reinit the tree, so we can have metadata

5 files changed, 152 insertions, 0 deletions

diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
new file mode 100644
index 000000000000..a6f2060da5e8
--- /dev/null
+++ b/sci-chemistry/tinker/Manifest
@@ -0,0 +1,7 @@
+AUX 7.1.2-openmp.patch 400 SHA256 67cf53b3801814ab39b4bdbb40db9f500cbc4740e2b7db94a945829ef1961cec SHA512 1af405acc753d602501589725374e88964a55e5954cb77eb1f3c0156fa73936552be9ce5fc4f36c855dfbd4043f12749dfc95aa9b946d80d0e5e6e8100e84ad4 WHIRLPOOL 6f20e980f63f79d3443f46d5608ad241723b73026cc3ec85437cb741a1c2b7b3fe74de428097583f3f34ac05d85e14edfe0490a04d48cccfd64d4ded2850dfb2
+AUX tinker-7.1.2-build.patch 360 SHA256 26fba46b9a72407cfd194cf74d5044b06b41164ae039b0b97f29b1840be4f765 SHA512 b20a4d8e75a781cd9c769dd0b5ae4e1039ea54d7ac61fc3605543b796afa2f4f3957be439f338fd47090a17e9153a466c2f76b364f4d9b7a2705b746f6cefbd3 WHIRLPOOL e102e8fafacc51160e191535355ae6fc7216c76b21234f6878c252eeebcb306bac8678413da26b44ff20a32b7652eda189eb66eb44efd577eb007e8685f8222f
+DIST tinker-7.1.2.tar.gz 28468683 SHA256 fdee18915cff9044fd083bb2271083c221db6d05de2cb98fc111b136e23e6899 SHA512 4524259754b0f11d7e2e8997ebd85eae7d28f8dbb1edb2d9818aa0a96640de0049aa4937236694f1a11743dee187d612f775b233a73cc96c2708d620457a7dc2 WHIRLPOOL f3e29eaf67d25ae6d4f3c4e3546798e66bd626929fddd45b9d1ff9f2143cd57dcc5079226f3ceaa142f4c6a168c4a150a51be1336a5ca13384338795ef3a6d46
+EBUILD tinker-7.1.2.ebuild 2275 SHA256 ddb245287de264e81e8c1ea7b0ef3749aaf9d218f49b6d165d3b1ecc41437c22 SHA512 d617f08cf03f35e78f0561214dcc0c7c4af0fedce69214a302ca8dee2c2a3577ba002671f4cce8a86cb3ca76084ce99eff6a2e90ecfc940c7aa56fd588edda2c WHIRLPOOL 6875ec865fd927d27c9fd5644da5b6a739f45e275f7e1a424a470e8610d5aa45e28ef03b5c200c6419e694928fc5841980c62c770cfe10c366a95d4ac9b1cf85
+MISC ChangeLog 2546 SHA256 40f1e60e2f001e8fc7c6cdb4c5effb89840a850c45347fe6e9e9fd74905ccd61 SHA512 fc9b14a4abb63367ae77af1c6eb7f49ac4169cb6df6250d5daa7b34559361860a6fda404976eacec50d0149c4b4d48eb59c45addf58e5133bcf9fb9be87e1588 WHIRLPOOL 107d50ddc5826ce1e19e9c9d47a1a7356b9aed04bcce26e95d73437215e5074a914320af789333ec4f1cfa6415277519d9191822b210265d353021e4bec125b7
+MISC ChangeLog-2015 5325 SHA256 628dfafc7626fc1bb8e814c00f4f80e559a5c14a539709499e196e848182c4cd SHA512 a8f802aca8a0e694569ddf5174d7a60c840435d11f745e705d9e381d93ebfdf636c6b790b9f02638b51101e28e688532f09566a6384ec83f7cc5d3af6bf34c86 WHIRLPOOL 81e4ec3bd16032f86598883c50e4a8e93123ef8f8394f8665d2268afbe154fd8b10178eb733188d11078d8f630662db048be7e105e953cd4b30ae90d59be9d38
+MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d
diff --git a/sci-chemistry/tinker/files/7.1.2-openmp.patch b/sci-chemistry/tinker/files/7.1.2-openmp.patch
new file mode 100644
index 000000000000..f3e8e2932b4a
--- /dev/null
+++ b/sci-chemistry/tinker/files/7.1.2-openmp.patch
@@ -0,0 +1,15 @@
+diff --git a/source/initial.f b/source/initial.f
+index 835f228..4099c74 100644
+--- a/source/initial.f
++++ b/source/initial.f
+@@ -73,8 +73,8 @@ c
+ c
+ c     Intel compiler extensions to OpenMP standard
+ c
+-!$    call kmp_set_stacksize_s (2**28)
+-!$    call kmp_set_blocktime (0)
++!    call kmp_set_stacksize_s (2**28)
++!    call kmp_set_blocktime (0)
+ c
+ c     values of machine precision constants
+ c
