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-rw-r--r--sci-chemistry/molrep/Manifest2
-rw-r--r--sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch61
-rw-r--r--sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch12
-rw-r--r--sci-chemistry/molrep/files/11.0.00-test.patch191
-rw-r--r--sci-chemistry/molrep/files/11.0.03-EOR.patch16
-rw-r--r--sci-chemistry/molrep/metadata.xml8
-rw-r--r--sci-chemistry/molrep/molrep-11.0.02.ebuild57
-rw-r--r--sci-chemistry/molrep/molrep-11.0.03-r1.ebuild59
8 files changed, 0 insertions, 406 deletions
diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest
deleted file mode 100644
index d91b8a448acd..000000000000
--- a/sci-chemistry/molrep/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST molrep-11.0.02.tar.gz 3594084 SHA256 6acb00bc91ad76027461ce6055eda72c8de34e5243449a31d5ede9e537e9adce SHA512 e22636e2d6b5558b66877960a64c0b990bb50d9e1b42016981b64e1311f83d5942fde7c1cd2dc8462ef1be814ce94ef566028079a7a091c9b3d7300f2d6ce03f WHIRLPOOL e507108a38be703e882ab3fd25e817c53c2d57b76fce578de3d308f10a85fce7a9febed39f748667a01c631b35787955d7d0290c944d4bfabfc936eab620daaf
-DIST molrep-11.0.03.tar.gz 3643087 SHA256 f4c317713b0dddf0ca883734f0bfe27600b50f8d4dd354ea8ae8245e21ce4392 SHA512 d9ff351e3754871d100c41aa9b8af48e3588768320f5ed92e536fac5e24114ca5df6497103d0b077455fc4e30e2d3d085aeb63854eb88dc8e74259b4e1683dc8 WHIRLPOOL b16e128e3ca7f1734ca79f70decab3e262d47b6a37c49e46c4c7d51f3fd8093cd3a0f20e487caeb5e9aa0a37a9fd050588cad3e99ad46e1866d05ff4a8ed0bb6
diff --git a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch
deleted file mode 100644
index d81ec793b510..000000000000
--- a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch
+++ /dev/null
@@ -1,61 +0,0 @@
---- src/makefile 2009-02-27 16:51:46.492890717 +0100
-+++ src/makefile.new 2009-02-27 16:52:18.295619642 +0100
-@@ -5,8 +5,8 @@
-
- BIN = $(MOLREP)/bin
-
--OBJS = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym.o molrep_unix.o
--OBJSL = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym.o molrep_unix.o
-+OBJS = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym_ccp4.o molrep_unix_ccp4.o
-+OBJSL = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym_ccp4.o molrep_unix_ccp4.o
-
-
- all: molrep
-@@ -19,31 +19,31 @@
- # -----------------------------
-
- molrep.o: molrep.f
-- $(MR_FORT) -c molrep.f
-+ $(MR_FORT) $(FFLAGS) -c molrep.f
- molrep1.o: molrep1.f
-- $(MR_FORT) -c molrep1.f
-+ $(MR_FORT) $(FFLAGS) -c molrep1.f
- molrep2.o: molrep2.f
-- $(MR_FORT) -c molrep2.f
-+ $(MR_FORT) $(FFLAGS) -c molrep2.f
- molrep3.o: molrep3.f
-- $(MR_FORT) -c molrep3.f
-+ $(MR_FORT) $(FFLAGS) -c molrep3.f
- molrep_prog.o: molrep_prog.f
-- $(MR_FORT) -c molrep_prog.f
-+ $(MR_FORT) $(FFLAGS) -c molrep_prog.f
- molrep_prog1.o: molrep_prog1.f
-- $(MR_FORT) -c molrep_prog1.f
-+ $(MR_FORT) $(FFLAGS) -c molrep_prog1.f
- molrep_prog2.o: molrep_prog2.f
-- $(MR_FORT) -c molrep_prog2.f
-+ $(MR_FORT) $(FFLAGS) -c molrep_prog2.f
- molrep_subr.o: molrep_subr.f
-- $(MR_FORT) -c molrep_subr.f
--molrep_sym.o: molrep_sym.f
-- $(MR_FORT) -c molrep_sym.f
-+ $(MR_FORT) $(FFLAGS) -c molrep_subr.f
-+molrep_sym_ccp4.o: molrep_sym.f
-+ $(MR_FORT) $(FFLAGS) -c molrep_sym_ccp4.f
- main_molrep_mtz.o: main_molrep_mtz.f molrep_version.fh molrep_keywords.fh
-- $(MR_FORT) -c main_molrep_mtz.f
--molrep_unix.o: molrep_unix.f
-- $(MR_FORT) -c molrep_unix.f
-+ $(MR_FORT) $(FFLAGS) -c main_molrep_mtz.f
-+molrep_unix_ccp4.o: molrep_unix.f
-+ $(MR_FORT) $(FFLAGS) -c molrep_unix_ccp4.f
- molrep_dummy.o: molrep_dummy.f
-- $(MR_FORT) -c molrep_dummy.f
-+ $(MR_FORT) $(FFLAGS) -c molrep_dummy.f
-
- molrep: $(OBJS)
-- $(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
-+ $(MR_FORT) $(FFLAGS) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
-
- # --------------------------------
-
diff --git a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch
deleted file mode 100644
index c18b9a1e3f0d..000000000000
--- a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/makefile b/src/makefile
-index 30d0de7..10dd68f 100755
---- a/src/makefile
-+++ b/src/makefile
-@@ -46,6 +46,6 @@ molrep_dummy.o: molrep_dummy.f
