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commit: eb7653c7d0b2c1ec08a436154d5d5623ad3ad3d1 |
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Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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AuthorDate: Sun Jun 2 16:42:24 2013 +0000 |
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Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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CommitDate: Sun Jun 2 16:42:24 2013 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=eb7653c7 |
7 |
|
8 |
sci-chemistry/coot: Update pc patches |
9 |
|
10 |
Package-Manager: portage-2.2.0_alpha177 |
11 |
|
12 |
--- |
13 |
sci-chemistry/coot/ChangeLog | 5 + |
14 |
sci-chemistry/coot/coot-9999.ebuild | 20 +- |
15 |
sci-chemistry/coot/files/9999-clipper-config.patch | 17 - |
16 |
sci-chemistry/coot/files/9999-goocanvas.patch | 25 - |
17 |
sci-chemistry/coot/files/9999-mmdb-config.patch | 18 - |
18 |
sci-chemistry/coot/files/9999-pc.patch | 1040 ++++++++++++++++++++ |
19 |
sci-chemistry/coot/files/9999-ssm.patch | 56 -- |
20 |
7 files changed, 1054 insertions(+), 127 deletions(-) |
21 |
|
22 |
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog |
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index c729ace..2bbf002 100644 |
24 |
--- a/sci-chemistry/coot/ChangeLog |
25 |
+++ b/sci-chemistry/coot/ChangeLog |
26 |
@@ -2,6 +2,11 @@ |
27 |
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 |
28 |
# $Header: $ |
29 |
|
30 |
+ 02 Jun 2013; Justin Lecher <jlec@g.o> coot-9999.ebuild, |
31 |
+ -files/9999-clipper-config.patch, -files/9999-goocanvas.patch, |
32 |
+ -files/9999-mmdb-config.patch, +files/9999-pc.patch, -files/9999-ssm.patch: |
33 |
+ Update pc patches |
34 |
+ |
35 |
02 Jun 2013; Justin Lecher <jlec@g.o> coot-9999.ebuild: |
36 |
Fix PYTHON() -> ${EPYTHON} for new eclasses |
37 |
|
38 |
|
39 |
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild |
40 |
index 4a7ee55..c8831ad 100644 |
41 |
--- a/sci-chemistry/coot/coot-9999.ebuild |
42 |
+++ b/sci-chemistry/coot/coot-9999.ebuild |
43 |
@@ -37,9 +37,9 @@ SCIDEPS=" |
44 |
>=sci-libs/gsl-1.3 |
45 |
>=sci-libs/mmdb-1.23 |
46 |
sci-libs/ssm |
47 |
- <sci-libs/monomer-db-1 |
48 |
+ sci-libs/monomer-db |
49 |
sci-chemistry/reduce |
50 |
- <sci-chemistry/refmac-5.6 |
51 |
+ sci-chemistry/refmac |
52 |
sci-chemistry/probe" |
53 |
|
54 |
XDEPS=" |
55 |
@@ -82,21 +82,19 @@ pkg_setup() { |
56 |
python-single-r1_pkg_setup |
57 |
} |
58 |
|
59 |
-PATCHES=( |
60 |
- "${FILESDIR}"/${PV}-clipper-config.patch |
61 |
- "${FILESDIR}"/${PV}-goocanvas.patch |
62 |
- "${FILESDIR}"/${PV}-mmdb-config.patch |
63 |
- "${FILESDIR}"/${PV}-ssm.patch |
64 |
- ) |
65 |
+PATCHES=( "${FILESDIR}"/${PV}-pc.patch ) |
66 |
|
67 |
src_unpack() { |
68 |
subversion_src_unpack |
69 |
- use test && unpack ${A} |
70 |
+ if use test; then |
71 |
+ unpack ${A} |
72 |
+ ln -sf . "${S}"/coot-ccp4 |
73 |
+ fi |
74 |
} |
75 |
|
76 |
src_prepare() { |
77 |
sed \ |
78 |
- -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${PYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ |
79 |
+ -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ |
80 |
-i configure.in || die |
81 |
|
82 |
autotools-utils_src_prepare |
83 |
@@ -128,7 +126,7 @@ src_configure() { |
84 |
|
85 |
src_compile() { |
86 |
autotools-utils_src_compile |
87 |
- python_fix_shebang "${S}"/src/coot_gtk2.py "${S}"/python-tests/coot_unittest.py |