diff --git a/sci-chemistry/tinker/files/tinker-7.1.2-build.patch b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch
new file mode 100644
index 000000000000..d6ef484b19a4
--- /dev/null
+++ b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch
@@ -0,0 +1,17 @@
+ make/Makefile | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/make/Makefile b/make/Makefile
+index 61d5037..9be384a 100644
+--- a/make/Makefile
++++ b/make/Makefile
+@@ -719,8 +719,7 @@ EXEFILES = alchemy.x \
+ %.x: %.o libtinker.a
+ 	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@
+ 
+-all:
+-	${EXEFILES}
++all: ${EXEFILES}
+ 
+ install:
+ 	rename
diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml
new file mode 100644
index 000000000000..da36ecbfcd6a
--- /dev/null
+++ b/sci-chemistry/tinker/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/tinker/tinker-7.1.2.ebuild b/sci-chemistry/tinker/tinker-7.1.2.ebuild
new file mode 100644
index 000000000000..46a8d2feb0f2
--- /dev/null
+++ b/sci-chemistry/tinker/tinker-7.1.2.ebuild
@@ -0,0 +1,105 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs
+
+DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM"
+HOMEPAGE="http://dasher.wustl.edu/tinker/"
+SRC_URI="http://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="Tinker"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+DEPEND="
+	>=virtual/jdk-1.6"
+
+RDEPEND="
+	>=sci-libs/fftw-3.2.2-r1[fortran,threads]
+	dev-libs/maloc
+	!sys-apps/bar
+	!dev-util/diffuse
+	>=virtual/jre-1.6"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${PN}/source
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	java-pkg-opt-2_pkg_setup
+	tc-has-openmp || die "Please use an openmp capable compiler like gcc[openmp]"
+}
+
+src_prepare() {
+	sed 's:strip:true:g' -i ../make/Makefile
+	[[ $(tc-getFC) =~ "ifort" ]] || epatch "${FILESDIR}"/${PV}-openmp.patch
+	cd .. && epatch "${FILESDIR}"/${P}-build.patch
+}
+
+src_compile() {
+	local javalib=
+	for i in $(java-config -g LDPATH | sed 's|:| |g'); do
+		[[ -f ${i}/libjvm.so ]] && javalib=${i}
+	done
+
+	# use dummy routines in pmpb.f instead of apbs calls
+	rm pmpb.c || die
+
+	if [[ $(tc-getFC) =~ "gfortran" ]]; then
+		append-flags -fopenmp
+		_omplib="-lgomp"
+	else
+		append-flags -openmp
+		_omplib="-liomp5"
+	fi
+
+	_fftwlib="$($(tc-getPKG_CONFIG) --libs fftw3 fftw3_threads)"
+
+	emake \
+		-f ../make/Makefile \
+		F77="$(tc-getFC)" \
+		CC="$(tc-getCC) -c" \
+		F77FLAGS=-c \
+		OPTFLAGS="${FFLAGS}" \
+		LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \
+		INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \
+		LIBS="-lmaloc -L${javalib} -ljvm ${_omplib} ${_fftwlib}" \
+		all
+
+	mkdir "${S}"/../bin || die
+
+	emake \
+		-f ../make/Makefile \
+		BINDIR="${S}"/../bin \
+		rename
+}
+
+src_test() {
+	cd "${WORKDIR}"/${PN}/test/
+	for test in *.run; do
+		einfo "Testing ${test} ..."
+		bash ${test} || die
+	done
+}
+
+src_install() {
+	dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/*
+
+	insinto /usr/share/${PN}/
+	doins -r "${WORKDIR}"/${PN}/params
+
+	dodoc \
+		"${WORKDIR}"/${PN}/doc/{*.txt,*.pdf,0README}
+
+	if use examples; then
+		insinto /usr/share/${P}
+		doins -r "${WORKDIR}"/${PN}/example
+
+		doins -r "${WORKDIR}"/${PN}/test
+	fi
+
+}