- $(MR_FORT) -c molrep_dummy.f
-
- molrep: $(OBJS)
-- $(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
-+ $(MR_FORT) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
-
- # --------------------------------
diff --git a/sci-chemistry/molrep/files/11.0.00-test.patch b/sci-chemistry/molrep/files/11.0.00-test.patch
deleted file mode 100644
index d90cfb8c7b35..000000000000
--- a/sci-chemistry/molrep/files/11.0.00-test.patch
+++ /dev/null
@@ -1,191 +0,0 @@
-diff --git a/molrep_check/em.bat b/molrep_check/em.bat
-index 2f0f992..96ddd75 100755
---- a/molrep_check/em.bat
-+++ b/molrep_check/em.bat
-@@ -8,6 +8,8 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
- # --------------------------------
- _NMON 6
- stop
-+echo $?
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 2. Atomic model --> EM map
-@@ -20,6 +22,7 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
- _NMON 6
- _prf y
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 3. Atomic model --> EM map
-@@ -36,6 +39,7 @@ _ncs 322
- _centre 0.500 0.490 0.490
- _angles 0.0 0.0 90.0
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- cp out/molrep.pdb hexamer.pdb
-@@ -52,6 +56,7 @@ $MR_TEST/molrep -mx hexamer.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
- # --------------------------------
- _DOM s
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 5. EM --> X-ray
-@@ -60,6 +65,7 @@ stop
- $MR_TEST/molrep -f ../em/p2.cif -m ../em/pel.map -po out/ -ps scr/ -i <<stop
- # --------------------------------
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 6. Placing the model to a particular orientation and position.
-@@ -72,4 +78,5 @@ $MR_TEST/molrep -f ../em/p2.cif -m ../em/pel.map -po out/ -ps scr/ -i <<stop
- _fun s
- _file_t ../em/tab
- stop
-+[[ $? ]] || exit 1
- #==========================================
-diff --git a/molrep_check/mr.bat b/molrep_check/mr.bat
-index 284a4cd..6e00695 100755
---- a/molrep_check/mr.bat
-+++ b/molrep_check/mr.bat
-@@ -10,6 +10,7 @@
- $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i <<stop
- # --------------------------------
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -26,6 +27,7 @@ _nmon 2
- _COMPL .5
- _SIM .7
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -46,6 +48,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -mx ../data/test_mod
- # --------------------------------
- _NP 3
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -67,6 +70,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -po out/ -ps scr/ -i
- _NMON 2
- _NP 3
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -85,6 +89,7 @@ _NPT 3
- _NPTD 3
- _DYAD D
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -103,6 +108,7 @@ _NP 3
- _NPT 10
- _NMR 3
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -118,6 +124,7 @@ _PRF Y
- _compl 1.
- _sim .2
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -136,6 +143,7 @@ _ph PH
- _fom FOM
- #
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- # 9. use sequence
-@@ -145,6 +153,7 @@ stop
- $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -s ../data/s100.seq -po out/ -ps scr/ -i <<stop
- # --------------------------------
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- # 10. Locked RF
-@@ -157,6 +166,7 @@ _lock y
- _file_tsrf ../data/srf.tab
- _nsrf 1
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- # 11. Multi-monomer search using NCS, SELF = 'A' means to compute Self RF and
-@@ -169,6 +179,7 @@ $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -m2 ../data/monomer.p
- _self a
- _nsrf 1
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- # 12. use pst
-@@ -179,6 +190,7 @@ $MR_TEST/molrep -f ../data/pst.mtz -m ../data/model_pst.pdb -po out/ -ps scr/ -i
- # --------------------------------
- #
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- # 13. space group check
-@@ -189,7 +201,8 @@ $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i
- # --------------------------------
- _sg all
- #
--stop
-+s[[ $? ]] || exit 1
-+top
- # ==========================================================
- #
- # 14. Example for finding HA position by MR solution.
