diff options
Diffstat (limited to 'sci-chemistry/coot/files/9999-pc.patch')
| -rw-r--r-- | sci-chemistry/coot/files/9999-pc.patch | 1047 |
1 files changed, 0 insertions, 1047 deletions
diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch deleted file mode 100644 index 32d08e119..000000000 --- a/sci-chemistry/coot/files/9999-pc.patch +++ /dev/null @@ -1,1047 +0,0 @@ -diff --git a/ChangeLog b/ChangeLog -index 46f6362..fd3fd9a 100644 ---- a/ChangeLog -+++ b/ChangeLog -@@ -1963,7 +1963,7 @@ - 2005-01-29 Paul Emsley <paulemsley@ysbl.york.ac.uk> - - * macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): use $with_ssmlib_prefix in -- MMDBSSM_CXXFLAGS [Oops]. Hopefully fixes problems spotted by Joel -+ MMDBSSM_CFLAGS [Oops]. Hopefully fixes problems spotted by Joel - Bard and Joseph Toth. - - * src/graphics-info-pick.cc: (symmetry_atom_pick): tried to add -@@ -2256,14 +2256,14 @@ - - 2004-11-20 Paul Emsley <paulemsley@ysbl.york.ac.uk> - -- * coords/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS [for -+ * coords/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS [for - coot-close.cc usage]. - - 2004-11-19 Paul Emsley <paulemsley@ysbl.york.ac.uk> - -- * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CXXFLAGS -+ * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CFLAGS - -- * analysis/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS -+ * analysis/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS - - 2004-11-16 Paul Emsley <emsley@localhost> - -@@ -2273,7 +2273,7 @@ - - 2004-11-15 Paul Emsley <emsley@localhost> - -- * coot-utils/Makefile.am: add MMDB_CXXFLAGS to INCLUDE [thanks -+ * coot-utils/Makefile.am: add MMDB_CFLAGS to INCLUDE [thanks - Joseph Toth]. - - * surface/CXXSphereNode.h: removed the ; again! -diff --git a/analysis/Makefile.am b/analysis/Makefile.am -index 8a873dc..ef4a9cf 100644 ---- a/analysis/Makefile.am -+++ b/analysis/Makefile.am -@@ -8,8 +8,8 @@ pkgincludedir = $(includedir)/coot/analysis - - INCLUDES = \ - -I$(top_srcdir) \ -- $(CLIPPER_CXXFLAGS) \ -- $(MMDB_CXXFLAGS) -+ $(CLIPPER_CFLAGS) \ -+ $(MMDB_CFLAGS) - - libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc kolmogorov.hh kolmogorov.cc cablam.hh cablam.cc - -diff --git a/angles/Makefile.am b/angles/Makefile.am -index b89276d..935ce06 100644 ---- a/angles/Makefile.am -+++ b/angles/Makefile.am -@@ -7,7 +7,7 @@ EXTRA_DIST = \ - pkginclude_HEADERS = AngleInfo.h ncube.h wrapped-ncube.h - pkgincludedir = $(includedir)/coot/angles - --INCLUDES = $(CLIPPER_CXXFLAGS) -+INCLUDES = $(CLIPPER_CFLAGS) - - libcoot_AngleInfo_a_sources = AngleInfo.cc AngleInfo.h \ - AngleInfo-angle-torsions-autogen.cc AngleInfo-theta_2-autogen.cc -diff --git a/auxil/catcheck/Makefile.am b/auxil/catcheck/Makefile.am -index 41e1766..69e6091 100644 ---- a/auxil/catcheck/Makefile.am -+++ b/auxil/catcheck/Makefile.am -@@ -1,7 +1,7 @@ - - EXTRA_DIST = Makefile.simple - --INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) -+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) - - check_PROGRAMS = catcheck - -diff --git a/auxil/catcheck/Makefile.simple b/auxil/catcheck/Makefile.simple -index 5157398..0e25fb2 100644 ---- a/auxil/catcheck/Makefile.simple -+++ b/auxil/catcheck/Makefile.simple -@@ -1,17 +1,17 @@ - --# CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include -+# CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include - - - BASE = /home/paule/autobuild/Linux-kalypso-pre-release --CLIPPER_CXXFLAGS = -I$(BASE)/include --MMDB_CXXFLAGS = -I$(BASE)/include/mmdb -+CLIPPER_CFLAGS = -I$(BASE)/include -+MMDB_CFLAGS = -I$(BASE)/include/mmdb - - CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \ - -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \ - -lclipper-core -lccp4c -L$(BASE)/lib \ - -L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm - --INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) - LDLIBS = $(CLIPPER_LIBS) - - catcheck: catcheck.cc catcheck.hh -diff --git a/auxil/rama/Makefile.am b/auxil/rama/Makefile.am -index cdbb54e..12c6731 100644 ---- a/auxil/rama/Makefile.am -+++ b/auxil/rama/Makefile.am -@@ -1,7 +1,7 @@ - - EXTRA_DIST = Makefile.simple fit-rama.scm