Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci

7 files changed, 69 insertions, 8 deletions

diff --git a/sci-chemistry/jligand/ChangeLog b/sci-chemistry/jligand/ChangeLog
new file mode 100644
index 000000000..c3d064bc1
--- /dev/null
+++ b/sci-chemistry/jligand/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/jligand
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*jligand-0.1 (26 Jul 2009)
+
+  26 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +jligand-0.1.ebuild, +metadata.xml:
+  new ebuild, written by me
+
diff --git a/sci-chemistry/jligand/Manifest b/sci-chemistry/jligand/Manifest
new file mode 100644
index 000000000..7e027ca5c
--- /dev/null
+++ b/sci-chemistry/jligand/Manifest
@@ -0,0 +1,4 @@
+DIST JLigand_0.1_Source.tar 583680 RMD160 be71bdaeb1991c96c05d6864427606dbcad5c2eb SHA1 1805e737124c9fc483279a1aa37b0612a9e8d062 SHA256 12578dbe2212a6cc12ede15beecb6e20c5ba28a467883a881f700b908f493de6
+EBUILD jligand-0.1.ebuild 821 RMD160 40a46b6b0b0d62b13a0cf9701ba30c1a24c88928 SHA1 a3aa4df92da4bed163b8711f2c7cfb96ce2b2465 SHA256 8d07a9a1369b3ae0d973d2ea9b56614e414f33975e5cdd81c38d24af0bf39c75
+MISC ChangeLog 274 RMD160 191da1077cab8086237bfbcb96e7d0fcd313a859 SHA1 7152a54527147adc6f35fbb0fec26a1cc70f7912 SHA256 a4c165f42617e7619b9eef2c3ae1266b6a4f465b41cd52497917c067bc4d4a49
+MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/jligand/jligand-0.1.ebuild b/sci-chemistry/jligand/jligand-0.1.ebuild
new file mode 100644
index 000000000..92d19bb3e
--- /dev/null
+++ b/sci-chemistry/jligand/jligand-0.1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit java-pkg-2 java-ant-2
+
+MY_PN="JLigand"
+
+DESCRIPTION="a Java interface which allows links descriptions to be created"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html"
+SRC_URI="http://www.ysbl.york.ac.uk/~pyoung/${MY_PN}/${MY_PN}_${PV}_Source.tar"
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND=">=virtual/jre-1.5
+	sci-chemistry/refmac
+	sci-libs/monomer-db"
+DEPEND=">=virtual/jdk-1.5"
+
+S="${WORKDIR}"/${MY_PN}
+
+src_install() {
+	java-pkg_dojar dist/${MY_PN}.jar
+	java-pkg_dolauncher ${PN} \
+		--main uk.ac.york.ysbl.JLigand \
+		--jar ${MY_PN}.jar \
+		--pkg_args "/usr/share/jligand /usr/share/ccp4/data/monomers /usr/bin/libcheck /usr/bin/refmac"
+}
diff --git a/sci-chemistry/jligand/metadata.xml b/sci-chemistry/jligand/metadata.xml
new file mode 100644
index 000000000..efb490d78
--- /dev/null
+++ b/sci-chemistry/jligand/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>
diff --git a/sci-chemistry/tinker/ChangeLog b/sci-chemistry/tinker/ChangeLog
index f45afcb07..ab0c5cae7 100644
--- a/sci-chemistry/tinker/ChangeLog
+++ b/sci-chemistry/tinker/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/ChangeLog,v 1.10 2008/11/06 23:53:23 dberkholz Exp $
 