-@@ -206,6 +219,7 @@ _SIGFD SIGFD3
- #
- _FUN d
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
- #
- # 15. Example for HA search by multi-copy search
-@@ -225,6 +239,7 @@ _diff h
- _dyad y
- _nmon 4
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
- #
- # 16. Example HA for search by translation function
-@@ -242,6 +257,7 @@ _FUN t
- _diff h
- _nmon 4
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
- #
- # 17. Example for Self RF for Heavy Atom structure in derivative.
-@@ -258,4 +274,5 @@ _SIGFD SIGFD3
- _FUN r
- _diff h
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
diff --git a/sci-chemistry/molrep/files/11.0.03-EOR.patch b/sci-chemistry/molrep/files/11.0.03-EOR.patch
deleted file mode 100644
index 430629e8dcc1..000000000000
--- a/sci-chemistry/molrep/files/11.0.03-EOR.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/molrep.f | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/src/molrep.f b/src/molrep.f
-index eac0cfc..94f74c6 100755
---- a/src/molrep.f
-+++ b/src/molrep.f
-@@ -1257,7 +1257,7 @@ C CHECK_DENS_FILE( 2 )
- LEN1 = 1
- IF(LEN.GT.60) LEN1 = LEN - 59
- WRITE(LINE,'(''Input MODEL_2(fixed)_file:'',A)')
-- * NAME2(LEN11:LEN)
-+ * NAME2(LEN1:LEN)
- CALL MSGDOC(MDoc,LINE)
-
- ENDIF
diff --git a/sci-chemistry/molrep/metadata.xml b/sci-chemistry/molrep/metadata.xml
deleted file mode 100644
index ae9ec7c5f6a4..000000000000
--- a/sci-chemistry/molrep/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-chemistry</herd>
- <maintainer>
- <email>jlec@gentoo.org</email>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/molrep/molrep-11.0.02.ebuild b/sci-chemistry/molrep/molrep-11.0.02.ebuild
deleted file mode 100644
index 51ff6cb26524..000000000000
--- a/sci-chemistry/molrep/molrep-11.0.02.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="molecular replacement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
- >=sci-libs/ccp4-libs-6.1.3
- sci-libs/mmdb
- virtual/lapack"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/11.0.00-respect-FLAGS.patch \
- "${FILESDIR}"/11.0.00-test.patch
-}
-
-src_compile() {
- cd "${S}"/src
- emake clean
- emake \
- MR_FORT="$(tc-getFC) ${FFLAGS}" \
- FFLAGS="${FFLAGS}" \
- LDFLAGS="${LDFLAGS}" \
- MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm"
-}
-
-src_test() {
- export MR_TEST="${S}/bin/"
- cd "${S}"/molrep_check/work
- mkdir out scr
- cp ../*.bat .
- bash em.bat || die
- bash mr.bat || die
-}
-
-src_install() {
- exeinto /usr/libexec/ccp4/bin/
- doexe bin/${PN}
- dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
- dodoc readme doc/${PN}.rtf
-}
diff --git a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
deleted file mode 100644
index 3373bbba6f97..000000000000
--- a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="molecular replacement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
- >=sci-libs/ccp4-libs-6.1.3
- sci-libs/mmdb
- virtual/lapack"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/11.0.00-respect-FLAGS.patch \
- "${FILESDIR}"/11.0.00-test.patch \
- "${FILESDIR}"/${PV}-EOR.patch
- [[ $(tc-getFC) =~ gfortran ]] && append-fflags -fno-second-underscore
-}
-
-src_compile() {
- cd "${S}"/src
- emake clean
- emake \
- MR_FORT="$(tc-getFC) ${FFLAGS}" \
- FFLAGS="${FFLAGS}" \
- LDFLAGS="${LDFLAGS}" \
- MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm"
-}
-
-src_test() {
- export MR_TEST="${S}/bin/"
- cd "${S}"/molrep_check/work
- mkdir out scr
- cp ../*.bat .
- bash em.bat || die
- bash mr.bat || die
-}
-
-src_install() {
- exeinto /usr/libexec/ccp4/bin/
- doexe bin/${PN}
- dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
- dodoc readme doc/${PN}.rtf
-}