run.scm test-arr.scm - --INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) - - - check_PROGRAMS = rama-data rama-doughnut -diff --git a/auxil/rama/Makefile.simple b/auxil/rama/Makefile.simple -index 10fe22e..715a270 100644 ---- a/auxil/rama/Makefile.simple -+++ b/auxil/rama/Makefile.simple -@@ -1,12 +1,12 @@ - --CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include -+CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include - - CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \ - -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \ - -lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \ - -L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm - --INCLUDES = $(CLIPPER_CXXFLAGS) -+INCLUDES = $(CLIPPER_CFLAGS) - LDLIBS = $(CLIPPER_LIBS) - - rama-data: rama-data.cc -diff --git a/auxil/sec-str/Makefile.am b/auxil/sec-str/Makefile.am -index 81f79e8..bfef73a 100644 ---- a/auxil/sec-str/Makefile.am -+++ b/auxil/sec-str/Makefile.am -@@ -1,6 +1,6 @@ - - EXTRA_DIST = Makefile.simple sec-str-dist-check.cc sec-str-dist-check.hh --INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) -+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) - - #check_PROGRAMS = sec-str-dist-check - -diff --git a/auxil/sec-str/Makefile.simple b/auxil/sec-str/Makefile.simple -index eb6db20..8b22930 100644 ---- a/auxil/sec-str/Makefile.simple -+++ b/auxil/sec-str/Makefile.simple -@@ -1,27 +1,27 @@ - --#CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include -+#CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include - - #CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \ - # -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \ - # -lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \ - # -L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm - --#INCLUDES = $(CLIPPER_CXXFLAGS) -+#INCLUDES = $(CLIPPER_CFLAGS) - #LDLIBS = $(CLIPPER_LIBS) - - - # - - BASE = /home/paule/autobuild/Linux-kalypso-pre-release --CLIPPER_CXXFLAGS = -I$(BASE)/include --MMDB_CXXFLAGS = -I$(BASE)/include/mmdb -+CLIPPER_CFLAGS = -I$(BASE)/include -+MMDB_CFLAGS = -I$(BASE)/include/mmdb - - CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \ - -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \ - -lclipper-core -lccp4c -L$(BASE)/lib \ - -L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm - --INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) - LDLIBS = $(CLIPPER_LIBS) - - sec-str-dist-check: sec-str-dist-check.cc sec-str-dist-check.hh -diff --git a/auxil/strand-analysis/Makefile.am b/auxil/strand-analysis/Makefile.am -index 11686ba..9c24b3b 100644 ---- a/auxil/strand-analysis/Makefile.am -+++ b/auxil/strand-analysis/Makefile.am -@@ -3,8 +3,8 @@ EXTRA_DIST = Makefile.simple strand-analysis.cc - - - INCLUDES = -I$(top_srcdir)/auxil/sec-str \ -- $(MMDB_CXXFLAGS) \ -- $(CLIPPER_CXXFLAGS) -+ $(MMDB_CFLAGS) \ -+ $(CLIPPER_CFLAGS) - - - check_PROGRAMS = -diff --git a/auxil/strand-analysis/Makefile.simple b/auxil/strand-analysis/Makefile.simple -index d5c21a4..2f58b8d 100644 ---- a/auxil/strand-analysis/Makefile.simple -+++ b/auxil/strand-analysis/Makefile.simple -@@ -2,13 +2,13 @@ - - CLIPPER = /Users/paulemsley/ccp4/ysbl-distro-based - --CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -+CLIPPER_CFLAGS = -I$(CLIPPER)/include - - CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-ccp4 \ - -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \ - -lclipper-core -lccp4c -lmmdb -lm -lrfftw -lfftw -lz -lm - --INCLUDES = -I../sec-str $(CLIPPER_CXXFLAGS) -+INCLUDES = -I../sec-str $(CLIPPER_CFLAGS) - LDLIBS = $(CLIPPER_LIBS) - - .cc: -diff --git a/auxil/vectors/Makefile.am b/auxil/vectors/Makefile.am -index 8826587..4a8d72e 100644 ---- a/auxil/vectors/Makefile.am -+++ b/auxil/vectors/Makefile.am -@@ -1,6 +1,6 @@ - - EXTRA_DIST = Makefile.simple diff-vec.cc --INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) -+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) - check_PROGRAMS = - - #diff_vec_SOURCES = diff-vec.cc -diff --git a/build/Makefile.am b/build/Makefile.am -index 6afe5a3..748341b 100644 ---- a/build/Makefile.am -+++ b/build/Makefile.am -@@ -25,8 +25,8 @@ pkgincludedir = $(includedir)/coot/build - - INCLUDES = \ - -I$(top_srcdir) \ -- $(CLIPPER_CXXFLAGS) \ -- $(MMDB_CXXFLAGS) -+ $(CLIPPER_CFLAGS) \ -+ $(MMDB_CFLAGS) - - noinst_PROGRAMS = testcabuild - -diff --git a/ccp4mg-utils/Makefile.am b/ccp4mg-utils/Makefile.am -index 7734f09..c58fe1d 100644 ---- a/ccp4mg-utils/Makefile.am -+++ b/ccp4mg-utils/Makefile.am -@@ -26,7 +26,7 @@ pkgincludedir = $(includedir)/coot/ccp4mg-utils - EXTRA_DIST = convert.sh get-new-utils.sh - - INCLUDES = \ -- $(MMDB_CXXFLAGS) \ -+ $(MMDB_CFLAGS) \ - $(LIBPNG_CFLAGS) - - libccp4mg_utils_la_SOURCES = geomutil.cc mgtree.cc cartesian.cc \ -diff --git a/ccp4mg-utils/mmut/Makefile.am b/ccp4mg-utils/mmut/Makefile.am -index d0651db..d4e0bf8 100755 ---- a/ccp4mg-utils/mmut/Makefile.am -+++ b/ccp4mg-utils/mmut/Makefile.am -@@ -70,9 +70,9 @@ INCLUDES = \ - $(LIBGLADE_CFLAGS) \ - @GTK_CFLAGS@ \ - $(GLUT_CFLAGS) \ -- $(MMDBSSM_CXXFLAGS) \ -- $(MMDB_CXXFLAGS) \ -- $(CLIPPER_CXXFLAGS) -+ $(MMDBSSM_CFLAGS) \ -+ $(MMDB_CFLAGS) \ -+ $(CLIPPER_CFLAGS) - - # $(WITH_SCRIPT_CFLAGS) - -diff --git a/ccp4mg-utils/pygl/Makefile.am b/ccp4mg-utils/pygl/Makefile.am -index a7e68b5..e26a6c8 100755 ---- a/ccp4mg-utils/pygl/Makefile.am -+++ b/ccp4mg-utils/pygl/Makefile.am -@@ -108,9 +108,9 @@ INCLUDES = \ - $(LIBGLADE_CFLAGS) \ - @GTK_CFLAGS@ \ - $(GLUT_CFLAGS) \ -- $(MMDBSSM_CXXFLAGS) \ -- $(MMDB_CXXFLAGS) \ -- $(CLIPPER_CXXFLAGS) -+ $(MMDBSSM_CFLAGS) \ -+ $(MMDB_CFLAGS) \ -+ $(CLIPPER_CFLAGS) - - # $(WITH_SCRIPT_CFLAGS) - -diff --git a/ccp4mg-utils/util/Makefile.am b/ccp4mg-utils/util/Makefile.am -index 399f453..3d2ff55 100755 ---- a/ccp4mg-utils/util/Makefile.am -+++ b/ccp4mg-utils/util/Makefile.am -@@ -73,9 +73,9 @@ INCLUDES = \ - $(LIBGLADE_CFLAGS) \ - @GTK_CFLAGS@ \ - $(GLUT_CFLAGS) \ -- $(MMDBSSM_CXXFLAGS) \ -- $(MMDB_CXXFLAGS) \ -- $(CLIPPER_CXXFLAGS) -+ $(MMDBSSM_CFLAGS) \ -+ $(MMDB_CFLAGS) \ -+ $(CLIPPER_CFLAGS) - - # $(WITH_SCRIPT_CFLAGS) - -diff --git a/configure.in b/configure.in -index cc549a5..d56f856 100644 ---- a/configure.in -+++ b/configure.in -@@ -108,14 +108,18 @@ esac - - - dnl Check for MMDB. --AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,) -+PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2],,[AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)]) - --AM_WITH_MMDBSSM -+PKG_CHECK_MODULES([MMDBSSM],[ssm],,[AM_WITH_MMDBSSM]) - AM_WITH_CCP4SRS - - dnl Check for Clipper. we exit if clipper is not found. - # --AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper])) -+PKG_CHECK_MODULES([CLIPPER], [clipper libccp4c], [ -+ CLIPPER_LIBS="${CLIPPER_LIBS} -lrfftw -lfftw"; AC_SUBST([CLIPPER_LIBS]) -+ ], [ -+ AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper])) -+ ]) - - # we set default coot_guile to true - coot_guile=true -@@ -186,11 +190,15 @@ AM_PATH_LIBGLADE - - dnl =========================== GooCanvas ================================ - --AM_PATH_GOOCANVAS --# give something for the preprocessor to chew on... --if test "$GOOCANVAS_CFLAGS" != "" ; then -- GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS" --fi -+PKG_CHECK_MODULES([GOOCANVAS], [goocanvas], -+ [GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"; AC_SUBST(GOOCANVAS_CFLAGS)], -+ [ -+ AM_PATH_GOOCANVAS -+ # give something for the preprocessor to chew on... -+ if test "$GOOCANVAS_CFLAGS" != "" ; then -+ GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS" -+ fi -+ ]) - - AC_ARG_WITH(enhanced-ligand-tools, [ --with-enhanced-ligand-tools with optional complicated/experimental ligand-related dependencies ], - coot_enhanced_ligand_additions="true", -diff --git a/coords/Makefile.am b/coords/Makefile.am -index 05fdf70..1e1c5d2 100644 ---- a/coords/Makefile.am -+++ b/coords/Makefile.am -@@ -29,7 +29,7 @@ INCLUDES = \ - -I$(top_srcdir) \ - $(ENHANCED_LIGAND_TOOLS_CFLAGS) \ - $(RDKIT_CXXFLAGS) \ -- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -+ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) - - AM_CXXFLAGS = \ - -DPKGDATADIR='"$(pkgdatadir)"' \ -diff --git a/coot-surface/Makefile.am b/coot-surface/Makefile.am -index d2243d6..2434219 100644 ---- a/coot-surface/Makefile.am -+++ b/coot-surface/Makefile.am -@@ -19,7 +19,7 @@ - # 02110-1301, USA - - INCLUDES = -I$(top_srcdir) \ -- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS) -+ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS) - - lib_LTLIBRARIES = libcoot-surface.la - -diff --git a/coot-utils/Makefile.am b/coot-utils/Makefile.am -index 87810dc..c5b05b4 100644 ---- a/coot-utils/Makefile.am -+++ b/coot-utils/Makefile.am -@@ -34,11 +34,10 @@ pkginclude_HEADERS = peak-search.hh coot-trim.hh \ - read-sm-cif.hh bonded-pairs.hh tree.hh helix-analysis.hh elastic.hh - pkgincludedir = $(includedir)/coot/coot-utils - -- - INCLUDES = \ - -I$(top_srcdir) \ -- $(CLIPPER_CXXFLAGS) \ -- $(MMDB_CXXFLAGS) \ -+ $(CLIPPER_CFLAGS) \ -+ $(MMDB_CFLAGS) \ - $(GSL_CFLAGS) \ - $(WITH_GUILE_CFLAGS) \ - $(WITH_PYTHON_CFLAGS) -diff --git a/cootaneer/Makefile.am b/cootaneer/Makefile.am -index 3a1d720..cfca0fd 100644 ---- a/cootaneer/Makefile.am -+++ b/cootaneer/Makefile.am -@@ -20,7 +20,7 @@ - EXTRA_DIST = \ - cootaneer-llk-2.40.dat - --INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) - - cootaneer_demo_SOURCES = cootaneer-demo.cpp - -diff --git a/cootilus/Makefile.am b/cootilus/Makefile.am -index 7e4169d..4492014 100644 ---- a/cootilus/Makefile.am -+++ b/cootilus/Makefile.am -@@ -20,7 +20,7 @@ - EXTRA_DIST = \ - nautilus_lib.pdb - --INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) - - cootilus_demo_SOURCES = cootilus-demo.cpp - -diff --git a/db-main/Makefile.am b/db-main/Makefile.am -index 3a85b9e..1a11cdf 100644 ---- a/db-main/Makefile.am -+++ b/db-main/Makefile.am -@@ -6,7 +6,7 @@ AM_CXXFLAGS = \ - -DDATADIR='"$(datadir)"' - - INCLUDES = -I$(top_srcdir) \ -- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) -+ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) - - pkginclude_HEADERS = db-main.hh db-strands.hh - pkgincludedir = $(includedir)/coot/db-main -diff --git a/db-main/Makefile.simple b/db-main/Makefile.simple -index cec561d..c207a43 100644 ---- a/db-main/Makefile.simple -+++ b/db-main/Makefile.simple -@@ -19,7 +19,7 @@ CLIPPER = $(HOME)/crystal - MCCP4 = $(HOME)/crystal - - CXX = g++ --MMDB_CXXFLAGS = -I$(MMDB)/include -+MMDB_CFLAGS = -I$(MMDB)/include - FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw - - MMDB_LIBS = -L$(MMDB)/lib -lmmdb -@@ -28,9 +28,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \ - -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS) - - MCCP4_CFLAGS = -I$(MCCP4)/include --CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include -+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include - --INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol -+INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol - - CXXFLAGS = -g $(INCLUDES) - LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS) -@@ -44,4 +44,4 @@ libcoot-db-main.a: db-main.o - db-main.o: db-main.cc db-main.hh - - testmmdbbits: testmmdbbits.cc -- $(CXX) $(MMDB_CXXFLAGS) $(MMDB_LIBS) $? -o $@ -+ $(CXX) $(MMDB_CFLAGS) $(MMDB_LIBS) $? -o $@ -diff --git a/density-contour/Makefile.am b/density-contour/Makefile.am -index 7f705e8..f5dcc00 100644 ---- a/density-contour/Makefile.am -+++ b/density-contour/Makefile.am -@@ -20,7 +20,7 @@ - - COORD_INCLUDES = -I$(top_srcdir) - --INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CXXFLAGS) -+INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CFLAGS) - - lib_LTLIBRARIES = libcoot-isosurface.la - -diff --git a/geometry/Makefile.am b/geometry/Makefile.am -index 6dd665f..57aaa04 100644 ---- a/geometry/Makefile.am -+++ b/geometry/Makefile.am -@@ -26,7 +26,7 @@ pkginclude_HEADERS = protein-geometry.hh read-sbase.hh lbg-graph.hh srs-interfa - pkgincludedir = $(includedir)/coot/geometry - - INCLUDES = -I$(top_srcdir) \ -- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) -+ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) - - AM_CXXFLAGS = \ - -DDATADIR='"$(datadir)"' \ -diff --git a/geometry/Makefile.simple b/geometry/Makefile.simple -index 370b2fa..c3b0106 100644 ---- a/geometry/Makefile.simple -+++ b/geometry/Makefile.simple -@@ -46,7 +46,7 @@ MCCP4 = $(HOME)/mapview - - - CXX = g++ --MMDB_CXXFLAGS = -I$(MMDB)/include -+MMDB_CFLAGS = -I$(MMDB)/include - FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw - - MMDB_LIBS = -L$(MMDB)/lib -lmmdb -@@ -55,9 +55,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \ - -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS) - - MCCP4_CFLAGS = -I$(MCCP4)/include --CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include -+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include - --INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -I$(top_srcdir)/coords -+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/coords - - top_srcdir = .. - -diff --git a/high-res/Makefile.am b/high-res/Makefile.am -index cf81182..3a2af5c 100644 ---- a/high-res/Makefile.am -+++ b/high-res/Makefile.am -@@ -29,8 +29,8 @@ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) - - INCLUDES = \ - -I$(top_srcdir) \ -- $(MMDB_CXXFLAGS) \ -- $(CLIPPER_CXXFLAGS) -+ $(MMDB_CFLAGS) \ -+ $(CLIPPER_CFLAGS) - - libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \ - sequence-assignment.cc -diff --git a/ideal/Makefile.am b/ideal/Makefile.am -index e52c271..c5c8e6a 100644 ---- a/ideal/Makefile.am -+++ b/ideal/Makefile.am -@@ -33,11 +33,11 @@ pkgincludedir = $(includedir)/coot/ideal - - INCLUDES = \ - -I$(top_srcdir) \ -- $(CLIPPER_CXXFLAGS) \ -- $(MMDB_CXXFLAGS) -+ $(CLIPPER_CFLAGS) \ -+ $(MMDB_CFLAGS) - - AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) $(COOT_WINDOWS_CFLAGS) \ -- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) $(COOT_GSL_FLAGS) -+ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) $(COOT_GSL_FLAGS) - AM_LDFLAGS = $(GSL_LIBS) $(MMDB_LIBS) $(CLIPPER_LIBS) - - -diff --git a/ideal/Makefile.simple b/ideal/Makefile.simple -index 3c32c3c..0abd514 100644 ---- a/ideal/Makefile.simple -+++ b/ideal/Makefile.simple -@@ -44,7 +44,7 @@ MMDB = $(HOME)/mapview - - - CXX = g++ --MMDB_CXXFLAGS = -I$(MMDB)/include -+MMDB_CFLAGS = -I$(MMDB)/include - FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw - - MMDB_LIBS = -L$(MMDB)/lib -lmmdb -@@ -53,9 +53,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \ - -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS) - - MCCP4_CFLAGS = -I$(MCCP4)/include --CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include -+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include - --INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) \ -+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) \ - -I$(top_srcdir)/coords \ - -I$(top_srcdir)/geometry - -diff --git a/lbg/Makefile.am b/lbg/Makefile.am -index df74b90..7f54567 100644 ---- a/lbg/Makefile.am -+++ b/lbg/Makefile.am -@@ -6,7 +6,7 @@ INCLUDES = \ - $(GSL_CFLAGS) \ - $(GOOCANVAS_CFLAGS) \ - $(GTK_CFLAGS) \ -- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \ -+ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \ - $(COOT_WINDOWS_CFLAGS) \ - $(ENHANCED_LIGAND_TOOLS_CFLAGS) \ - $(RDKIT_CXXFLAGS) \ -diff --git a/lbg/Makefile.simple b/lbg/Makefile.simple -index 48d091b..5b148b4 100644 ---- a/lbg/Makefile.simple -+++ b/lbg/Makefile.simple -@@ -24,11 +24,11 @@ GSL_LDFLAGS=$(CRYST)/lib/libgsl.la $(CRYST)/lib/libgslcblas.la -lm - MMDB=$(CRYST) - # MMDB=$(HOME)/test/mmdb - --MMDB_CXXFLAGS=-I$(MMDB)/include/mmdb -+MMDB_CFLAGS=-I$(MMDB)/include/mmdb - MMDB_LDFLAGS=$(MMDB)/lib/libmmdb.la - - CLIPPER=$(CRYST) --CLIPPER_CXXFLAGS=-I$(CLIPPER)/include -+CLIPPER_CFLAGS=-I$(CLIPPER)/include - CLIPPER_LDFLAGS=$(CLIPPER)/lib/libclipper-core.la \ - $(CLIPPER)/lib/librfftw.la \ - $(CLIPPER)/lib/libfftw.la -@@ -40,7 +40,7 @@ LIDIA_CORE_CXXFLAGS = -I ../lidia-core - LIDIA_CORE_LDFLAGS = $(COOT_INSTALLED)/lib/libcoot-lidia-core.la - - --CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(LIDIA_CORE_CXXFLAGS) \ -+CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(LIDIA_CORE_CXXFLAGS) \ - -I$(top_srcdir)/compat - - lbg: lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o residue-circles.o -diff --git a/lidia-core/Makefile.am b/lidia-core/Makefile.am -index 72b28ca..2a184b4 100644 ---- a/lidia-core/Makefile.am -+++ b/lidia-core/Makefile.am -@@ -24,13 +24,13 @@ pkgincludedir = $(includedir)/coot/lidia-core - - # 20110408 I add a CResidue,dictionary_residue_restraints_t constructor to