88 |
+ python_fix_shebang "${S}"/src/coot_gtk2.py |
89 |
cp "${S}"/src/coot_gtk2.py python/coot.py || die |
90 |
} |
91 |
|
92 |
|
93 |
diff --git a/sci-chemistry/coot/files/9999-clipper-config.patch b/sci-chemistry/coot/files/9999-clipper-config.patch |
94 |
deleted file mode 100644 |
95 |
index 311b5e8..0000000 |
96 |
--- a/sci-chemistry/coot/files/9999-clipper-config.patch |
97 |
+++ /dev/null |
98 |
@@ -1,17 +0,0 @@ |
99 |
- macros/clipper.m4 | 3 +++ |
100 |
- 1 files changed, 3 insertions(+), 0 deletions(-) |
101 |
- |
102 |
-diff --git a/macros/clipper.m4 b/macros/clipper.m4 |
103 |
-index 0bf087a..d0e8b6b 100644 |
104 |
---- a/macros/clipper.m4 |
105 |
-+++ b/macros/clipper.m4 |
106 |
-@@ -98,6 +98,9 @@ case $ac_cv_build_alias in |
107 |
- ;; |
108 |
- esac |
109 |
- |
110 |
-+CLIPPER_CXXFLAGS=`clipper-config --cflags` |
111 |
-+CLIPPER_LDOPTS=`clipper-config --libs` |
112 |
-+ |
113 |
- AC_MSG_CHECKING([for Clipper]) |
114 |
- |
115 |
- LIBS="$save_LIBS $CLIPPER_LDOPTS" |
116 |
|
117 |
diff --git a/sci-chemistry/coot/files/9999-goocanvas.patch b/sci-chemistry/coot/files/9999-goocanvas.patch |
118 |
deleted file mode 100644 |
119 |
index ce0d4a0..0000000 |
120 |
--- a/sci-chemistry/coot/files/9999-goocanvas.patch |
121 |
+++ /dev/null |
122 |
@@ -1,25 +0,0 @@ |
123 |
-Index: macros/goo-canvas.m4 |
124 |
-=================================================================== |
125 |
---- macros/goo-canvas.m4 (revision 3307) |
126 |
-+++ macros/goo-canvas.m4 (working copy) |
127 |
-@@ -56,9 +56,9 @@ |
128 |
- fi |
129 |
- fi |
130 |
- |
131 |
--AC_MSG_CHECKING([for Goocanvas]) |
132 |
-+PKG_CHECK_MODULES(GOOCANVAS, goocanvas) |
133 |
- |
134 |
--LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS" |
135 |
-+LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS" |
136 |
- CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS" |
137 |
- # |
138 |
- # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will |
139 |
-@@ -76,7 +76,7 @@ |
140 |
- if test x$have_goocanvas = xyes; then |
141 |
- |
142 |
- GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS" |
143 |
-- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS" |
144 |
-+ GOOCANVAS_LIBS="$GOOCANVAS_LIBS" |
145 |
- |
146 |
- ifelse([$1], , :, [$1]) |
147 |
- |
148 |
|
149 |
diff --git a/sci-chemistry/coot/files/9999-mmdb-config.patch b/sci-chemistry/coot/files/9999-mmdb-config.patch |
150 |
deleted file mode 100644 |
151 |
index b3b66ab..0000000 |
152 |
--- a/sci-chemistry/coot/files/9999-mmdb-config.patch |
153 |
+++ /dev/null |
154 |
@@ -1,18 +0,0 @@ |
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-Index: macros/mmdb.m4 |
156 |
-=================================================================== |
157 |
---- macros/mmdb.m4 (revision 3579) |
158 |
-+++ macros/mmdb.m4 (working copy) |
159 |
-@@ -86,8 +86,12 @@ |
160 |
- ac_MMDB_LDOPTS="-lmmdb -lm" |
161 |
- fi |
162 |
- |
163 |
--AC_MSG_CHECKING([for MMDB]) |
164 |
-+PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2]) |
165 |
-+ac_MMDB_LDOPTS="${MMDB_LIBS}" |
166 |
-+ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}" |
167 |
- |
168 |
-+AC_MSG_CHECKING([for CISPEP in MMDB]) |
169 |
-+ |
170 |
- LIBS="$save_LIBS $ac_MMDB_LDOPTS" |
171 |
- CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS" |
172 |
- # |
173 |
|
174 |
diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch |
175 |
new file mode 100644 |
176 |
index 0000000..a6bc18e |
177 |
