refmac splitted from ccp4 package

Package-Manager: portage-2.2_rc62/cvs/Linux x86_64

6 files changed, 205 insertions, 0 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
new file mode 100644
index 000000000000..15650f6a03bb
--- /dev/null
+++ b/sci-chemistry/refmac/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/refmac
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.1 2010/02/02 22:43:56 jlec Exp $
+
+*refmac-5.5.0109 (02 Feb 2010)
+
+  02 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/5.5-allow-dynamic-linking.patch, +files/5.5-test.log.patch,
+  +refmac-5.5.0109.ebuild, +metadata.xml:
+  refmac splitted from ccp4 package
+
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
new file mode 100644
index 000000000000..f8c1f0dc3cb3
--- /dev/null
+++ b/sci-chemistry/refmac/Manifest
@@ -0,0 +1,17 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 5.5-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a
+AUX 5.5-test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f01b SHA1 d026fdea6a487754f7e48ec24bcf4851a613b6d1 SHA256 d2c2a09f44e525dc255bc2ac93ca4194b24ca1fe58c31f0e3b5c32e439dfe2e7
+DIST refmac_5.5.0109.tar.gz 1326779 RMD160 3b603c13638407cceb907bd43ac0a971b587c116 SHA1 3cc35a55df71bac4de3eec9cf0e690e221ae3c86 SHA256 38d416c94e1f86a0676d48d7ddaeb4af272970b8cd6b084e70aa38481327c59e
+DIST test-framework.tar.gz 130933173 RMD160 7122539dc713615dca2ddaddfd8d152cd22624d0 SHA1 1d3e3019a67afb9b2346e919c859d402d3250fea SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605
+EBUILD refmac-5.5.0109.ebuild 1671 RMD160 a33b551a19ba91ffb854f60c284403b6f107766a SHA1 a7c8c77ccf1e03ac0fe3652965033749642d5891 SHA256 410dae6405894ed3d2d3cf6784a03e6cd5d40ec4943768968f6161468e3e3e1a
+MISC ChangeLog 445 RMD160 1cd1e894ea4e6a92aef5dd35a93038900dad0c49 SHA1 6ccfb0984bd50bb07fef701c27cbc598908ae6d6 SHA256 486c3286314f636d654c1c486589191ccaae92a6c07506427bf57a99a0aa161c
+MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAktoqrEACgkQgAnW8HDreRbpvgCfaH47B1YS+q1Aq5MFMnSPPeY5
+dNQAoMHWoRvwlh33FLnIyTT1oOtbpPuh
+=6QBn
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/refmac/files/5.5-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5-allow-dynamic-linking.patch
new file mode 100644
index 000000000000..415ba9d08cb0
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.5-allow-dynamic-linking.patch
@@ -0,0 +1,66 @@
+--- makefile_refmac.inc1.orig	2008-08-01 22:17:14.000000000 -0700
++++ makefile_refmac.inc1	2008-08-01 22:18:46.000000000 -0700
+@@ -69,9 +69,7 @@
+ bridge.o                    \
+ i0.o                        \
+ i1.o                        \
+-chbevl.o                    \
+-$(LLIBCIF)                  \
+-$(LLIBLAPACK)
++chbevl.o                    
+ #$(LLIBCCP)                  \
+ #crt0.o                      \
+ 
+@@ -95,8 +93,7 @@
+ emin.o                      \
+ libcheck_min.o              \
+ mol2_file.o                 \
+-sdf_files.o                 \
+-$(LLIBCCP)
++sdf_files.o                 
+ 
+ SUBM =                      \
+ main_makecif.o              \
+@@ -116,9 +113,7 @@
+ make_PDB.o                  \
+ makecif.o                   \
+ make_unix_ccp4.o            \
+-make_vdw.o                  \
+-$(LLIBCCP)                  \
+-$(LLIBCIF)
++make_vdw.o                  
+ 
+ SUBT =                      \
+ tlsgroups.o                 \
+@@ -142,9 +137,7 @@
+ inout_routines.o            \
+ errwrt_1.o                  \
+ linalgebra.o                \
+-subnumrec.o                 \
+-$(LLIBCCP)                  \
+-$(LLIBCIF)
++subnumrec.o                 
+ #--------------------------------------------------------------------------------
+ 
+ ed = echo 'g/^CMDW-5.0/s//        /@w@q@' | tr "@" "\012" | ed -s
+@@ -154,16 +147,16 @@
+ all:	refmac libcheck makecif
+ 
+ refmac:	$(SUBR)
+-	$(FC) $(FFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
+ 
+ libcheck:	$(SUBL)
+-	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP)
+ 
+ makecif:	$(SUBM)