molfile_molecule_t - # simple --#INCLUDES = $(CLIPPER_CXXFLAGS) -+#INCLUDES = $(CLIPPER_CFLAGS) - # - INCLUDES = \ - -I$(top_srcdir) \ - $(ENHANCED_LIGAND_TOOLS_CFLAGS) \ - $(RDKIT_CXXFLAGS) \ -- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -+ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) - - libcoot_lidia_core_la_SOURCES = lbg-shared.cc lbg-molfile.cc lig-build.cc rdkit-interface.cc \ - cod-types.cc -diff --git a/ligand/Makefile.am b/ligand/Makefile.am -index 202979e..5173204 100644 ---- a/ligand/Makefile.am -+++ b/ligand/Makefile.am -@@ -27,7 +27,7 @@ INCLUDES = \ - -I$(top_srcdir) \ - $(COOT_GSL_FLAGS) \ - $(GSL_CFLAGS) \ -- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -+ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) - - pkginclude_HEADERS = ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh \ - chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh \ -diff --git a/macros/clipper.m4 b/macros/clipper.m4 -index da11e74..ad2af81 100644 ---- a/macros/clipper.m4 -+++ b/macros/clipper.m4 -@@ -56,7 +56,7 @@ if test x$clipper_prefix != x; then - # - # should use clipper-config --cflags - # -- CLIPPER_CXXFLAGS="-I$clipper_prefix/include" -+ CLIPPER_CFLAGS="-I$clipper_prefix/include" - # -I$clipper_prefix/cctbx - - # yes, libmmtz.a is in -L$clipper_prefix/umtz! -@@ -75,7 +75,7 @@ if test x$clipper_prefix != x; then - # - ccp4c=ccp4c - -- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm" -+ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm" - # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx - - -@@ -102,8 +102,8 @@ else - # this needs to be 'configured' - typically either s or blank. - fftw_pre= - -- CLIPPER_CXXFLAGS="$CCP4_CFLAGS" -- CLIPPER_LDOPTS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm" -+ CLIPPER_CFLAGS="$CCP4_CFLAGS" -+ CLIPPER_LIBS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm" - fi - - # BL: workaround needed for new MinGW -@@ -113,17 +113,17 @@ ac_cv_build_alias=${ac_cv_build_alias:=$build_alias} - case $ac_cv_build_alias in - # BL says:: same as for cygwin in mingw - MINGW*|Mingw*|*mingw*|Cygwin*|CYGWIN*|*cygwin*) -- CLIPPER_LDOPTS=$CLIPPER_LDOPTS -+ CLIPPER_LIBS=$CLIPPER_LIBS - ;; - *) -- CLIPPER_LDOPTS=$CLIPPER_LDOPTS" -lpthread" -+ CLIPPER_LIBS=$CLIPPER_LIBS" -lpthread" - ;; - esac - - AC_MSG_CHECKING([for Clipper]) - -- LIBS="$save_LIBS $CLIPPER_LDOPTS" -- CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS" -+ LIBS="$save_LIBS $CLIPPER_LIBS" -+ CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS" - # AC_TRY_LINK uses the c compiler, so we will temporarily - # reassign $CC to the c++ compiler. - # -@@ -140,7 +140,7 @@ if test x$have_clipper = xyes; then - - LIBS="$saved_LIBS" - CFLAGS="$saved_CFLAGS" -- CLIPPER_LIBS="$CLIPPER_LDOPTS" -+ CLIPPER_LIBS="$CLIPPER_LIBS" - ifelse([$1], , :, [$1]) - - else -@@ -148,12 +148,12 @@ else - LIBS="$saved_LIBS" - CFLAGS="$saved_CFLAGS" - CLIPPER_LIBS="" -- CLIPPER_CXXFLAGS="" -+ CLIPPER_CFLAGS="" - ifelse([$2], , :, [$2]) - - fi - --AC_SUBST(CLIPPER_CXXFLAGS) -+AC_SUBST(CLIPPER_CFLAGS) - AC_SUBST(CLIPPER_LIBS) - - ]) -diff --git a/macros/clipper.m4.old b/macros/clipper.m4.old -index de8ab65..4c1b418 100644 ---- a/macros/clipper.m4.old -+++ b/macros/clipper.m4.old -@@ -34,7 +34,7 @@ if test x$clipper_prefix != x; then - # should ideally be CLIPPER_CFLAGS="-I$clipper_prefix/include", and the like - # when clipper and dependencies get installed. - # -- CLIPPER_CXXFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include" -+ CLIPPER_CFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include" - # -I$clipper_prefix/cctbx - - # yes, libmmtz.a is in -L$clipper_prefix/umtz! -@@ -45,20 +45,20 @@ if test x$clipper_prefix != x; then - # HACK! FIXME - # added lz, we should have proper autoconf check for this. - # -- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm" -+ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm" - # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx - else - # the compiler looks in the "standard" places for clipper. In real life, - # it would be quite unlikely that clipper would be installed in /usr/include, - # /usr/lib etc. so this