sci-chemistry/ambertools added

5 files changed, 154 insertions, 0 deletions

diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
new file mode 100644
index 000000000..492da0ce5
--- /dev/null
+++ b/sci-chemistry/ambertools/Manifest
@@ -0,0 +1,5 @@
+AUX 1.2-Makefile_at.patch 830 RMD160 a6e007e5f86ea244e95b2e24955f487d2e5c4f72 SHA1 50c3d7cd3691a2d9e189f0f0c8138dbaf7111c3c SHA256 ed157fad8d36c35636ea2377723b1623669434c8ddac3c050beeea85f90cc178
+AUX 1.2-configure_at.patch 852 RMD160 57bd7b529c3be0ed5c94856f1603d5288e1fd338 SHA1 a9d7d003f6926cc79289d6924d44a5488a85f3d4 SHA256 84b219694b85edf6ed40546e769666e67844da1b68f44cfdae6c4bbf484bc627
+DIST AmberTools-1.2.tar.bz2 50621801 RMD160 01dd22dd86b90148111dc0616964384dfeda467c SHA1 001db6742fdbf0f0f8c862d1b08a59ea3da0b684 SHA256 1630e0c0135de05441226a08a5f60d861faeb7a06f5d1a4bc38e9eeff4b2f991
+EBUILD ambertools-1.2.ebuild 2030 RMD160 b4428ce5a569b03fdaa4e8cc9f36426de3ba304e SHA1 014451ef55d5060a941ee59476d61e149bd0a81b SHA256 e8479895c644cd3efc26f1daeb0ddd88c3adf31dcd92448abfa0cf69e57d9d50
+MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/ambertools/ambertools-1.2.ebuild b/sci-chemistry/ambertools/ambertools-1.2.ebuild
new file mode 100644
index 000000000..6275b486d
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-1.2.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit toolchain-funcs eutils fortran
+
+FORTRAN="g77 gfortran ifc"
+
+DESCRIPTION="A suite of programs for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="AmberTools-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="mpi openmp scalapack X"
+RESTRICT="fetch"
+
+RDEPEND=""
+DEPEND="${RDEPEND}"
+S="${WORKDIR}"/amber10
+
+pkg_nofetch() {
+	einfo "Go to ${HOMEPAGE} and get ${A}"
+	einfo "Place it in ${DISTDIR}"
+}
+
+pkg_setup() {
+	need_fortran "${FORTRAN}"
+	if use openmp &&
+	[[ $(tc-getCC)$ == *gcc* ]] &&
+		( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
+		! built_with_use sys-devel/gcc openmp )
+	then
+		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
+		ewarn "If you want to build ${PN} with OpenMP, abort now,"
+		ewarn "and switch CC to an OpenMP capable compiler"
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-configure_at.patch
+	epatch "${FILESDIR}"/${PV}-Makefile_at.patch
+}
+
+src_configure() {
+	cd src
+	sed -e "s:\\\\\$(LIBDIR)/arpack.a:/usr/$(get_libdir)/libarpack.a:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:/usr/$(get_libdir)/liblapack.a:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:/usr/$(get_libdir)/libcblas.a:g" \
+		-e "s:\\\\\$(LIBDIR)/f2c.a:/usr/$(get_libdir)/libf2c.a:g" \
+		-e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
+		-e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \
+		-e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \
+		-e "s:fc=g77:fc=${FORTRANC}:g" \
+		-e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=/usr/$(get_libdir)/libnetcdf.a:g" \
+		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+		-e "s:-O3::g" \
+		-i configure_at
+
+	local myconf
+
+	use X || myconf="${myconf} -noX11"
+
+	for x in mpi openmp scalapack; do
+		use ${x} && myconf="${myconf} -${x}"
+	done
+
+	./configure_at \
+		${myconf} \
+		-nobintraj \
+		$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+}
+
+src_compile() {
+	cd src
+	emake -f Makefile_at || die
+}
diff --git a/sci-chemistry/ambertools/files/1.2-Makefile_at.patch b/sci-chemistry/ambertools/files/1.2-Makefile_at.patch
new file mode 100644
index 000000000..36a9b75d3
--- /dev/null
+++ b/sci-chemistry/ambertools/files/1.2-Makefile_at.patch
@@ -0,0 +1,32 @@
+--- src/Makefile_at	2008-07-11 00:09:01.000000000 +0200
++++ src/Makefile_at.new	2009-03-22 20:44:20.818437912 +0100
+@@ -5,29 +5,19 @@
+ install:
+ 	-mkdir $(BINDIR) $(LIBDIR) $(INCDIR)
+ #	utility routines and libraries:
+-	(cd ucpp-1.3 && make $(UCPP) )
+-	(cd byacc && make install )
+-	(cd carpack && make install );
+-	(cd clapack && make $(LAPACK) )
+-	(cd cblas && make $(BLAS) )
+-	(cd f2c &&  make $(F2C)  )
+-	(cd c9x-complex && make $(C9XCOMPLEX) )
+ 
+ #	nab, leap, and sleap:
+-	(cd cifparse && make install )
+ 	(cd nab && make install )
+ 	(cd nss && make install )
+ 
+ #	antechamber:
+ 	(cd antechamber && make install )
+-	(cd mopac6/src && make $(G77) )
+ 	(cd resp && make $(G77) )
+ 
+ #   ptraj:
+ 	(cd ptraj && make install )
+ 
+ #   miscellaneous:
+-	(cd reduce && make install )
+ 
+ #   leap and gleap:
+ 	(cd leap && make install )
diff --git a/sci-chemistry/ambertools/files/1.2-configure_at.patch b/sci-chemistry/ambertools/files/1.2-configure_at.patch
new file mode 100644
index 000000000..69e902131
--- /dev/null
+++ b/sci-chemistry/ambertools/files/1.2-configure_at.patch
@@ -0,0 +1,29 @@
+--- src/configure_at	2009-03-22 20:55:51.394457545 +0100
++++ src/configure_at.new	2009-03-22 20:50:01.155363408 +0100
+@@ -163,7 +163,7 @@
+ blas=install
+ f2c=install
+ ucpp=install
+-cpp="\$(BINDIR)/ucpp -l"
++cpp="/usr/bin/ucpp -l"
+ 
+ #-----------------------------------
+ # skip building of sleap?
+@@ -501,7 +501,7 @@
+         echo ""
+         echo "Obtaining the C++ compiler version:"
+         echo "      $cplusplus -v"
+-        version=`$cplusplus -v 2>&1 | grep version | cut -d' ' -f3`
++        version=`$cplusplus -v 2>&1 | grep " version " | cut -d' ' -f3`
+         echo "The version is $version"
+         majorversion=`echo $version | cut -d'.' -f1`
+         minorversion=`echo $version | cut -d'.' -f2`
+@@ -698,7 +698,7 @@
+ LDFLAGS=$ldflags
+ 
+ LEX=   $lex
+-YACC=  \$(BINDIR)/yacc
++YACC=  /usr/bin/yacc
+ AR=    ar rv
+ M4=    $m4
+ RANLIB=$ranlib
diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml
new file mode 100644
index 000000000..efb490d78
--- /dev/null
+++ b/sci-chemistry/ambertools/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+  <email>sci@gentoo.org</email>
+</maintainer>
+</pkgmetadata>