+-	$(FC) $(FFLAGS) -o makecif${VERSION} $(SUBM)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o makecif${VERSION} $(SUBM) $(LLIBCCP) $(LLIBCIF)
+ 
+ tlsgroups:	$(SUBT)
+-	$(FC) $(FFLAGS) -o tlsgroups${VERSION} $(SUBT)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o tlsgroups${VERSION} $(SUBT) $(LLIBCCP) $(LLIBCIF)
+ 
+ clean:
+ 	/bin/rm *.o
diff --git a/sci-chemistry/refmac/files/5.5-test.log.patch b/sci-chemistry/refmac/files/5.5-test.log.patch
new file mode 100644
index 000000000000..61858be357a0
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.5-test.log.patch
@@ -0,0 +1,32 @@
+--- test-framework/refmac5/test_refmac5.py	2009-06-29 15:45:37.000000000 +0200
++++ test-framework/refmac5/test_refmac5.py.new	2009-06-29 15:48:05.000000000 +0200
+@@ -88,7 +88,8 @@
+              'make hydr no',
+              'labin IP=IMEAN SIGIP=SIGIMEAN FREE=FreeR_flag',
+              'labout FC=FC PHIC=PHIC'],
+-            working_directory = self.test_dir)
++            working_directory = self.test_dir,
++            log_file = 'test_twinned_refinement.log')
+ 
+         self.assertEqual(status, 0)
+ 
+@@ -123,7 +124,8 @@
+              'weight auto',
+              'ncyc 20',
+              'labout FC=FC PHIC=PHIC'],
+-            working_directory = self.test_dir)
++            working_directory = self.test_dir,
++            log_file = 'test_4_domain_tls.log')
+ 
+         self.assertEqual(status, 0)
+ 
+@@ -156,7 +158,8 @@
+              'anomalous form SE -9.9 3.9',
+              'anomalous wavelength 0.97966',
+              'labout FC=FC PHIC=PHIC'],
+-            working_directory = self.test_dir)
++            working_directory = self.test_dir,
++            log_file = 'test_sad_refinement.log')
+ 
+         self.assertEqual(status, 0)
+ 
diff --git a/sci-chemistry/refmac/metadata.xml b/sci-chemistry/refmac/metadata.xml
new file mode 100644
index 000000000000..a4525fd92784
--- /dev/null
+++ b/sci-chemistry/refmac/metadata.xml
@@ -0,0 +1,12 @@
+<?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>
+<maintainer>
+ <email>jlec@gentoo.org</email>
+  <name>Justin Lecher (jlec)</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/refmac/refmac-5.5.0109.ebuild b/sci-chemistry/refmac/refmac-5.5.0109.ebuild
new file mode 100644
index 000000000000..2455aa9aaaeb
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.5.0109.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0109.ebuild,v 1.1 2010/02/02 22:43:56 jlec Exp $
+
+EAPI="2"
+
+inherit fortran base toolchain-funcs versionator
+
+DESCRIPTION="Macromolecular crystallographic refinement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/"
+SRC_URI="${HOMEPAGE}data/refmac_stable/refmac_${PV}.tar.gz
+	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
+
+SLOT="0"
+LICENSE="ccp4"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="
+	sci-libs/ccp4-libs
+	sci-libs/mmdb
+	virtual/blas
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+PATCHES=(
+	"${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-allow-dynamic-linking.patch
+	)
+
+src_prepare() {
+	base_src_prepare
+	use test && epatch "${FILESDIR}"/test.log.patch
+}
+
+src_compile() {
+	emake \
+		FC=$(tc-getFC) \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		COPTIM="${CFLAGS}" \
+		FOPTIM="${FFLAGS:- -O2}" \
+		VERSION="" \
+		XFFLAGS="-fno-second-underscore" \
+		LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \
+		LLIBLAPACK="-llapack -lblas" \
+		|| die
+}
+
+src_test() {
+	einfo "Starting tests ..."
+	export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}"
+	export CCP4_TEST="${WORKDIR}"/test-framework
+	export CCP4_SCR="${T}"
+	ln -sf refmac "${S}"/refmac5
+	sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb
+	ccp4-run-thorough-tests -v test_refmac5 || die
+}
+
+src_install() {
+	for i in refmac libcheck makecif; do
+		dobin ${i} || die
+	done
+	dosym refmac /usr/bin/refmac5 || die
+	dodoc refmac_keywords.pdf bugs_and_features.pdf || die
+}