--- /dev/null |
178 |
+++ b/sci-chemistry/coot/files/9999-pc.patch |
179 |
@@ -0,0 +1,1040 @@ |
180 |
+Index: ChangeLog |
181 |
+=================================================================== |
182 |
+--- ChangeLog (revision 4651) |
183 |
++++ ChangeLog (working copy) |
184 |
+@@ -1959,7 +1959,7 @@ |
185 |
+ 2005-01-29 Paul Emsley <paulemsley@××××××××××××.uk> |
186 |
+ |
187 |
+ * macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): use $with_ssmlib_prefix in |
188 |
+- MMDBSSM_CXXFLAGS [Oops]. Hopefully fixes problems spotted by Joel |
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++ MMDBSSM_CFLAGS [Oops]. Hopefully fixes problems spotted by Joel |
190 |
+ Bard and Joseph Toth. |
191 |
+ |
192 |
+ * src/graphics-info-pick.cc: (symmetry_atom_pick): tried to add |
193 |
+@@ -2252,14 +2252,14 @@ |
194 |
+ |
195 |
+ 2004-11-20 Paul Emsley <paulemsley@××××××××××××.uk> |
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+ |
197 |
+- * coords/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS [for |
198 |
++ * coords/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS [for |
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+ coot-close.cc usage]. |
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+ |
201 |
+ 2004-11-19 Paul Emsley <paulemsley@××××××××××××.uk> |
202 |
+ |
203 |
+- * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CXXFLAGS |
204 |
++ * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CFLAGS |
205 |
+ |
206 |
+- * analysis/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS |
207 |
++ * analysis/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS |
208 |
+ |
209 |
+ 2004-11-16 Paul Emsley <emsley@localhost> |
210 |
+ |
211 |
+@@ -2269,7 +2269,7 @@ |
212 |
+ |
213 |
+ 2004-11-15 Paul Emsley <emsley@localhost> |
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+ |
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+- * coot-utils/Makefile.am: add MMDB_CXXFLAGS to INCLUDE [thanks |
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++ * coot-utils/Makefile.am: add MMDB_CFLAGS to INCLUDE [thanks |
217 |
+ Joseph Toth]. |
218 |
+ |
219 |
+ * surface/CXXSphereNode.h: removed the ; again! |
220 |
+Index: analysis/Makefile.am |
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+=================================================================== |
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+--- analysis/Makefile.am (revision 4651) |
223 |
++++ analysis/Makefile.am (working copy) |
224 |
+@@ -11,8 +11,8 @@ |
225 |
+ -I$(top_srcdir)/coot-utils \ |
226 |
+ -I$(top_srcdir)/mini-mol \ |
227 |
+ -I$(top_srcdir)/utils \ |
228 |
+- $(CLIPPER_CXXFLAGS) \ |
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+- $(MMDB_CXXFLAGS) |
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++ $(CLIPPER_CFLAGS) \ |
231 |
++ $(MMDB_CFLAGS) |
232 |
+ |
233 |
+ libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc |
234 |
+ |
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+Index: angles/Makefile.am |
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+=================================================================== |
237 |
+--- angles/Makefile.am (revision 4651) |
238 |
++++ angles/Makefile.am (working copy) |
239 |
+@@ -6,7 +6,7 @@ |
240 |
+ |
241 |
+ include_HEADERS = AngleInfo.h ncube.h wrapped-ncube.h |
242 |
+ |
243 |
+-INCLUDES = $(CLIPPER_CXXFLAGS) |
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++INCLUDES = $(CLIPPER_CFLAGS) |
