From 05970f2776bdcc6a987f985fac3383de0bb584e2 Mon Sep 17 00:00:00 2001 From: "Justin Lecher (jlec)" Date: Sat, 3 Oct 2009 20:38:42 +0200 Subject: coot fixes as-needed patch not needed anymore Same for reduce sed rappermc patch added --- sci-chemistry/coot/files/9999-as-needed2.patch | 481 +++++++++++++++++++++++++ sci-chemistry/coot/files/9999-rappermc.patch | 15 + 2 files changed, 496 insertions(+) create mode 100644 sci-chemistry/coot/files/9999-as-needed2.patch create mode 100644 sci-chemistry/coot/files/9999-rappermc.patch (limited to 'sci-chemistry/coot/files') diff --git a/sci-chemistry/coot/files/9999-as-needed2.patch b/sci-chemistry/coot/files/9999-as-needed2.patch new file mode 100644 index 000000000..0cfce54dd --- /dev/null +++ b/sci-chemistry/coot/files/9999-as-needed2.patch @@ -0,0 +1,481 @@ +Index: mini-mol/Makefile.am +=================================================================== +--- mini-mol/Makefile.am (revision 2293) ++++ mini-mol/Makefile.am (working copy) +@@ -35,8 +35,9 @@ + testminimol_SOURCES = testminimol.cc + + libcoot_mini_mol_la_SOURCES = mini-mol.cc mini-mol-utils.cc atom-quads.cc ++libcoot_mini_mol_la_LIBADD = \ ++ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ ++ $(CLIPPER_LIBS) + + testminimol_LDADD = libcoot-mini-mol.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) ++ $(MMDB_LIBS) +Index: coords/Makefile.am +=================================================================== +--- coords/Makefile.am (revision 2293) ++++ coords/Makefile.am (working copy) +@@ -40,3 +40,7 @@ + mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \ + Bond_lines_ext.cc coot-close.cc + ++libcoot_coords_la_LIBADD = \ ++ $(top_builddir)/coot-utils/libcoot-shelx.la \ ++ $(top_builddir)/mini-mol/libcoot-mini-mol.la ++ +Index: ligand/Makefile.am +=================================================================== +--- ligand/Makefile.am (revision 2293) ++++ ligand/Makefile.am (working copy) +@@ -49,6 +49,17 @@ + torsion-general.cc rotamer-tables.cc primitive-chi-angles.cc dipole.cc\ + base-pairing.cc backrub-rotamer.cc + ++libcoot_ligand_la_LIBADD = \ ++ $(top_builddir)/ideal/libcoot-ideal.la \ ++ $(top_builddir)/coords/libcoot-coords.la \ ++ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ ++ $(top_builddir)/coot-utils/libcoot-map-utils.la \ ++ $(top_builddir)/db-main/libcoot-db-main.la \ ++ $(top_builddir)/coot-utils/libcoot-shelx.la \ ++ $(top_builddir)/geometry/libcoot-geometry.la \ ++ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ ++ $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la ++ + AM_CXXFLAGS = \ + -DPKGDATADIR='"$(pkgdatadir)"' \ + $(COOT_WINDOWS_CFLAGS) +@@ -68,7 +79,6 @@ + + test_random_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/coot-utils/libcoot-coord-extras.la \ + $(top_builddir)/coot-utils/libcoot-map-utils.la \ +@@ -85,31 +95,14 @@ + + test_ligand_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + + test_helix_placement_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ +@@ -120,18 +113,9 @@ + + test_fffear_in_coot_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coot-utils/libcoot-map-heavy.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + +@@ -143,23 +127,13 @@ + + findligand_real_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ +- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + + findwaters_real_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ +@@ -190,16 +164,7 @@ + testdunbrack_SOURCES = testdunbrack.cc + + testdunbrack_LDADD = ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + +Index: analysis/Makefile.am +=================================================================== +--- analysis/Makefile.am (revision 2293) ++++ analysis/Makefile.am (working copy) +@@ -9,6 +9,7 @@ + $(MMDB_CXXFLAGS) + + libcoot_analysis_la_SOURCES = bfkurt.cc ++libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la + + bin_PROGRAMS = bfactan + +@@ -16,7 +17,6 @@ + + bfactan_LDADD = \ + libcoot-analysis.