code will not usually find the right dependencies. -- CLIPPER_CXXFLAGS="" -- CLIPPER_LDOPTS="" -+ CLIPPER_CFLAGS="" -+ CLIPPER_LIBS="" - fi - - AC_MSG_CHECKING([for Clipper]) - -- LIBS="$save_LIBS $CLIPPER_LDOPTS" -- CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS" -+ LIBS="$save_LIBS $CLIPPER_LIBS" -+ CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS" - # AC_TRY_LINK uses the c compiler, so we will temporarily - # reassign $CC to the c++ compiler. - # -@@ -72,7 +72,7 @@ if test x$have_clipper = xyes; then - - LIBS="$saved_LIBS" - CFLAGS="$saved_CFLAGS" -- CLIPPER_LIBS="$CLIPPER_LDOPTS" -+ CLIPPER_LIBS="$CLIPPER_LIBS" - ifelse([$1], , :, [$1]) - - else -@@ -80,12 +80,12 @@ else - LIBS="$saved_LIBS" - CFLAGS="$saved_CFLAGS" - CLIPPER_LIBS="" -- CLIPPER_CXXFLAGS="" -+ CLIPPER_CFLAGS="" - ifelse([$2], , :, [$2]) - - fi - --AC_SUBST(CLIPPER_CXXFLAGS) -+AC_SUBST(CLIPPER_CFLAGS) - AC_SUBST(CLIPPER_LIBS) - - ]) -diff --git a/macros/goo-canvas.m4 b/macros/goo-canvas.m4 -index e2494a5..89c908e 100644 ---- a/macros/goo-canvas.m4 -+++ b/macros/goo-canvas.m4 -@@ -35,8 +35,7 @@ if test x$goocanvas_prefix != x; then - # SGI compiler CC (CXX=CC) needs -lm to link maths library, but - # GCC c++ does not. - # -- GOOCANVAS_LDOPTS="-L$goocanvas_prefix/lib -lgoocanvas" -- -+ GOOCANVAS_LIBS="-L$goocanvas_prefix/lib -lgoocanvas" - else - # the compiler looks in the "standard" places for GOOCANVAS. (or uses pkgconfig) - -@@ -54,18 +53,16 @@ else - break;; - esac - if test -z "${PKG_CONFIG}"; then -- GOOCANVAS_LDOPTS="-lgoocanvas" -+ GOOCANVAS_LIBS="-lgoocanvas" - else -- GOOCANVAS_LDOPTS=`$PKG_CONFIG goocanvas --libs` -+ GOOCANVAS_LIBS=`$PKG_CONFIG goocanvas --libs` - fi - fi - - AC_MSG_CHECKING([for Goocanvas]) - --LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS" -+LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS" - CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS" -- -- - dnl # 20130929: why do I do this? I don't remember. Using libtool - dnl # in this way is not a good idea (configure makes libtool). - dnl # -@@ -85,18 +82,15 @@ dnl # note that we use ./libtool (running in the build dir) because $LIBTOOL - dnl CXX="libtool --mode=link $CXX" - dnl break;; - dnl esac -- -- - AC_LANG_PUSH(C++) - AC_TRY_LINK([#include "goocanvas.h"] ,[ GooCanvas *a; ], have_goocanvas=yes, have_goocanvas=no) - AC_LANG_POP -- - AC_MSG_RESULT($have_goocanvas) - - if test x$have_goocanvas = xyes; then - - GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS" -- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS" -+ GOOCANVAS_LIBS="$GOOCANVAS_LIBS" - - ifelse([$1], , :, [$1]) - -diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4 -index 25dc502..21646a5 100644 ---- a/macros/mmdb-ssm.m4 -+++ b/macros/mmdb-ssm.m4 -@@ -34,11 +34,11 @@ if test x$with_ssmlib_prefix != x; then - - if test -r "$with_ssmlib_prefix/include/ssm/ssm_superpose.h"; then - -- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB" -+ MMDBSSM_CFLAGS="-DHAVE_SSMLIB" - # AFAICS, ssm does not put its libs in $acl_libdirstem - # MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm" - MMDBSSM_LIBS="-L$with_ssmlib_prefix/lib -lssm" -- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/include" -+ ac_MMDBSSM_CFLAGS="-I$with_ssmlib_prefix/include" - - # saved_LIBS="$LIBS" - # saved_CPPFLAGS="$CPPFLAGS" -@@ -50,11 +50,11 @@ if test x$with_ssmlib_prefix != x; then - else - AC_MSG_FAILURE([ --with-ssmlib-prefix specified but include files not found]) - fi -- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS" -+ MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS" - - else - -- MMDBSSM_CXXFLAGS="" -+ MMDBSSM_CFLAGS="" - MMDBSSM_LIBS="" - with_ssmlib_prefix=no - -@@ -62,6 +62,6 @@ fi - - AC_MSG_RESULT([$with_ssmlib_prefix]) - --AC_SUBST(MMDBSSM_CXXFLAGS) -+AC_SUBST(MMDBSSM_CFLAGS) - AC_SUBST(MMDBSSM_LIBS) - ]) -diff --git a/macros/mmdb.m4 b/macros/mmdb.m4 -index 7c1cbcf..72613f3 100644 ---- a/macros/mmdb.m4 -+++ b/macros/mmdb.m4 -@@ -55,7 +55,7 @@ if test x$mmdb_prefix != x; then - # --with-mmdb=/some/thing - # - -- # should ideally be MMDB_CXXFLAGS="-I$MMDB_prefix/include", and the like -+ # should ideally