[sci-chemistry/ambertools] Updates for ambertools and gcc-4.6

(Portage version: 2.2.0_alpha47/git/Linux x86_64, signed Manifest commit with key F82F92E6)

2 files changed, 156 insertions, 4 deletions

diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
index 98d79e2e3..0636d23e2 100644
--- a/sci-chemistry/ambertools/Manifest
+++ b/sci-chemistry/ambertools/Manifest
@@ -1,20 +1,32 @@
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-Hash: SHA1
+Hash: SHA256
 
 AUX ambertools-1.4-gentoo.patch 9926 RMD160 d84b121e1fa940cbf949855de3a5f0bee7566330 SHA1 08ea41b969bed5320230420d047e71a28333f76c SHA256 8f520c01146a704173ca31c68dc9440e2938263416f6d0c95de22d138426e01f
 AUX ambertools-1.5-gentoo.patch 14083 RMD160 762c52626c4eda51839caf74c001bb660052706a SHA1 ab0afa1f5b73569539515dba4cf6638a594c7d6e SHA256 82a83f660701c192272e79f5bab17a8a8be945d78fdab454ade3918281749922
 DIST AmberTools-1.4.tar.bz2 67331137 RMD160 b499e18b583a0b454dd3a554986c19c111822e6a SHA1 ef0f9a44c8767ed35f942fd41afc636b67da0389 SHA256 af61da2f3643b4ec7f41620242b734a3cb4a79c5d422100fbd1fd1c402fecfc1
 DIST AmberTools-1.5.tar.bz2 121062582 RMD160 4a086b42c378f0904f7bf0b16adb042f1677be55 SHA1 92e47e7337fb4901a5a145d808c5ffd42c82d08d SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c
 DIST ambertools-1.4-bugfix_1-18.patch.xz 48136 RMD160 83fe98ef2f4620cd4c85fc72147f830ddfa47b51 SHA1 7a5a2cba9172d017d83aed16ece06d6fed6a5196 SHA256 7ea936442ce1b29943e867adaeb69932d297ae50e0a63b0e03cfb18953e9f7c2
+DIST ambertools-1.5-bugfix_1-10.patch.xz 38396 RMD160 680e64bb7071ea126650c79cd41fc9b8272207bd SHA1 1aec1063902cd3681550f04ba106a14b6b2aaa37 SHA256 469a45b079a3b67a2b58bc6d4dcc46a115305869ddf4ab5890f293e1c5ec05f7
 DIST ambertools-1.5-bugfix_1-3.patch.xz 27268 RMD160 18a74e2e84e81d39417f656ef93e8ee4d4d4583d SHA1 bc52c0776d151a8db005bb7bfb40bf9e963bdeba SHA256 edec6ccc275ee0a70b2ecc9316c031249c4f32d89b1aa145cee32c862516049a
 EBUILD ambertools-1.4.ebuild 3201 RMD160 b2f4331166bafc5093f04c4e7ad9bf2eee9ee0e5 SHA1 4033d6225f7e86d42292eed5ddecd7edeb6742ec SHA256 e3a77f1a006832c46117a5c6a6a641685965f8dfe0c949c0ec1e2f7e57f73835
+EBUILD ambertools-1.5-r1.ebuild 3337 RMD160 a5826024f12a9a070c4f1cdd87878d09f3ba62de SHA1 97e45fbbaf16b126d240d95c3fc3896e372f5086 SHA256 d07ed914b461ebb2a0443b6fb0b334f2912e7e3a0f77ee9a44fce0b75f3580ea
 EBUILD ambertools-1.5.ebuild 3336 RMD160 d97fc7eade8bcf0d12596d42a512560671751d18 SHA1 0427a45349e95be91e274d0e12eb2eb484da6dd3 SHA256 8f8f33770cb12253fef10e9b651a567de36a2863d674b82ca3b1959ab8684353
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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 000000000..bebe61538
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
@@ -0,0 +1,140 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit eutils fortran-2 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"
+IUSE="mpi openmp 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
+	virtual/fortran"
+DEPEND="${RDEPEND}
+	dev-util/byacc
+	dev-libs/libf2c
+	sys-devel/ucpp"
+S="${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_1-3.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:$(pkg-config lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):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=$(tc-getFC):g" \
+		-e "s:\$netcdflib:$(pkg-config netcdf --libs):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 || die
+}
+
+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 "${ED}/usr/bin/tleap" || die
+	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
+	dolib.a lib/*
+	insinto /usr/include/${PN}
+	doins include/*
+	insinto /usr/share/${PN}
+	doins -r dat
+	cd AmberTools
+	doins -r benchmarks
+	doins -r examples
+	doins -r test
+	cat >> "${T}"/99ambertools <<- EOF
+	AMBERHOME="${EPREFIX}/usr/share/ambertools"
+	EOF
+	doenvd "${T}"/99ambertools
+}