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(CLIPPER_LIBS) \ +Index: skeleton/Makefile.am +=================================================================== +--- skeleton/Makefile.am (revision 2293) ++++ skeleton/Makefile.am (working copy) +@@ -39,8 +39,8 @@ + + + libcoot_skeleton_la_SOURCES = $(libskeleton_a_sources) ++libcoot_skeleton_la_LIBADD = ../atom-utils/libcoot-atomutils.la + +- + # bin_PROGRAMS = ncssearch test_various test_torsion test_theta_2 + + # ncssearch_SOURCES = ncs-search.cc ncs-search.h +Index: coot-surface/Makefile.am +=================================================================== +--- coot-surface/Makefile.am (revision 2293) ++++ coot-surface/Makefile.am (working copy) +@@ -25,3 +25,4 @@ + + libcoot_surface_la_SOURCES = \ + coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h ++libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la +Index: high-res/Makefile.am +=================================================================== +--- high-res/Makefile.am (revision 2293) ++++ high-res/Makefile.am (working copy) +@@ -39,13 +39,16 @@ + + libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \ + sequence-assignment.cc ++libcoot_high_res_la_LIBADD = \ ++ $(top_builddir)/ligand/libcoot-ligand.la \ ++ $(top_builddir)/coot-utils/libcoot-map-utils.la \ ++ $(CLIPPER_LIBS) $(MMDB_LIBS) + + check_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein + + testatomgraph_SOURCES = test-atom-graph.cc + + testatomgraph_LDADD = libcoot-high-res.la \ +- $(top_builddir)/ligand/libcoot-ligand.la \ + $(top_builddir)/db-main/libcoot-db-main.la \ + $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ +@@ -53,71 +56,60 @@ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coot-utils/libcoot-coord-extras.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ + $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ +- $(GSL_LIBS) \ +- $(CLIPPER_LIBS) ++ $(GSL_LIBS) + + testseqassignment_SOURCES = testseqassignment.cc + testseqassignment_LDADD = libcoot-high-res.la \ +- $(top_builddir)/ligand/libcoot-ligand.la \ + $(top_builddir)/db-main/libcoot-db-main.la \ + $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ +- $(GSL_LIBS) \ +- $(CLIPPER_LIBS) ++ $(GSL_LIBS) + + # tracehighres_LDFLAGS = -static + tracehighres_SOURCES = trace-high-res.cc + tracehighres_LDADD = libcoot-high-res.la \ +- $(top_builddir)/ligand/libcoot-ligand.la \ + $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/db-main/libcoot-db-main.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ +- $(GSL_LIBS) \ +- $(CLIPPER_LIBS) ++ $(GSL_LIBS) + + + testseqalign_SOURCES = testseqalign.cc + + # why do we need to link with all this (junk)? + testseqalign_LDADD = libcoot-high-res.la \ +- $(top_builddir)/ligand/libcoot-ligand.la \ + $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/db-main/libcoot-db-main.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ +- $(GSL_LIBS) \ +- $(CLIPPER_LIBS) ++ $(GSL_LIBS) + + + globularize_protein_SOURCES = globularize.cc +Index: cootaneer/Makefile.am +=================================================================== +--- cootaneer/Makefile.am (revision 2293) ++++ cootaneer/Makefile.am (working copy) +@@ -34,6 +34,7 @@ + buccaneer-sequence.cpp cootaneer-sequence.cpp \ + buccaneer-lib.h buccaneer-prot.h \ + buccaneer-sequence.h cootaneer-sequence.h ++libcootaneer_la_LIBADD = $(CLIPPER_LIBS) + + subpkgdatadir = $(pkgdatadir) + subpkgdata_DATA = cootaneer-llk-2.40.dat +Index: geometry/Makefile.am +=================================================================== +--- geometry/Makefile.am (revision 2293) ++++ geometry/Makefile.am (working copy) +@@ -35,6 +35,9 @@ + # -DHAVE_SYS_STDTYPES_H + + libcoot_geometry_la_SOURCES = protein-geometry.cc protein-geometry-mmdb.cc ++libcoot_geometry_la_LIBADD = \ ++ $(top_builddir)/coot-utils/libcoot-utils.la \ ++ $(CLIPPER_LIBS) $(MMDB_LIBS) + + # libcoot_geometry_la_CXXFLAGS = -g -O1 + +@@ -44,12 +47,7 @@ + + test_read_components_SOURCES = test-read-components.cc test-read-components.hh + +-test_geometry_LDADD = ./libcoot-geometry.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) ++test_geometry_LDADD = ./libcoot-geometry.la ++ ++test_read_components_LDADD = ./libcoot-geometry.la + +-test_read_components_LDADD = \ +- ./libcoot-geometry.