diff options
Diffstat (limited to 'sci-chemistry/balbes/files')
| -rw-r--r-- | sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch | 107 | ||||
| -rw-r--r-- | sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch | 28 |
2 files changed, 0 insertions, 135 deletions
diff --git a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch b/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch deleted file mode 100644 index da17240642d7..000000000000 --- a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch +++ /dev/null @@ -1,107 +0,0 @@ -diff --git a/makefile b/makefile -index baaceb5..85a7baf 100755 ---- a/makefile -+++ b/makefile -@@ -70,6 +70,15 @@ OBJDB_G = get_pdb_list.o - - #OBJDB_Z = blanc2mtz.o libutils.o - -+# incomplete targets: -+# dimer_search_db domain_search_db domain align3 -+all: search_db get_structure_db manage_db search_dm dom2ch \ -+ save_si get_pdb_list_db update_db \ -+ update_dom_db bl2mtz check_file_db fobs2cif sol_check \ -+ get_trns p2s check_cell alt_sg \ -+ align cell_list create_bins \ -+ get_pdb_list_db get_ch get_nm get_mod -+ - search_db: sdb_l - - get_structure_db: tdb_l -@@ -201,58 +210,58 @@ save_seg_id.o: save_seg_id.f - $(BLANC_FORT) -c save_seg_id.f - - sdb_l: $(OBJDB_S) -- $(BLANC_FORT) -o ../bin/search_DB $(OBJDB_S) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DB $(OBJDB_S) - tdb_l: $(OBJDB_T) -- $(BLANC_FORT) -o ../bin/get_structure_DB $(OBJDB_T) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_structure_DB $(OBJDB_T) - mdb_l: $(OBJDB_M) -- $(BLANC_FORT) -o ../bin/manage_DB $(OBJDB_M) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/manage_DB $(OBJDB_M) - mdm_l: $(OBJDB_MD) -- $(BLANC_FORT) -o ../bin/search_DOM $(OBJDB_MD) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DOM $(OBJDB_MD) - d2c_l: $(OBJDB_A) -- $(BLANC_FORT) -o ../bin/domain2chain $(OBJDB_A) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain2chain $(OBJDB_A) - upd_l: $(OBJDB_U) -- $(BLANC_FORT) -o ../bin/update_DB $(OBJDB_U) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_DB $(OBJDB_U) - dom_l: $(OBJDB_V) -- $(BLANC_FORT) -o ../bin/update_domain_DB $(OBJDB_V) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_domain_DB $(OBJDB_V) - ddb_l: $(OBJDB_D) -- $(BLANC_FORT) -o ../bin/dimer_search $(OBJDB_D) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/dimer_search $(OBJDB_D) - dmdb_l: $(OBJDB_N) -- $(BLANC_FORT) -o ../bin/domain_search $(OBJDB_N) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain_search $(OBJDB_N) - gdb_l: $(OBJDB_G) -- $(BLANC_FORT) -o ../bin/get_pdb_list $(OBJDB_G) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_pdb_list $(OBJDB_G) - b2m_l: blanc2mtz.o libutils.o -- $(BLANC_FORT) -o ../bin/blanc2mtz blanc2mtz.o libutils.o $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/blanc2mtz blanc2mtz.o libutils.o -lccp4f -lccp4c - f2c_l: f2cif.o libutils.o -- $(BLANC_FORT) -o ../bin/f2cif f2cif.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/f2cif f2cif.o libutils.o - chf_l: check_file_DB.o libutils.o -- $(BLANC_FORT) -o ../bin/check_file_DB check_file_DB.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_file_DB check_file_DB.o libutils.o - chc_l: check_cell_sg.o libutils.o -- $(BLANC_FORT) -o ../bin/check_cell_sg check_cell_sg.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_cell_sg check_cell_sg.o libutils.o - asl_l: alt_sg_list.o libutils.o -- $(BLANC_FORT) -o ../bin/alt_sg_list alt_sg_list.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/alt_sg_list alt_sg_list.o libutils.o - sc_l: $(OBJDB_C) -- $(BLANC_FORT) -o ../bin/solution_check $(OBJDB_C) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/solution_check $(OBJDB_C) - gt_l: $(OBJDB_R) -- $(BLANC_FORT) -o ../bin/get_trans $(OBJDB_R) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_trans $(OBJDB_R) - dmn_l: domain.o libutils.o -- $(BLANC_FORT) -o ../bin/domain domain.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain domain.o libutils.o - pack: pdb_pack.o libutils.o -- $(BLANC_FORT) -o ../bin/pdb_pack pdb_pack.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb_pack pdb_pack.o libutils.o - p2s_l: $(OBJDB_P) -- $(BLANC_FORT) -o ../bin/pdb2s $(OBJDB_P) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb2s $(OBJDB_P) - aln_l: align_DB.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/align_DB align_DB.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB align_DB.o DB_subr.o libutils.o - aln3_l: align_DB_new.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o - cell_l: create_cell_list.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o - getch_l: get_chain.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/get_chain get_chain.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_chain get_chain.o DB_subr.o libutils.o - getnmr_l: get_nmr.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o - getmod_l: get_model.o libutils.o -- $(BLANC_FORT) -o ../bin/get_model get_model.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_model get_model.o libutils.o - crb_l: create_binaries.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o - save_si_l: save_seg_id.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o diff --git a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch deleted file mode 100644 index d29b0b6a9eb2..000000000000 --- a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch +++ /dev/null @@ -1,28 +0,0 @@ -diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py ---- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:54:36.000000000 +0900 -+++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:57:02.000000000 +0900 -@@ -24,8 +24,8 @@ class ParsedAbbreviatedAbsoluteLocationP - self._rel = rel - nt = ParsedNodeTest.ParsedNodeTest('node', '') - ppl = ParsedPredicateList.ParsedPredicateList([]) -- as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') -- self._step = ParsedStep.ParsedStep(as, nt, ppl) -+ as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') -+ self._step = ParsedStep.ParsedStep(as_, nt, ppl) - return - - def evaluate(self, context): -diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py ---- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:54:36.000000000 +0900 -+++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:58:58.000000000 +0900 -@@ -28,8 +28,8 @@ class ParsedAbbreviatedRelativeLocationP - self._right = right - nt = ParsedNodeTest.ParsedNodeTest('node','') - ppl = ParsedPredicateList.ParsedPredicateList([]) -- as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') -- self._middle = ParsedStep.ParsedStep(as, nt, ppl) -+ as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') -+ self._middle = ParsedStep.ParsedStep(as_, nt, ppl) - - def evaluate(self, context): - res = [] |