+*tinker-5.0 (26 Jul 2009)
+
+  26 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -tinker-4.2-r2.ebuild, +tinker-5.0.ebuild:
+  version bump
+
   24 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   tinker-4.2-r2.ebuild:
   ~amd64 added see bug 263006
diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
index 558cb6b85..d1e0331d8 100644
--- a/sci-chemistry/tinker/Manifest
+++ b/sci-chemistry/tinker/Manifest
@@ -1,4 +1,4 @@
 DIST tinker.tar.gz 8177555 RMD160 95f904f03f6a1767bbf73b00f326d19a164b7a1c SHA1 b42c5763958869894ee91fcd2ed4c5e03d8c1e5d SHA256 ad0cc9782dabdb0cce490fe26508761a36078e741f019090cbaa3e6cacf71055
-EBUILD tinker-4.2-r2.ebuild 1845 RMD160 f2f6aea11bd427d0d6a2e8ac55c99955c2973cb7 SHA1 defb9d66d120c1f3556a4223b64a32069c3fde40 SHA256 0af0b95c61c33ddb64de255911e78d88c7c4710e9825b43c61efb8d39a4f6cdb
-MISC ChangeLog 2225 RMD160 d9bd5aa28ebc0d496c2b24dde56a8d65e4b8f0ec SHA1 d7b97aa53272cac7ba4f06f8d9908e7d87178dd6 SHA256 07b64eeb84df091b330ed343329753e47067b6045a24ceeb1bc80d8a194524b8
+EBUILD tinker-5.0.ebuild 1845 RMD160 9099d5e35f26521a1daced4e2c420d749f51cb14 SHA1 aa2953ee8745008a6a999687b49603e09ca8904b SHA256 22c6bb14b4a9b2992ac690afea8b0f251aabd52a809bbb210d570c72ff999e97
+MISC ChangeLog 2370 RMD160 8b5d727c2720d348f6f00ff0846c505b71746e27 SHA1 f34a340ee01f2a597b8e17acc2f2da39c9d85dcb SHA256 5395df8360f6dd6700e0bc1c8957a5f42c663be966c6319c6e86e7f8bf1a88b0
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/tinker/tinker-4.2-r2.ebuild b/sci-chemistry/tinker/tinker-5.0.ebuild
index 32ecab9b7..84f989021 100644
--- a/sci-chemistry/tinker/tinker-4.2-r2.ebuild
+++ b/sci-chemistry/tinker/tinker-5.0.ebuild
@@ -4,7 +4,7 @@
 
 inherit fortran toolchain-funcs
 
-FORTRAN="g77 gfortran ifc"
+FORTRAN="gfortran ifc"
 
 DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM."
 HOMEPAGE="http://dasher.wustl.edu/tinker/"
@@ -27,17 +27,17 @@ src_compile() {
 	if [[ ${FORTRANC} == "ifc" ]]; then
 		cp ../linux/intel/* .
 	else
-		cp ../linux/gnu/* .
+		cp ../linux/gfortran/* .
 	fi
 
 	cp ../make/* .
 
 	# Prep build scripts
-	sed -i -e "s:g77:${FORTRANC} ${LDFLAGS}:g" ${LINK}
+	sed -i -e "s:gfortran:${FORTRANC} ${LDFLAGS}:g" ${LINK}
 
 	# Default to -O2 if FFLAGS is unset
-	sed -i -e "s:-O3 -ffast-math:${FFLAGS:- -O2}:" ${COMPILE}
-	sed -i -e "s:g77:${FORTRANC}:g" ${COMPILE}
+	sed -i -e "s:-O:${FFLAGS:- -O2}:" ${COMPILE}
+	sed -i -e "s:gfortran:${FORTRANC}:g" ${COMPILE}
 
 	einfo "Compiling ..."
 	${COMPILE} || die "compile failed"
@@ -52,7 +52,7 @@ src_install() {
 
 	dodoc \
 		"${WORKDIR}"/tinker/doc/*.txt \
-		"${WORKDIR}"/tinker/doc/release-4.2 \
+		"${WORKDIR}"/tinker/doc/release-${PV} \
 		"${WORKDIR}"/tinker/doc/*.pdf
 
 	dolib.a libtinker.a