245 |
+ |
246 |
+ libcoot_AngleInfo_a_sources = AngleInfo.cc AngleInfo.h \ |
247 |
+ AngleInfo-angle-torsions-autogen.cc AngleInfo-theta_2-autogen.cc |
248 |
+Index: auxil/catcheck/Makefile.am |
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+=================================================================== |
250 |
+--- auxil/catcheck/Makefile.am (revision 4651) |
251 |
++++ auxil/catcheck/Makefile.am (working copy) |
252 |
+@@ -1,7 +1,7 @@ |
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+ |
254 |
+ EXTRA_DIST = Makefile.simple |
255 |
+ |
256 |
+-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) |
257 |
++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) |
258 |
+ |
259 |
+ check_PROGRAMS = catcheck |
260 |
+ |
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+Index: auxil/catcheck/Makefile.simple |
262 |
+=================================================================== |
263 |
+--- auxil/catcheck/Makefile.simple (revision 4651) |
264 |
++++ auxil/catcheck/Makefile.simple (working copy) |
265 |
+@@ -1,17 +1,17 @@ |
266 |
+ |
267 |
+-# CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include |
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++# CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include |
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+ |
270 |
+ |
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+ BASE = /home/paule/autobuild/Linux-kalypso-pre-release |
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+-CLIPPER_CXXFLAGS = -I$(BASE)/include |
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+-MMDB_CXXFLAGS = -I$(BASE)/include/mmdb |
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++CLIPPER_CFLAGS = -I$(BASE)/include |
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++MMDB_CFLAGS = -I$(BASE)/include/mmdb |
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+ |
277 |
+ CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \ |
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+ -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \ |
279 |
+ -lclipper-core -lccp4c -L$(BASE)/lib \ |
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+ -L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm |
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+ |
282 |
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) |
283 |
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) |
284 |
+ LDLIBS = $(CLIPPER_LIBS) |
285 |
+ |
286 |
+ catcheck: catcheck.cc catcheck.hh |
287 |
+Index: auxil/rama/Makefile.am |
288 |
+=================================================================== |
289 |
+--- auxil/rama/Makefile.am (revision 4651) |
290 |
++++ auxil/rama/Makefile.am (working copy) |
291 |
+@@ -1,7 +1,7 @@ |
292 |
+ |
293 |
+ EXTRA_DIST = Makefile.simple fit-rama.scm run.scm test-arr.scm |
294 |
+ |
295 |
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) |
296 |
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) |
297 |
+ |
298 |
+ |
299 |
+ check_PROGRAMS = rama-data rama-doughnut |
300 |
+Index: auxil/rama/Makefile.simple |
301 |
+=================================================================== |
302 |
+--- auxil/rama/Makefile.simple (revision 4651) |
303 |
++++ auxil/rama/Makefile.simple (working copy) |
304 |
+@@ -1,12 +1,12 @@ |
305 |
+ |
306 |
+-CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include |
307 |
++CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include |
