diff -urN coot-0.3.1.orig/analysis/Makefile.am coot-0.3.1/analysis/Makefile.am --- coot-0.3.1.orig/analysis/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/analysis/Makefile.am 2007-05-28 19:58:13.000000000 -0700 @@ -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) \ diff -urN coot-0.3.1.orig/coords/Makefile.am coot-0.3.1/coords/Makefile.am --- coot-0.3.1.orig/coords/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/coords/Makefile.am 2007-05-29 00:42:28.000000000 -0700 @@ -18,4 +18,6 @@ libcoot_coords_la_SOURCES = Bond_lines.cc Cartesian.cc cos-sin.cc \ 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 diff -urN coot-0.3.1.orig/coot-surface/Makefile.am coot-0.3.1/coot-surface/Makefile.am --- coot-0.3.1.orig/coot-surface/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/coot-surface/Makefile.am 2007-05-29 00:34:34.000000000 -0700 @@ -6,3 +6,4 @@ libcoot_surface_la_SOURCES = \ coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h +libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la diff -urN coot-0.3.1.orig/coot-utils/Makefile.am coot-0.3.1/coot-utils/Makefile.am --- coot-0.3.1.orig/coot-utils/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/coot-utils/Makefile.am 2007-05-28 20:08:39.000000000 -0700 @@ -20,9 +20,11 @@ # for pure coordinates (mmdb) things libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc +libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la # 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 @@ -32,21 +34,20 @@ # 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) + ./libcoot-utils.la testcootutils_SOURCES = test-utils.cc testcootutils_LDADD = \ ./libcoot-shelx.la \ ./libcoot-coord-utils.la \ ./libcoot-utils.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) + $(MMDB_LIBS) diff -urN coot-0.3.1.orig/geometry/Makefile.am coot-0.3.1/geometry/Makefile.am --- coot-0.3.1.orig/geometry/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/geometry/Makefile.am 2007-05-28 18:02:38.000000000 -0700 @@ -15,6 +15,9 @@ libcoot_geometry_a_sources = protein-geometry.cc protein-geometry-mmdb.cc libcoot_geometry_la_SOURCES = $(libcoot_geometry_a_sources) +libcoot_geometry_la_LIBADD = \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) # libcoot_geometry_la_CXXFLAGS = -g -O1 @@ -22,6 +25,4 @@ test_geometry_SOURCES = test-geometry.cc -test_geometry_LDADD = ./libcoot-geometry.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) +test_geometry_LDADD = ./libcoot-geometry.la diff -urN coot-0.3.1.orig/high-res/Makefile.am coot-0.3.1/high-res/Makefile.am --- coot-0.3.1.orig/high-res/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/high-res/Makefile.am 2007-05-28 19:52:12.000000000 -0700 @@ -20,13 +20,16 @@ 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) noinst_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 \ @@ -34,90 +37,73 @@ $(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 globularize_protein_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)/ccp4mg-utils/libccp4mg-utils.la \ $(top_builddir)/compat/libcoot-compat.la \ - $(GSL_LIBS) \ - $(CLIPPER_LIBS) - + $(GSL_LIBS) diff -urN coot-0.3.1.orig/ideal/Makefile.am coot-0.3.1/ideal/Makefile.am --- coot-0.3.1.orig/ideal/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/ideal/Makefile.am 2007-05-28 19:00:33.000000000 -0700 @@ -24,6 +24,12 @@ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) libcoot_ideal_la_SOURCES = simple-restraint.cc pepflip.cc regularize-minimol.cc +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 # bin_PROGRAMS = @@ -41,31 +47,20 @@ with_geometry_LDADD = \ ./libcoot-ideal.la \ $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.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 \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + $(CLIPPER_LIBS) $(MMDB_LIBS) with_map_LDADD = \ ./libcoot-ideal.la \ $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.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 \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + $(top_builddir)/coot-utils/libcoot-coord-utils.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) diff -urN coot-0.3.1.orig/ligand/Makefile.am coot-0.3.1/ligand/Makefile.am --- coot-0.3.1.orig/ligand/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/ligand/Makefile.am 2007-05-28 19:33:52.000000000 -0700 @@ -23,6 +23,16 @@ libcoot_ligand_la_SOURCES = ligand.cc ligand-extras.cc residue_by_phi_psi.cc \ wiggly-ligand.cc monomer-utils.cc dunbrack.cc chi-angles-autogen.cc \ chi-angles.cc helix-placement.cc rigid-body.cc ideal-rna.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)"' \ @@ -40,35 +50,17 @@ test_random_SOURCES = test-random.cc test_random_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)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ $(top_builddir)/coot-utils/libcoot-utils.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)/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)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ $(top_builddir)/compat/libcoot-compat.la \ $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) @@ -76,19 +68,10 @@ test_fffear_in_coot_LDADD = \ ./libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ $(top_builddir)/mini-mol/libcoot-mini-mol.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)/mini-mol/libcoot-mini-mol.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)/ccp4mg-utils/libccp4mg-utils.la \ $(top_builddir)/compat/libcoot-compat.la \ $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) @@ -100,33 +83,15 @@ findligand_real_LDADD = \ ./libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ $(top_builddir)/mini-mol/libcoot-mini-mol.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)/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)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/db-main/libcoot-db-main.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-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ $(top_builddir)/compat/libcoot-compat.la \ $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) @@ -147,17 +112,8 @@ testdunbrack_SOURCES = testdunbrack.cc testdunbrack_LDADD = ./libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ $(top_builddir)/mini-mol/libcoot-mini-mol.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 \ $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) # lib coot-coords depends on mmdb, even though Cartesian doesn't diff -urN coot-0.3.1.orig/Makefile.am coot-0.3.1/Makefile.am --- coot-0.3.1.orig/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/Makefile.am 2007-05-29 00:46:45.000000000 -0700 @@ -5,8 +5,8 @@ # 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 \ + skeleton ccp4mg-utils density-contour mini-mol coords angles \ + db-main geometry \ ideal ligand high-res build \ analysis sequence-view tw atom-utils src doc diff -urN coot-0.3.1.orig/mini-mol/Makefile.am coot-0.3.1/mini-mol/Makefile.am --- coot-0.3.1.orig/mini-mol/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/mini-mol/Makefile.am 2007-05-28 17:52:14.000000000 -0700 @@ -13,8 +13,9 @@ testminimol_SOURCES = testminimol.cc libcoot_mini_mol_la_SOURCES = mini-mol.cc mini-mol-utils.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) diff -urN coot-0.3.1.orig/tw/Makefile.am coot-0.3.1/tw/Makefile.am --- coot-0.3.1.orig/tw/Makefile.am 2007-05-28 17:08:04.000000000 -0700 +++ coot-0.3.1/tw/Makefile.am 2007-05-28 20:17:13.000000000 -0700 @@ -20,15 +20,15 @@ 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