
- fi
- done
- fi
-fi
-#
-# if found set environment
-#
-if [ $cns_found -eq 1 ]; then
- #
- # set installation and source directory
- #
- export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv
- export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source
- #
- # path for CNSsolve utility programs
- #
- if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then
- export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils`
- fi
- #
- # path for CNSsolve executable if installed
- #
- if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then
- export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin`
- fi
-fi
-#
-unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor
-unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same
-unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test
-#
+++ /dev/null
-#!/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
-#
-# ==========================================================================
-#
-# get the machine architecture
-#
-if [ -d $CNS_SOLVE ]; then
- if [ ! "$CNS_ARCH" ]; then
- export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch`
- fi
-else
- export CNS_ARCH; CNS_ARCH='unknown'
-fi
-#
-# ==========================================================================
-#
-# system variables for OpenMP
-#
-# The default stack sizes are usually insufficient, especially when
-# CNS is compiled using OpenMP. If the stack sizes are too
-# small segfaults may occur. Recommended setting for "stacksize":
-limit stacksize unlimited
-#
-# KMP_STACKSIZE is specific for Intel ifort, icc:
-##setenv KMP_STACKSIZE 256m
-#
-# OMP_STACKSIZE is used by all compilers:
-setenv OMP_STACKSIZE 256m
-#
-# Uncomment the following line and change as appropriate to set the number
-# of processors (threads) to use.
-###setenv OMP_NUM_THREADS 4
-#
-# ==========================================================================
-#
-# general environmental variables
-#
-export CNS_LIB; CNS_LIB=$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
-#
-# 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
- done
- fi
-#
-# now look for a backwards compatible match (with os version major/minor)
-#
- if [ $cns_found -eq 0 ]; then
- for cns_dir in $cns_dirs ; do
- if [ $cns_found -eq 0 ]; then
- cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'`
- if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
- if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then
- osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'`
- if [ $osv_test -eq 1 ]; then
- cns_archenv=$cns_dir
- cns_found=1
- fi
- fi
- fi
- fi
- done
- fi
-#
-# now look for a wildcard match on cpu
-#
- if [ $cns_found -eq 0 ]; then
- cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'`
- cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'`
- for cns_dir in $cns_dirs ; do
- if [ $cns_found -eq 0 ]; then
- cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'`
- cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'`
- if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
- if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \
- $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then
- cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'`
- if [ $cpu_test -eq 1 ]; then
- cns_archenv=$cns_dir
- cns_found=1
- fi
- fi
- fi
- fi
- done
- fi
-fi
-#
-# if found set environment
-#
-if [ $cns_found -eq 1 ]; then
- #
- # set installation and source directory
- #
- export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv
- export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source
- #
- # path for CNSsolve utility programs
- #
- if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then
- export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils`
- fi
- #
- # path for CNSsolve executable if installed
- #
- if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then
- export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin`
- fi
-fi
-#
-unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor
-unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same
-unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test
-#
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
- <use>
- <flag name="aria"> Support patch for sci-chemistry/aria</flag>
- </use>
- <longdescription>
-Crystallography and NMR System (CNS) is the result of an international
-collaborative effort among several research groups. The program has
-been designed to provide a flexible multi-level hierachical approach for the
-most commonly used algorithms in macromolecular structure determination.
-Highlights include heavy atom searching, experimental phasing (including
-MAD and MIR), density modification, crystallographic refinement with maximum
-likelihood targets, and NMR structure calculation using NOEs, J-coupling,
-chemical shift, and dipolar coupling data.
