(#35945) New molecular mechanics package. Heavily modified ebuild based on that of Jeremy Warren <jwarren@cheesefoam.dyndns.org>.

Package-Manager: portage-2.0.53

5 files changed, 156 insertions, 0 deletions

diff --git a/sci-chemistry/tinker/ChangeLog b/sci-chemistry/tinker/ChangeLog
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+++ b/sci-chemistry/tinker/ChangeLog
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+# ChangeLog for sci-chemistry/tinker
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/ChangeLog,v 1.1 2005/12/03 20:20:35 spyderous Exp $
+
+*tinker-4.2 (03 Dec 2005)
+
+  03 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; +metadata.xml,
+  +tinker-4.2.ebuild:
+  (#35945) New molecular mechanics package. Heavily modified ebuild based on
+  that of Jeremy Warren <jwarren@cheesefoam.dyndns.org>.
+
diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
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index 000000000000..818530d11e02
--- /dev/null
+++ b/sci-chemistry/tinker/Manifest
@@ -0,0 +1,4 @@
+MD5 9240d32cddc2ab3d96d838f169531e54 ChangeLog 470
+MD5 c336619e5cd4eb1ef174a15514c99a88 files/digest-tinker-4.2 59
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
+MD5 92f7b9be4fee0cf3b13967ab7cc6fd3f tinker-4.2.ebuild 3370
diff --git a/sci-chemistry/tinker/files/digest-tinker-4.2 b/sci-chemistry/tinker/files/digest-tinker-4.2
new file mode 100644
index 000000000000..3381b743c27f
--- /dev/null
+++ b/sci-chemistry/tinker/files/digest-tinker-4.2
@@ -0,0 +1 @@
+MD5 5618d8a373896f00e452b137200223fd tinker.tar.gz 8177555
diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
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+++ b/sci-chemistry/tinker/metadata.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/tinker/tinker-4.2.ebuild b/sci-chemistry/tinker/tinker-4.2.ebuild
new file mode 100644
index 000000000000..fe3202ad50c9
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+++ b/sci-chemistry/tinker/tinker-4.2.ebuild
@@ -0,0 +1,131 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/tinker-4.2.ebuild,v 1.1 2005/12/03 20:20:35 spyderous Exp $
+
+inherit fortran toolchain-funcs
+
+FORTRAN="ifc g77"
+
+DESCRIPTION="TINKER is a molecular modeling package that includes force fields for handing large molecules and large systems, such as AMBER and CHARMM.  A Java based visualization front end is included."
+HOMEPAGE="http://dasher.wustl.edu/tinker/"
+SRC_URI="ftp://dasher.wustl.edu/pub/tinker.tar.gz"
+IUSE="X"
+LICENSE="Tinker"
+SLOT="0"
+KEYWORDS="~x86"
+
+DEPEND="X? (
+			|| ( dev-java/blackdown-java3d-bin
+			dev-java/sun-java3d-bin )
+		)"
+S="${WORKDIR}/tinker/source"
+
+src_compile() {
+	if use X; then
+		COMPGUI="./compgui.make"
+		LINK="./linkgui.make"
+		if use ppc-macos; then
+			cp ../jar/macosx/sockets.c .
+		else
+			cp ../jar/linux/sockets.c .
+		fi
+	else
+		LINK="./link.make"
+	fi
+
+	COMPILE="./compile.make"
+	LIBRARY="./library.make"
+
+	# Need to make sure all of the appropriate config files are in place
+	# for the build.
+	# This should be easily customizable for other Fortran compilers, e.g. pg77.
+	if use ppc-macos; then
+		cp ../apple/gnu/* .
+	elif [ "${FORTRANC}" = "ifc" ]; then
+		cp ../linux/intel/* .
+	elif [ "${FORTRANC}" = "g77" ]; then
+		cp ../linux/gnu/* .
+	fi
+
+	cp ../make/* .
+
+	# Prep build scripts
+	if use X; then
+		sed -i \
+			-e "s:-O3:${CFLAGS}:" \
+			-e "s:gcc:$(tc-getCC):" \
+			${COMPGUI}
+		local JAVA_HOME=$(java-config --jdk-home)
+		local JAVA_LIB_PATH="${JAVA_HOME}/jre/lib/i386/client"
+		ln -s ${JAVA_LIB_PATH}/libjvm.so
+		sed -i -e "s:/local/java/j2sdk1.4.2_05:${JAVA_HOME}:g" ${COMPGUI}
+		sed -i -e "s:g77:${FORTRANC}:g" ${LINK}
+	fi
+	# Default to -O2 if FFLAGS is unset
+	sed -i -e "s:-O3 -ffast-math:${FFLAGS:- -O2}:" ${COMPILE}
+	sed -i -e "s:g77:${FORTRANC}:g" ${COMPILE}
+
+	# Prep executable script - the one packaged with the distro is b0rked
+	if use X; then
+		echo 'java -jar /usr/lib/tinker/ffe.jar -Djava.library.path=$(java-config -i blackdown-java3d-bin) -cp $(java-config -p blackdown-java3d-bin)' > tinker
+	fi
+
+	einfo "Compiling ..."
+	if use X; then
+		${COMPGUI} || die "GUI compile failed"
+	fi
+	${COMPILE} || die "compile failed"
+	einfo "Building libraries ..."
+	${LIBRARY} || die "library creation failed"
+	einfo "Linking ..."
+	${LINK} || die "link failed"
+}
+
+src_install() {
+	exeinto /usr/bin
+
+	dodoc \
+		${WORKDIR}/tinker/doc/*.txt \
+		${WORKDIR}/tinker/doc/release-4.2 \
+		${WORKDIR}/tinker/doc/*.pdf
+
+	if use X; then
+		if use ppc-macos; then
+			dolib.so ${WORKDIR}/tinker/jar/macosx/libffe.jnilib
+		else
+			dolib.so ${WORKDIR}/tinker/jar/linux/libffe.so
+		fi
+	fi
+
+	dolib.a libtinker.a
+
+	insinto /usr/lib/tinker
+	if use X; then
+		doins ${WORKDIR}/tinker/jar/ffe.jar
+	fi
+
+	for EXE in *.x; do
+		newexe ${EXE} ${EXE%.x}
+	done
+
+	if use X; then
+		doexe tinker
+	fi
+
+	docinto example
+	dodoc ${WORKDIR}/tinker/example/*
+	docinto test
+	dodoc ${WORKDIR}/tinker/test/*
+
+	doexe ${WORKDIR}/tinker/perl/mdavg
+
+	insinto /usr/share/tinker/params
+	doins ${WORKDIR}/tinker/params/*
+}
+
+pkg_postinst() {
+	einfo "Tinker binaries installed to ${ROOT}usr/bin."
+	einfo "Parameter files installed to ${ROOT}usr/share/tinker/params."
+	einfo "Call the Java X front-end, Force-Field Explorer, with 'tinker.'"
+	einfo "It doesn't seem to detect installed Java3D yet, fixes welcome."
+}