308 |
+ |
309 |
+ CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \ |
310 |
+ -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \ |
311 |
+ -lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \ |
312 |
+ -L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm |
313 |
+ |
314 |
+-INCLUDES = $(CLIPPER_CXXFLAGS) |
315 |
++INCLUDES = $(CLIPPER_CFLAGS) |
316 |
+ LDLIBS = $(CLIPPER_LIBS) |
317 |
+ |
318 |
+ rama-data: rama-data.cc |
319 |
+Index: auxil/sec-str/Makefile.am |
320 |
+=================================================================== |
321 |
+--- auxil/sec-str/Makefile.am (revision 4651) |
322 |
++++ auxil/sec-str/Makefile.am (working copy) |
323 |
+@@ -1,6 +1,6 @@ |
324 |
+ |
325 |
+ EXTRA_DIST = Makefile.simple sec-str-dist-check.cc sec-str-dist-check.hh |
326 |
+-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) |
327 |
++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) |
328 |
+ |
329 |
+ #check_PROGRAMS = sec-str-dist-check |
330 |
+ |
331 |
+Index: auxil/sec-str/Makefile.simple |
332 |
+=================================================================== |
333 |
+--- auxil/sec-str/Makefile.simple (revision 4651) |
334 |
++++ auxil/sec-str/Makefile.simple (working copy) |
335 |
+@@ -1,27 +1,27 @@ |
336 |
+ |
337 |
+-#CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include |
338 |
++#CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include |
339 |
+ |
340 |
+ #CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \ |
341 |
+ # -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \ |
342 |
+ # -lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \ |
343 |
+ # -L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm |
344 |
+ |
345 |
+-#INCLUDES = $(CLIPPER_CXXFLAGS) |
346 |
++#INCLUDES = $(CLIPPER_CFLAGS) |
347 |
+ #LDLIBS = $(CLIPPER_LIBS) |
348 |
+ |
349 |
+ |
350 |
+ # |
351 |
+ |
352 |
+ BASE = /home/paule/autobuild/Linux-kalypso-pre-release |
353 |
+-CLIPPER_CXXFLAGS = -I$(BASE)/include |
354 |
+-MMDB_CXXFLAGS = -I$(BASE)/include/mmdb |
355 |
++CLIPPER_CFLAGS = -I$(BASE)/include |
356 |
++MMDB_CFLAGS = -I$(BASE)/include/mmdb |
357 |
+ |
358 |
+ CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \ |
359 |
+ -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \ |
360 |
+ -lclipper-core -lccp4c -L$(BASE)/lib \ |
361 |
+ -L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm |
362 |
+ |
363 |
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) |
364 |
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) |
365 |
+ LDLIBS = $(CLIPPER_LIBS) |
366 |
+ |
367 |
+ sec-str-dist-check: sec-str-dist-check.cc sec-str-dist-check.hh |
368 |
+Index: auxil/strand-analysis/Makefile.am |
369 |
+=================================================================== |
370 |
+--- auxil/strand-analysis/Makefile.am (revision 4651) |
371 |
++++ auxil/strand-analysis/Makefile.am (working copy) |
372 |
+@@ -3,8 +3,8 @@ |
373 |
+ |
374 |
+ |
375 |
+ INCLUDES = -I$(top_srcdir)/auxil/sec-str \ |
376 |
+- $(MMDB_CXXFLAGS) \ |
377 |
+- $(CLIPPER_CXXFLAGS) |
378 |
++ $(MMDB_CFLAGS) \ |
379 |
++ $(CLIPPER_CFLAGS) |
380 |
+ |
381 |
+ |
382 |
+ check_PROGRAMS = |
383 |
+Index: auxil/strand-analysis/Makefile.simple |
384 |
+=================================================================== |
385 |
+--- auxil/strand-analysis/Makefile.simple (revision 4651) |
386 |
++++ auxil/strand-analysis/Makefile.simple (working copy) |
387 |
+@@ -2,13 +2,13 @@ |
