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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
PYTHON_COMPAT=( python2_7 )
inherit fortran-2 python-r1 toolchain-funcs
DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
HOMEPAGE="http://ambermd.org/#AmberTools"
SRC_URI="
AmberTools${PV%_p*}.tar.bz2"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux"
IUSE="X"
RESTRICT="fetch"
RDEPEND="${PYTHON_DEPS}
virtual/cblas
virtual/lapack
sci-libs/clapack
sci-libs/arpack
sci-chemistry/mopac7
sci-libs/netcdf
sci-libs/netcdf-fortran
>=sci-libs/fftw-3.3:3.0
sci-chemistry/reduce"
DEPEND="${RDEPEND}
app-shells/tcsh
dev-util/byacc
dev-libs/libf2c
sys-devel/ucpp"
S="${WORKDIR}/amber14"
pkg_nofetch() {
einfo "Go to ${HOMEPAGE} and get AmberTools${PV%_p*}.tar.bz2"
einfo "Place it into ${DISTDIR}"
}
pkg_setup() {
fortran-2_pkg_setup
export AMBERHOME="${S}"
}
src_prepare() {
eapply \
"${FILESDIR}"/${PN}-15-gentoo.patch
eapply -p0 \
"${FILESDIR}"/${PN}-15-update.{1..6}.patch
eapply_user
cd "${S}"/AmberTools/src || die
rm -r \
arpack \
blas \
byacc \
lapack \
fftw-3.3 \
c9x-complex \
netcdf-fortran-4.2 \
netcdf-4.3.0 \
reduce \
ucpp-1.3 \
|| die
cd "${S}"/AmberTools/src || die
sed \
-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
-e "s:-llapack:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
-e "s:-lblas:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
-e "s:GENTOO_CFLAGS:${CFLAGS}:g" \
-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
-e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \
-e "s:GENTOO_FFTW3_LIBS:$($(tc-getPKG_CONFIG) fftw3 --libs):" \
-e "s:fc=g77:fc=$(tc-getFC):g" \
-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
-e "s:\$netcdf_flag:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
-e "s:\$netcdfflagc:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
-e "s:\$netcdfflagf:$($(tc-getPKG_CONFIG) netcdf-fortran --libs):g" \
-i configure2 || die
sed \
-e "s:arsecond_:arscnd_:g" \
-i sff/time.c sff/sff.h sff/sff.c || die
}
src_configure() {
python_setup
local myconf="--no-updates"
use X || myconf="${myconf} -noX11"
cd "${S}" || die
sed \
-e '/patch_amber.py/d' \
-i configure || die
./configure \
${myconf} \
-nomtkpp \
--with-python ${PYTHON} \
--with-netcdf /usr \
gnu || die
}
src_compile() {
emake \
CC=$(tc-getCC) \
FC=$(tc-getFC)
}
src_test() {
source ${AMBERHOME}/amber.sh
emake test
}
src_install() {
local x
for x in bin/*
do
[ ! -d ${x} ] && dobin ${x}
done
dobin AmberTools/src/antechamber/mopac.sh
sed \
-e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
-i "${ED}/usr/bin/mopac.sh" || die
# Make symlinks untill binpath for amber will be fixed
dodir /usr/share/${PN}/bin
cd "${ED}/usr/bin" || die
for x in *
do
dosym ../../../bin/${x} /usr/share/${PN}/bin/${x}
done
cd "${S}" || die
dodoc doc/Amber15.pdf
dolib.a lib/*.a
dolib.so lib/*.so
local m=(
chemistry
compat24.py
cpinutils
fortranformat
interface
mcpb
mdoutanalyzer
MMPBSA_mods
ParmedTools
pymsmtexp.py
pymsmtlib
pymsmtmol
sander
sanderles
)
for x in ${m[@]}
do
python_domodule lib/${EPYTHON}/site-packages/${x}
done
insinto /usr/include/${PN}
doins include/*
insinto /usr/share/${PN}
doins -r dat
cd AmberTools || die
doins -r benchmarks examples test
cat >> "${T}"/99ambertools <<- EOF
AMBERHOME="${EPREFIX}/usr/share/ambertools"
EOF
doenvd "${T}"/99ambertools
}
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