-</longdescription>
-</pkgmetadata>
+++ /dev/null
-DIST analysis2.3.1r2.tar.gz 21683215 BLAKE2B 9eaf77987ff47be3d2ce4f9e9d9a94ce917fd57114181fb2beea56658e5d8e6b6b5b14765b198b29035e6d3b60d3f8fb87b7b21883292a86c3fcf3a36f6f3b50 SHA512 96bf75d1e958340d83836348f5a3045e5b2632913c66d9d74272140085800ea096f1ae53eadfb5bc0eba76804f1864553e82a517d637bdc3bace71b0c1c785ee
-DIST analysis2.4.0.tar.gz 36047222 BLAKE2B 6d38abb06922a4487eed77e19bb920e11f7c6a94e8e62554289310da0ca3555f9ba62e3f9cc52dc9df022ff0d0aebb95d60edd11ce54c645ffaa6efd9cfadab5 SHA512 2f9c5abd401675796d64c620f6142b484084c54af98e0a4800b2bea81de447d711d594ccf773f86ef6631f0482fe0a0ad2881da713d6e022e0704f8dea8d65d9
-DIST analysis2.4.1.tar.gz 36088236 BLAKE2B 8aaf4ffe5a8dc7a6b805a7a66e163cb03b0fc8a45617ebf892268a2f3658e49c48e3c2de4ea654a840eef2c01cf3a3f28f45e053697e68bbc83ce22d19a29cf3 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1
-DIST analysis2.4.2.tar.gz 36390919 BLAKE2B 5e7fa44b2029d834ef634b2cd9f2c34d7e6dbfd3e257b9344cff92d13750a21325a2a2f82eb072ae385c528a7406796959c8201edbc1422bc54a17e176d7db33 SHA512 694faefd3c085b559b6bb4729141a9ab885334f578bfbb0ebf260366dbca38c31738d5f5af50b5c7ea16b304b27adf80411082859796a5afeec630c36d56bd8b
-DIST ccpn-update-2.3.1-140425.patch.xz 19020 BLAKE2B 6d86ef7ddeb639b1c7ef50b3b206f4db726369e4c81bb0cd47f1aeec2f1a06d57573e378c1366feca2f35c4db18dc0ae19a9e35de5804595370b8d80f9d41b0c SHA512 071e1a0c4f589a76a6878cb5636516304c3eb9d929924ed1d03c1838cb1d894cc330cc5c6c0b222a71e24513e212f469a69fc3e746ea82e34eb669292d7ce52e
-DIST ccpn-update-2.4.0-140425.patch.xz 1096 BLAKE2B 64aaa083771e84616dd193f3a8ca181386c0784597868d6105744376919e7bab20ec24cdb864e01f6ae5d61b73f304f698824d949a380d7773d03c98f2078816 SHA512 8c1d3df4210f02e8fbb07caabab740c115769457296ae62903f5401ca875b006e355b99dcda32f9606c93c84b0e0cee07acff53fc953bc77918597b58f826e0f
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils portability python-r1 versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN/-data}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})r2"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR - Data"
-HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software"
-SRC_URI="http://www2.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
- ${PYTHON_DEPS}
- !<sci-chemistry/ccpn-${PVR}"
-DEPEND=""
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"/ccpnmr/ccpnmr2.3
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
- cp "${FILESDIR}"/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml data/ccp/nmr/NmrExpPrototype/ || die
-}
-
-src_install() {
- local i pydocs in_path ein_path
-
- dodir /usr/share/doc/${PF}/html
- sed \
- -e "s:../ccpnmr2.1:${EPREFIX}/usr/share/doc/${PF}/html:g" \
- ../doc/index.html > "${ED}"/usr/share/doc/${PF}/html/index.html || die
- treecopy $(find python/ -name doc -type d) "${ED}"/usr/share/doc/${PF}/html/
-
- pydocs="$(find python -name doc -type d)"
-
- symlinking() {
- in_path=$(python_get_sitedir)/ccpn
- ein_path="${in_path#${EPREFIX}}"
- dosym ../../../../share/doc/${PF}/html ${ein_path}/doc
- for i in ${pydocs}; do
- dosym /usr/share/doc/${PF}/html/${i} ${ein_path}/${i}
- done
- dosym /usr/share/ccpn/data ${ein_path}/data
- dosym /usr/share/ccpn/model ${ein_path}/model
- }
- python_foreach_impl symlinking
-
- dohtml -r doc/*
- insinto /usr/share/ccpn
- doins -r data model
-}
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils portability python-r1 versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN/-data}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR - Data"
-HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software"
-SRC_URI="http://www2.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
- ${PYTHON_DEPS}
- !<sci-chemistry/ccpn-${PVR}"
-DEPEND=""
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"/ccpnmr/ccpnmr2.4
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
- cp "${FILESDIR}"/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml data/ccp/nmr/NmrExpPrototype/ || die
-}
-
-src_install() {
- local i pydocs in_path ein_path
-
- dodir /usr/share/doc/${PF}/html
- sed \
- -e "s:../ccpnmr2.1:${EPREFIX}/usr/share/doc/${PF}/html:g" \
- ../doc/index.html > "${ED}"/usr/share/doc/${PF}/html/index.html || die
- treecopy $(find python/ -name doc -type d) "${ED}"/usr/share/doc/${PF}/html/
-
- pydocs="$(find python -name doc -type d)"
-
- symlinking() {
- in_path=$(python_get_sitedir)/ccpn
- ein_path="${in_path#${EPREFIX}}"
- dosym ../../../../share/doc/${PF}/html ${ein_path}/doc
- for i in ${pydocs}; do
- dosym /usr/share/doc/${PF}/html/${i} ${ein_path}/${i}
- done
- dosym /usr/share/ccpn/data ${ein_path}/data
- dosym /usr/share/ccpn/model ${ein_path}/model
- }
- python_foreach_impl symlinking
-
- dohtml -r doc/*
- insinto /usr/share/ccpn
- doins -r data model
-}
+++ /dev/null
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils portability python-r1 versionator
-
-#PATCHSET="${PV##*_p}"
-MY_PN="${PN/-data}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR - Data"
-HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software"
-SRC_URI="http://www2.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
- ${PYTHON_DEPS}
- !<sci-chemistry/ccpn-${PVR}"
-DEPEND=""
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"/ccpnmr/ccpnmr2.4
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
- cp "${FILESDIR}"/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml data/ccp/nmr/NmrExpPrototype/ || die
-}
-
-src_install() {
- local i pydocs in_path ein_path
-
- dodir /usr/share/doc/${PF}/html
- sed \
- -e "s:../ccpnmr2.1:${EPREFIX}/usr/share/doc/${PF}/html:g" \
- ../doc/index.html > "${ED}"/usr/share/doc/${PF}/html/index.html || die
- treecopy $(find python/ -name doc -type d) "${ED}"/usr/share/doc/${PF}/html/
-
- pydocs="$(find python -name doc -type d)"
-
- symlinking() {
- in_path=$(python_get_sitedir)/ccpn
- ein_path="${in_path#${EPREFIX}}"
- dosym ../../../../share/doc/${PF}/html ${ein_path}/doc
- for i in ${pydocs}; do
- dosym /usr/share/doc/${PF}/html/${i} ${ein_path}/${i}
- done
- dosym /usr/share/ccpn/data ${ein_path}/data
- dosym /usr/share/ccpn/model ${ein_path}/model
- }
- python_foreach_impl symlinking
-
- dohtml -r doc/*
- insinto /usr/share/ccpn
- doins -r data model
-}
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils portability python-r1 versionator
-
-#PATCHSET="${PV##*_p}"
-MY_PN="${PN/-data}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR - Data"
-HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software"
-SRC_URI="http://www2.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
- ${PYTHON_DEPS}
- !<sci-chemistry/ccpn-${PVR}"
-DEPEND=""
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"/ccpnmr/ccpnmr2.4
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
- cp "${FILESDIR}"/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml data/ccp/nmr/NmrExpPrototype/ || die
-}
-
-src_install() {
- local i pydocs in_path ein_path
-
- dodir /usr/share/doc/${PF}/html
- sed \
- -e "s:../ccpnmr2.1:${EPREFIX}/usr/share/doc/${PF}/html:g" \