388 |
+ |
389 |
+ CLIPPER = /Users/paulemsley/ccp4/ysbl-distro-based |
390 |
+ |
391 |
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include |
392 |
++CLIPPER_CFLAGS = -I$(CLIPPER)/include |
393 |
+ |
394 |
+ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-ccp4 \ |
395 |
+ -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \ |
396 |
+ -lclipper-core -lccp4c -lmmdb -lm -lrfftw -lfftw -lz -lm |
397 |
+ |
398 |
+-INCLUDES = -I../sec-str $(CLIPPER_CXXFLAGS) |
399 |
++INCLUDES = -I../sec-str $(CLIPPER_CFLAGS) |
400 |
+ LDLIBS = $(CLIPPER_LIBS) |
401 |
+ |
402 |
+ .cc: |
403 |
+Index: auxil/vectors/Makefile.am |
404 |
+=================================================================== |
405 |
+--- auxil/vectors/Makefile.am (revision 4651) |
406 |
++++ auxil/vectors/Makefile.am (working copy) |
407 |
+@@ -1,6 +1,6 @@ |
408 |
+ |
409 |
+ EXTRA_DIST = Makefile.simple diff-vec.cc |
410 |
+-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) |
411 |
++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) |
412 |
+ check_PROGRAMS = |
413 |
+ |
414 |
+ #diff_vec_SOURCES = diff-vec.cc |
415 |
+Index: build/Makefile.am |
416 |
+=================================================================== |
417 |
+--- build/Makefile.am (revision 4651) |
418 |
++++ build/Makefile.am (working copy) |
419 |
+@@ -24,8 +24,8 @@ |
420 |
+ |
421 |
+ INCLUDES = \ |
422 |
+ -I$(top_srcdir)/angles \ |
423 |
+- $(CLIPPER_CXXFLAGS) \ |
424 |
+- $(MMDB_CXXFLAGS) |
425 |
++ $(CLIPPER_CFLAGS) \ |
426 |
++ $(MMDB_CFLAGS) |
427 |
+ |
428 |
+ noinst_PROGRAMS = testcabuild |
429 |
+ |
430 |
+Index: ccp4mg-utils/Makefile.am |
431 |
+=================================================================== |
432 |
+--- ccp4mg-utils/Makefile.am (revision 4651) |
433 |
++++ ccp4mg-utils/Makefile.am (working copy) |
434 |
+@@ -25,7 +25,7 @@ |
435 |
+ EXTRA_DIST = convert.sh get-new-utils.sh |
436 |
+ |
437 |
+ INCLUDES = \ |
438 |
+- $(MMDB_CXXFLAGS) \ |
439 |
++ $(MMDB_CFLAGS) \ |
440 |
+ $(LIBPNG_CFLAGS) |
441 |
+ |
442 |
+ libccp4mg_utils_la_SOURCES = geomutil.cc mgtree.cc cartesian.cc \ |
443 |
+Index: ccp4mg-utils/mmut/Makefile.am |
444 |
+=================================================================== |
445 |
+--- ccp4mg-utils/mmut/Makefile.am (revision 4651) |
446 |
++++ ccp4mg-utils/mmut/Makefile.am (working copy) |
447 |
+@@ -70,9 +70,9 @@ |
448 |
+ $(LIBGLADE_CFLAGS) \ |
449 |
+ @GTK_CFLAGS@ \ |
450 |
+ $(GLUT_CFLAGS) \ |
451 |
+- $(MMDBSSM_CXXFLAGS) \ |
452 |
+- $(MMDB_CXXFLAGS) \ |
453 |
+- $(CLIPPER_CXXFLAGS) |
454 |
++ $(MMDBSSM_CFLAGS) \ |
455 |
++ $(MMDB_CFLAGS) \ |
456 |
++ $(CLIPPER_CFLAGS) |
457 |
+ |
458 |
+ # $(WITH_SCRIPT_CFLAGS) |
459 |
+ |
460 |
+Index: ccp4mg-utils/pygl/Makefile.am |
461 |
+=================================================================== |
462 |
+--- ccp4mg-utils/pygl/Makefile.am (revision 4651) |
463 |
++++ ccp4mg-utils/pygl/Makefile.am (working copy) |
464 |
+@@ -108,9 +108,9 @@ |
465 |
+ $(LIBGLADE_CFLAGS) \ |
466 |
+ @GTK_CFLAGS@ \ |
467 |
+ $(GLUT_CFLAGS) \ |
468 |
+- $(MMDBSSM_CXXFLAGS) \ |
469 |
+- $(MMDB_CXXFLAGS) \ |
470 |
+- $(CLIPPER_CXXFLAGS) |
471 |
++ $(MMDBSSM_CFLAGS) \ |
472 |
++ $(MMDB_CFLAGS) \ |
473 |
++ $(CLIPPER_CFLAGS) |
474 |
+ |
475 |
+ # $(WITH_SCRIPT_CFLAGS) |
476 |
+ |
477 |
+Index: ccp4mg-utils/util/Makefile.am |
478 |
+=================================================================== |
479 |
+--- ccp4mg-utils/util/Makefile.am (revision 4651) |
