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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
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committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-chemistry/molrep/files | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-chemistry/molrep/files')
-rw-r--r-- | sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch | 61 | ||||
-rw-r--r-- | sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch | 12 | ||||
-rw-r--r-- | sci-chemistry/molrep/files/11.0.00-test.patch | 191 | ||||
-rw-r--r-- | sci-chemistry/molrep/files/11.0.03-EOR.patch | 16 |
4 files changed, 280 insertions, 0 deletions
diff --git a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch new file mode 100644 index 000000000000..d81ec793b510 --- /dev/null +++ b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch @@ -0,0 +1,61 @@ +--- 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 new file mode 100644 index 000000000000..c18b9a1e3f0d --- /dev/null +++ b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch @@ -0,0 +1,12 @@ +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 new file mode 100644 index 000000000000..d90cfb8c7b35 --- /dev/null +++ b/sci-chemistry/molrep/files/11.0.00-test.patch @@ -0,0 +1,191 @@ +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 new file mode 100644 index 000000000000..430629e8dcc1 --- /dev/null +++ b/sci-chemistry/molrep/files/11.0.03-EOR.patch @@ -0,0 +1,16 @@ + 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 |