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) +- +Index: ideal/Makefile.am +=================================================================== +--- ideal/Makefile.am (revision 2293) ++++ ideal/Makefile.am (working copy) +@@ -54,6 +54,12 @@ + + + libcoot_ideal_la_SOURCES = simple-restraint.cc pepflip.cc regularize-minimol.cc lograma.cpp ++libcoot_ideal_la_LIBADD = \ ++ $(top_builddir)/coot-utils/libcoot-utils.la \ ++ $(top_builddir)/mini-mol/libcoot-mini-mol.la \ ++ $(top_builddir)/coot-utils/libcoot-shelx.la \ ++ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ ++ $(GSL_LIBS) + + + noinst_PROGRAMS = test-indexing with-geometry with-map logramatest +@@ -75,12 +81,8 @@ + ./libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) ++ $(CLIPPER_LIBS) $(MMDB_LIBS) + + # add libcoot-map-utils for the debugging density_around_point function + with_map_LDADD = \ +@@ -88,22 +90,16 @@ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/compat/libcoot-compat.la \ +- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) ++ $(top_builddir)/compat/libcoot-compat.la \ ++ $(CLIPPER_LIBS) $(MMDB_LIBS) + + test_indexing_LDADD = \ + ./libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ +- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) ++ $(CLIPPER_LIBS) $(MMDB_LIBS) + + # Why do I need all these libraries to simply link a trivial test program? + # Badness.... +Index: tw/Makefile.am +=================================================================== +--- tw/Makefile.am (revision 2293) ++++ tw/Makefile.am (working copy) +@@ -39,14 +39,15 @@ + include_HEADERS = coot-tw.hh + + libcoot_tw_la_SOURCES = tw.cc ++libcoot_tw_la_LIBADD = \ ++ $(GTKCANVAS_LIBS) \ ++ @GTK_LIBS@ + + noinst_PROGRAMS = coot-tiddly + + coot_tiddly_SOURCES = tiddly.cc + +-coot_tiddly_LDADD = libcoot-tw.la \ +- $(GTKCANVAS_LIBS) \ +- @GTK_LIBS@ ++coot_tiddly_LDADD = libcoot-tw.la + + + # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao +Index: coot-utils/Makefile.am +=================================================================== +--- coot-utils/Makefile.am (revision 2293) ++++ coot-utils/Makefile.am (working copy) +@@ -49,6 +49,7 @@ + # for simple things: + libcoot_utils_la_SOURCES = coot-utils.cc coot-fasta.cc atomic-numbers.cc \ + gdk-keysyms.cc ++libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la + + # for pure coordinates (mmdb) things + libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc \ +@@ -56,6 +57,7 @@ + + # shelx + libcoot_shelx_la_SOURCES = coot-shelx-ins.cc ++libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la + + # for non-simple coordinates things + libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc \ +@@ -63,24 +65,23 @@ + + # for (map) things that need to link mmdb and clipper: + libcoot_map_utils_la_SOURCES = coot-map-utils.cc peak-search.cc trim.cc xmap-stats.cc ++libcoot_map_utils_la_LIBADD = $(CLIPPER_LIBS) + + # for map things that need mmdb, clipper, gsl and other things + libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc ++libcoot_map_heavy_la_LIBADD = $(GSL_LIBS) + + noinst_PROGRAMS = testshelxreader testcootutils + + testshelxreader_SOURCES = test-shelx-reader.cc + testshelxreader_LDADD = \ + ./libcoot-shelx.la \ +- ./libcoot-coord-utils.la \ + ./libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) ++ $(MMDB_LIBS) + + testcootutils_SOURCES = test-utils.cc + testcootutils_LDADD = \ + ./libcoot-shelx.la \ +- ./libcoot-coord-utils.la \ + ./libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) ++ $(MMDB_LIBS) + +- +Index: Makefile.am +=================================================================== +--- Makefile.am (revision 2293) ++++ Makefile.am (working copy) +@@ -25,10 +25,10 @@ + + # see configure.in for po intl + SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \ +- skeleton ccp4mg-utils density-contour coords angles \ +- mini-mol db-main geometry \ ++ atom-utils skeleton ccp4mg-utils density-contour mini-mol coords angles \ ++ db-main geometry \ + ideal ligand high-res build greg-tests python-tests \ +- analysis sequence-view tw atom-utils cootaneer src rama-data doc ++ analysis sequence-view tw cootaneer src rama-data doc + + # po, no po today. + diff --git a/sci-chemistry/coot/files/9999-rappermc.patch b/sci-chemistry/coot/files/9999-rappermc.patch new file mode 100644 index 000000000..1ecd9c529 --- /dev/null +++ b/sci-chemistry/coot/files/9999-rappermc.patch @@ -0,0 +1,15 @@ +Index: /data/svn-src/coot/trunk/python/a_rapper_gui.py +=================================================================== +--- /data/svn-src/coot/trunk/python/a_rapper_gui.py (revision 2398) ++++ /data/svn-src/coot/trunk/python/a_rapper_gui.py (working copy) +@@ -20,8 +20,8 @@ + home_dir = os.getenv('COOT_HOME') + else: + home_dir = os.getenv('HOME') +-rapper_dir = os.path.join(os.path.normpath(home_dir), "rappermc") +-rapper_command = "rapper" ++rapper_dir = "/usr/share/rapper" ++rapper_command = "rappermc" + + def rapper_process(): + #needed? -- cgit v1.2.3-65-gdbad