New addition, unbundled from sci-chemistry/refmac

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

5 files changed, 134 insertions, 0 deletions

diff --git a/sci-chemistry/makecif/ChangeLog b/sci-chemistry/makecif/ChangeLog
new file mode 100644
index 000000000000..665055a12388
--- /dev/null
+++ b/sci-chemistry/makecif/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/makecif
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/makecif/ChangeLog,v 1.1 2010/06/15 08:16:52 jlec Exp $
+
+*makecif-5.6.6 (15 Jun 2010)
+
+  15 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/5.6.6-makefile.patch,
+  +makecif-5.6.6.ebuild, +metadata.xml:
+  New addition, unbundled from sci-chemistry/refmac
+
+
diff --git a/sci-chemistry/makecif/Manifest b/sci-chemistry/makecif/Manifest
new file mode 100644
index 000000000000..eeaaa4ab781a
--- /dev/null
+++ b/sci-chemistry/makecif/Manifest
@@ -0,0 +1,15 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 5.6.6-makefile.patch 3713 RMD160 9ea6ed99a99132dee094148162ddbf6a66718d69 SHA1 3b7455469a573033646b1cebcaab2b24b7c23659 SHA256 a0ceb0a8e68c58c3bb568f7700a9594956f4dae6f63920d0ce812ef1650abf43
+DIST makecif-5.6.6.tar.gz 3797710 RMD160 f5b914ccf135e8adf2867d6fd19113d7f2808fad SHA1 3ffa1543980cc8babfcf08786a46ef8850cb42d6 SHA256 fdcc1bee70583da3161f0d46eb792d965c04f08f0ad3033f730486550e859d1f
+EBUILD makecif-5.6.6.ebuild 842 RMD160 1771dfb1a144fc98a4444b6b9ef4d57d7bf776ad SHA1 dfc959e91684e8899060cb817dfb8dd45b09d716 SHA256 7a8e3f5db088f6706a68a0754b992110a3b359766c7eea2e62ae0e371ba476fc
+MISC ChangeLog 413 RMD160 f142ae9bc2c20c6e22698c07b6c1a39a0d36409b SHA1 96140f7c187f9ce45e6adf701bce8a576d30687f SHA256 37f8b00ce2356b1b5faaa142db9d0978ec0321edc8eca33c4bd433b0d262d8b9
+MISC metadata.xml 446 RMD160 40e5c82b5b17d257029c66d4a72fbac1aac28aed SHA1 5fd98c72f667351bd74570f3c04515d613b9fcdc SHA256 afd71c5775de3828022164f8fbc6d39f111013fa57f89132528d8f0c21714ae5
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.15 (GNU/Linux)
+
+iEYEARECAAYFAkwXNwMACgkQgAnW8HDreRYJPwCgyb5XxGtVjdZ/KKFc4j4kZToo
+ZPAAn3pLIpE0LqiU5NLzQ5UwMnQ6gd4L
+=Evq/
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/makecif/files/5.6.6-makefile.patch b/sci-chemistry/makecif/files/5.6.6-makefile.patch
new file mode 100644
index 000000000000..186abb92b7d8
--- /dev/null
+++ b/sci-chemistry/makecif/files/5.6.6-makefile.patch
@@ -0,0 +1,49 @@
+diff --git a/src/makefile b/src/makefile
+index 6c8264a..acdec20 100755
+--- a/src/makefile
++++ b/src/makefile
+@@ -22,6 +22,8 @@ MAKEDIC = $(MAKECIF)/dic/
+ # setenv BLANC_FORT "f77  -O1" 
+ #
+ 
++all: makecif_all libcheck_all modcheck_all emin_all
++
+ clean:
+ 	rm -f temp_makecif_path.fh
+ 	rm -f ../bin/*
+@@ -118,7 +120,7 @@ makecif.o: makecif.f  lib_com.fh crd_com.fh
+ 	$(BLANC_FORT) -c makecif.f  
+ 
+ mkcif: main_makecif.o make_lib11.o make_lib12.o make_lib2.o make_vdw.o make_CIF.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_PDB.o makecif.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o 
+-	$(BLANC_FORT) -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o  libcheck.o 
++	$(BLANC_FORT) ${LDFLAGS} -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o  libcheck.o 
+ # -------------
+ libcheck.o: libcheck.f  lib_com.fh crd_com.fh 
+ 	$(BLANC_FORT) -c libcheck.f
+@@ -130,7 +132,7 @@ main_libcheck.o: main_libcheck.f libcheck_version.fh
+ 	$(BLANC_FORT) -c main_libcheck.f
+ 
+ lbcheck: main_libcheck.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o libcheck.o  make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_unix.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o
+-	$(BLANC_FORT) -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o  mol2_file.o sdf_files.o 
++	$(BLANC_FORT) ${LDFLAGS} -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o  mol2_file.o sdf_files.o 
+ # ------------
+ 
+ emin.o: emin.f crd_com.fh atom_com.fh
+@@ -143,7 +145,7 @@ main_emin.o: main_emin.f
+ 	$(BLANC_FORT) -c main_emin.f 
+ 
+ emn: main_emin.o emin_new.o angle_subr.o make_unix.o make_CIF.o make_subr_2.o make_subr.o
+-	$(BLANC_FORT) -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o
++	$(BLANC_FORT) ${LDFLAGS} -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o
+ 
+ # -------------
+ 
+@@ -155,7 +157,7 @@ main_modcheck.o: main_modcheck.f
+ 	$(BLANC_FORT) -c main_modcheck.f 
+ 
+ mdcheck: main_modcheck.o modcheck.o mod_subr.o make_CIF.o make_unix.o make_subr_2.o make_subr.o 
+-	$(BLANC_FORT) -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o  
++	$(BLANC_FORT) ${LDFLAGS} -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o  
+ 
+ 
+ # ======================================
diff --git a/sci-chemistry/makecif/makecif-5.6.6.ebuild b/sci-chemistry/makecif/makecif-5.6.6.ebuild
new file mode 100644
index 000000000000..fe041c47c902
--- /dev/null
+++ b/sci-chemistry/makecif/makecif-5.6.6.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/makecif/makecif-5.6.6.ebuild,v 1.1 2010/06/15 08:16:52 jlec Exp $
+
+EAPI="3"
+
+FORTRANC="ifc gfortran"
+
+inherit eutils fortran
+
+DESCRIPTION="PDB --> CIF convertor"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html"
+SRC_URI="mirror://gentoo/${P}.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="ccp4"
+IUSE=""
+
+S="${WORKDIR}"/${PN}
+
+DEPEND=""
+RDEPEND="
+	sci-libs/monomer-db
+	!<sci-chemistry/refmac-5.5.0110-r1"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-makefile.patch
+}
+
+src_compile() {
+	cd src && emake clean
+	emake \
+		BLANC_FORT="$(tc-getFC) ${FFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		|| die
+}
+
+src_install() {
+	dobin bin/* || die
+	dodoc readme || die
+}
diff --git a/sci-chemistry/makecif/metadata.xml b/sci-chemistry/makecif/metadata.xml
new file mode 100644
index 000000000000..b8cee3034ed8
--- /dev/null
+++ b/sci-chemistry/makecif/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+<maintainer>
+  <email>jlec@gentoo.org</email>
+</maintainer>
+<longdescription>
+PDB --> CIF convertor
+check and create correct structure description
+create the list of restraints
+create dictionary description of new ligands
+rebuild missing atoms
+create tree like structure
+also the part of REFMAC
+can use additional user's dictionary
+</longdescription>
+</pkgmetadata>