be MMDB_CFLAGS="-I$MMDB_prefix/include", and the like - # when MMDB and dependencies get installed - we infact, include both - # directories. - # -@@ -69,7 +69,7 @@ lib/src - lib/src/mmdb' - for ac_dir in $ac_mmdb_dirs; do - if test -r "$mmdb_prefix/$ac_dir/mmdb/mmdb_manager.h"; then -- ac_MMDB_CXXFLAGS="-I$mmdb_prefix/$ac_dir" -+ ac_MMDB_CFLAGS="-I$mmdb_prefix/$ac_dir" - break - fi - done -@@ -82,14 +82,14 @@ else - # the compiler looks in the "standard" places for MMDB. In real life, - # it would be quite unlikely that MMDB would be installed in /usr/include, - # /usr/lib etc. so this code will not usually find the right dependencies. -- ac_MMDB_CXXFLAGS="" -+ ac_MMDB_CFLAGS="" - ac_MMDB_LDOPTS="-lmmdb -lm" - fi - - AC_MSG_CHECKING([for MMDB]) - - LIBS="$save_LIBS $ac_MMDB_LDOPTS" -- CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS" -+ CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CFLAGS" - # - # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will - # temporarily reassign $CC to the c++ compiler. -@@ -118,7 +118,7 @@ if test x$have_mmdb = xyes; then - CLINKR_FLAG=-DMMDB_WITHOUT_LINKR - fi - CXXFLAGS="$saved_CXXFLAGS" -- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG" -+ MMDB_CFLAGS="$ac_MMDB_CFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG" - MMDB_LIBS="$ac_MMDB_LDOPTS" - ifelse([$1], , :, [$1]) - -@@ -134,12 +134,12 @@ else - LIBS="$saved_LIBS" - CXXFLAGS="$saved_CXXFLAGS" - MMDB_LIBS="" -- MMDB_CXXFLAGS="" -+ MMDB_CFLAGS="" - ifelse([$2], , :, [$2]) - - fi - --AC_SUBST(MMDB_CXXFLAGS) -+AC_SUBST(MMDB_CFLAGS) - AC_SUBST(MMDB_LIBS) - - ]) -diff --git a/mini-mol/Makefile.am b/mini-mol/Makefile.am -index 2f6e3a3..4865b0b 100644 ---- a/mini-mol/Makefile.am -+++ b/mini-mol/Makefile.am -@@ -25,8 +25,8 @@ pkgincludedir = $(includedir)/coot/mini-mol - - INCLUDES = \ - -I$(top_srcdir) \ -- $(CLIPPER_CXXFLAGS) \ -- $(MMDB_CXXFLAGS) -+ $(CLIPPER_CFLAGS) \ -+ $(MMDB_CFLAGS) - - AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS) - -diff --git a/protein_db/Makefile.am b/protein_db/Makefile.am -index 268fcf6..cdd5c9e 100644 ---- a/protein_db/Makefile.am -+++ b/protein_db/Makefile.am -@@ -19,7 +19,7 @@ - - lib_LTLIBRARIES=libcoot-protein-db.la - --INCLUDES= $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -+INCLUDES= $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) - - pkginclude_HEADERS=protein_db.h protein_db_utils.h rna_db.h - pkgincludedir = $(includedir)/coot/protein_db -diff --git a/sequence-view/Makefile.am b/sequence-view/Makefile.am -index 7af6384..742e6d7 100644 ---- a/sequence-view/Makefile.am -+++ b/sequence-view/Makefile.am -@@ -55,9 +55,9 @@ INCLUDES = \ - -I$(top_srcdir)/analysis \ - -I$(top_srcdir)/cootaneer \ - -I$(top_srcdir)/src \ -- $(CLIPPER_CXXFLAGS) \ -- $(MMDB_CXXFLAGS) \ -- $(MMDBSSM_CXXFLAGS) \ -+ $(CLIPPER_CFLAGS) \ -+ $(MMDB_CFLAGS) \ -+ $(MMDBSSM_CFLAGS) \ - $(GLUT_CFLAGS) \ - $(CANVAS_CFLAGS) \ - $(GTKGL_CONTEXT_CFLAGS) \ -diff --git a/skeleton/Makefile.am b/skeleton/Makefile.am -index 54872fe..bef7d0e 100644 ---- a/skeleton/Makefile.am -+++ b/skeleton/Makefile.am -@@ -23,7 +23,7 @@ lib_LTLIBRARIES=libcoot-skeleton.la - - INCLUDES = \ - -I$(top_srcdir) \ -- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) -+ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) - - AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS) - -diff --git a/src/Makefile.am b/src/Makefile.am -index af5276b..d0ab482 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -195,11 +195,11 @@ INCLUDES = \ - $(GOOCANVAS_CFLAGS) \ - @GTK_CFLAGS@ \ - $(GLUT_CFLAGS) \ -- $(MMDBSSM_CXXFLAGS) \ -- $(MMDB_CXXFLAGS) \ -+ $(MMDBSSM_CFLAGS) \ -+ $(MMDB_CFLAGS) \ - $(CCP4SRS_CXXFLAGS) \ - $(GSL_CFLAGS) \ -- $(CLIPPER_CXXFLAGS) \ -+ $(CLIPPER_CFLAGS) \ - $(PYGTK_CFLAGS) \ - $(GLOB_CFLAGS) \ - $(CURL_CFLAGS) -diff --git a/surface/Makefile.am b/surface/Makefile.am -index 3de5953..2461f58 100644 ---- a/surface/Makefile.am -+++ b/surface/Makefile.am -@@ -1,5 +1,5 @@ - --INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(FFTW_CXXFLAGS) -+INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(FFTW_CXXFLAGS) - - AM_CXXFLAGS = $(OPENMP_CFLAGS) - |