- ../doc/index.html > "${ED}"/usr/share/doc/${PF}/html/index.html || die
- treecopy $(find python/ -name doc -type d) "${ED}"/usr/share/doc/${PF}/html/
-
- pydocs="$(find python -name doc -type d)"
-
- symlinking() {
- in_path=$(python_get_sitedir)/ccpn
- ein_path="${in_path#${EPREFIX}}"
- dosym ../../../../share/doc/${PF}/html ${ein_path}/doc
- for i in ${pydocs}; do
- dosym /usr/share/doc/${PF}/html/${i} ${ein_path}/${i}
- done
- dosym /usr/share/ccpn/data ${ein_path}/data
- dosym /usr/share/ccpn/model ${ein_path}/model
- }
- python_foreach_impl symlinking
-
- dohtml -r doc/*
- insinto /usr/share/ccpn
- doins -r data model
-}
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<_StorageUnit release="2.1.2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-16-14:22:45_00019" time="Wed Oct 2 16:22:49 2013">
-
-<NMRX.NmrExpPrototype _ID="_1" createdBy="ccpnRef" guid="ccpn_rhf22_2013-10-02-16-17-30-923_00001" lastUnlockedBy="editor" serial="312">
- <NMRX.NmrExpPrototype.category>
- <NMRX.ExpCategory>through-bond</NMRX.ExpCategory>
- </NMRX.NmrExpPrototype.category>
- <NMRX.NmrExpPrototype.details>
- <IMPL.Text>e.g. POST-C7, INADEQUATE</IMPL.Text>
- </NMRX.NmrExpPrototype.details>
- <NMRX.NmrExpPrototype.name>
- <IMPL.Line>C[DQ(CC)]_C.through-space</IMPL.Line>
- </NMRX.NmrExpPrototype.name>
- <NMRX.NmrExpPrototype.synonym>
- <IMPL.Line>13C DQ</IMPL.Line>
- </NMRX.NmrExpPrototype.synonym>
- <NMRX.NmrExpPrototype.atomSites>
- <NMRX.AtomSite _ID="_2" isotopeCode="13C" name="C" serial="1">
- <NMRX.AtomSite.expMeasurements> _3 _4</NMRX.AtomSite.expMeasurements>
- <NMRX.AtomSite.expTransfers> _5 _6</NMRX.AtomSite.expTransfers>
- </NMRX.AtomSite>
- <NMRX.AtomSite _ID="_7" isotopeCode="13C" name="C" serial="2">
- <NMRX.AtomSite.expMeasurements> _4</NMRX.AtomSite.expMeasurements>
- <NMRX.AtomSite.expTransfers> _5</NMRX.AtomSite.expTransfers>
- </NMRX.AtomSite>
- <NMRX.AtomSite _ID="_8" isotopeCode="13C" name="C" serial="3">
- <NMRX.AtomSite.expMeasurements> _9</NMRX.AtomSite.expMeasurements>
- <NMRX.AtomSite.expTransfers> _6</NMRX.AtomSite.expTransfers>
- </NMRX.AtomSite>
- </NMRX.NmrExpPrototype.atomSites>
- <NMRX.NmrExpPrototype.expGraphs>
- <NMRX.ExpGraph _ID="_10" serial="1">
- <NMRX.ExpGraph.expSteps>
- <NMRX.ExpStep _ID="_11" serial="1" stepNumber="1">
- </NMRX.ExpStep>
- <NMRX.ExpStep _ID="_12" serial="2" stepNumber="2">
- </NMRX.ExpStep>
- <NMRX.ExpStep _ID="_13" serial="3" stepNumber="3">
- </NMRX.ExpStep>
- <NMRX.ExpStep _ID="_14" serial="4" stepNumber="4">
- </NMRX.ExpStep>
- </NMRX.ExpGraph.expSteps>
- <NMRX.ExpGraph.expTransfers>
- <NMRX.ExpTransfer _ID="_5" serial="1" transferType="onebond">
- <NMRX.ExpTransfer.atomSites> _7 _2</NMRX.ExpTransfer.atomSites>
- </NMRX.ExpTransfer>
- <NMRX.ExpTransfer _ID="_6" serial="2" transferToSelf="true" transferType="through-space">
- <NMRX.ExpTransfer.atomSites> _8 _2</NMRX.ExpTransfer.atomSites>
- </NMRX.ExpTransfer>
- </NMRX.ExpGraph.expTransfers>
- </NMRX.ExpGraph>
- </NMRX.NmrExpPrototype.expGraphs>
- <NMRX.NmrExpPrototype.expMeasurements>
- <NMRX.ExpMeasurement _ID="_3" serial="1">
- <NMRX.ExpMeasurement.measurementType>
- <NMRX.ExpMeasurementType>Shift</NMRX.ExpMeasurementType>
- </NMRX.ExpMeasurement.measurementType>
- <NMRX.ExpMeasurement.atomSites> _2</NMRX.ExpMeasurement.atomSites>
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-<!--End of Memops Data-->
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
-</pkgmetadata>
projects / gentoo.git / commitdiff