480 |
++++ ccp4mg-utils/util/Makefile.am (working copy) |
481 |
+@@ -73,9 +73,9 @@ |
482 |
+ $(LIBGLADE_CFLAGS) \ |
483 |
+ @GTK_CFLAGS@ \ |
484 |
+ $(GLUT_CFLAGS) \ |
485 |
+- $(MMDBSSM_CXXFLAGS) \ |
486 |
+- $(MMDB_CXXFLAGS) \ |
487 |
+- $(CLIPPER_CXXFLAGS) |
488 |
++ $(MMDBSSM_CFLAGS) \ |
489 |
++ $(MMDB_CFLAGS) \ |
490 |
++ $(CLIPPER_CFLAGS) |
491 |
+ |
492 |
+ # $(WITH_SCRIPT_CFLAGS) |
493 |
+ |
494 |
+Index: configure.in |
495 |
+=================================================================== |
496 |
+--- configure.in (revision 4651) |
497 |
++++ configure.in (working copy) |
498 |
+@@ -108,14 +108,18 @@ |
499 |
+ |
500 |
+ |
501 |
+ dnl Check for MMDB. |
502 |
+-AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,) |
503 |
++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2],,[AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)]) |
504 |
+ |
505 |
+-AM_WITH_MMDBSSM |
506 |
++PKG_CHECK_MODULES([MMDBSSM],[ssm],,[AM_WITH_MMDBSSM]) |
507 |
+ AM_WITH_CCP4SRS |
508 |
+ |
509 |
+ dnl Check for Clipper. we exit if clipper is not found. |
510 |
+ # |
511 |
+-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])) |
512 |
++PKG_CHECK_MODULES([CLIPPER], [clipper libccp4c], [ |
513 |
++ CLIPPER_LIBS="${CLIPPER_LIBS} -lrfftw -lfftw"; AC_SUBST([CLIPPER_LIBS]) |
514 |
++ ], [ |
515 |
++ 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])) |
516 |
++ ]) |
517 |
+ |
518 |
+ # we set default coot_guile to true |
519 |
+ coot_guile=true |
520 |
+@@ -189,11 +193,15 @@ |
521 |
+ |
522 |
+ dnl =========================== GooCanvas ================================ |
523 |
+ |
524 |
+-AM_PATH_GOOCANVAS |
525 |
+-# give something for the preprocessor to chew on... |
526 |
+-if test "$GOOCANVAS_CFLAGS" != "" ; then |
527 |
+- GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS" |
528 |
+-fi |
529 |
++PKG_CHECK_MODULES([GOOCANVAS], [goocanvas], |
530 |
++ [GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"; AC_SUBST(GOOCANVAS_CFLAGS)], |
531 |
++ [ |
532 |
++ AM_PATH_GOOCANVAS |
533 |
++ # give something for the preprocessor to chew on... |
534 |
++ if test "$GOOCANVAS_CFLAGS" != "" ; then |
535 |
++ GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS" |
536 |
++ fi |
537 |
++ ]) |
538 |
+ |
539 |
+ AC_ARG_WITH(enterprise-tools, [ --with-enterprise-tools with optional complicated/experimental ligand-related dependencies ], |
540 |
+ coot_enterprise_additions="true", |
541 |
+Index: coords/Makefile.am |
542 |
+=================================================================== |
543 |
+--- coords/Makefile.am (revision 4651) |
544 |
++++ coords/Makefile.am (working copy) |
545 |
+@@ -34,7 +34,7 @@ |
546 |
+ -I$(top_srcdir)/compat \ |
547 |
+ $(ENTERPRISE_TOOLS_CFLAGS) \ |
548 |
+ $(RDKIT_CXXFLAGS) \ |
549 |
+- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) |
550 |
++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) |
551 |
+ |
552 |
+ AM_CXXFLAGS = \ |
553 |
+ -DPKGDATADIR='"$(pkgdatadir)"' \ |
554 |
+Index: coot-surface/Makefile.am |
555 |
+=================================================================== |
556 |
+--- coot-surface/Makefile.am (revision 4651) |
557 |
++++ coot-surface/Makefile.am (working copy) |
558 |
+@@ -21,7 +21,7 @@ |
559 |
+ INCLUDES = -I$(top_srcdir)/surface \ |
560 |
+ -I$(top_srcdir)/coot-utils \ |
561 |
+ -I$(top_srcdir)/mini-mol \ |
562 |
+- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS) |
563 |
++ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS) |
564 |
+ |
565 |
+ lib_LTLIBRARIES = libcoot-surface.la |
566 |
+ |
567 |
+Index: coot-utils/Makefile.am |
568 |
+=================================================================== |
569 |
+--- coot-utils/Makefile.am (revision 4651) |
570 |
++++ coot-utils/Makefile.am (working copy) |
571 |
+@@ -38,8 +38,8 @@ |
572 |
+ -I$(top_srcdir)/geometry \ |
573 |
+ -I$(top_srcdir)/compat \ |
574 |
+ -I$(top_srcdir)/mini-mol \ |
575 |
+- $(CLIPPER_CXXFLAGS) \ |
576 |
+- $(MMDB_CXXFLAGS) \ |
577 |
++ $(CLIPPER_CFLAGS) \ |
578 |
++ $(MMDB_CFLAGS) \ |
579 |
+ $(GSL_CFLAGS) \ |
580 |
+ $(WITH_GUILE_CFLAGS) \ |
581 |
+ $(WITH_PYTHON_CFLAGS) |
582 |
+Index: cootaneer/Makefile.am |
583 |
+=================================================================== |
584 |
+--- cootaneer/Makefile.am (revision 4651) |
585 |
++++ cootaneer/Makefile.am (working copy) |
586 |
+@@ -20,7 +20,7 @@ |
587 |
+ EXTRA_DIST = \ |
588 |
+ cootaneer-llk-2.40.dat |
589 |
+ |
590 |
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) |
591 |
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) |
592 |
+ |
593 |
+ cootaneer_demo_SOURCES = cootaneer-demo.cpp |
594 |
+ |
595 |
+Index: cootilus/Makefile.am |
596 |
+=================================================================== |
597 |
+--- cootilus/Makefile.am (revision 4651) |
598 |
++++ cootilus/Makefile.am (working copy) |
599 |
+@@ -20,7 +20,7 @@ |
600 |
+ EXTRA_DIST = \ |
601 |
+ nautilus_lib.pdb |
602 |
+ |
603 |
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) |
604 |
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) |
605 |
+ |
606 |
+ cootilus_demo_SOURCES = cootilus-demo.cpp |
607 |
+ |
608 |
+Index: db-main/Makefile.am |
609 |
+=================================================================== |
610 |
+--- db-main/Makefile.am (revision 4651) |
611 |
++++ db-main/Makefile.am (working copy) |
612 |
+@@ -6,7 +6,7 @@ |
613 |
+ -DDATADIR='"$(datadir)"' |
614 |
+ |
615 |
+ INCLUDES = -I$(top_srcdir)/utils -I$(top_srcdir)/coot-utils -I$(top_srcdir)/mini-mol \ |
616 |
+- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) |
617 |
++ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) |
618 |
+ |
619 |
+ include_HEADERS = db-main.hh db-strands.hh |
620 |
+ |
621 |
+Index: db-main/Makefile.simple |
622 |
+=================================================================== |
623 |
+--- db-main/Makefile.simple (revision 4651) |
624 |
++++ db-main/Makefile.simple (working copy) |
625 |
+@@ -19,7 +19,7 @@ |
626 |
+ MCCP4 = $(HOME)/crystal |
627 |
+ |
628 |
+ CXX = g++ |
629 |
+-MMDB_CXXFLAGS = -I$(MMDB)/include |
630 |
++MMDB_CFLAGS = -I$(MMDB)/include |
631 |
+ FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw |
632 |
+ |
633 |
+ MMDB_LIBS = -L$(MMDB)/lib -lmmdb |
634 |
+@@ -28,9 +28,9 @@ |
635 |
+ -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS) |
636 |
+ |
637 |
+ MCCP4_CFLAGS = -I$(MCCP4)/include |
638 |
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include |
639 |
++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include |
640 |
+ |
641 |
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol |
642 |
++INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol |
643 |
+ |
644 |
+ CXXFLAGS = -g $(INCLUDES) |
645 |
+ LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS) |
646 |
+@@ -44,4 +44,4 @@ |
647 |
+ db-main.o: db-main.cc db-main.hh |
648 |
+ |
649 |
+ testmmdbbits: testmmdbbits.cc |
650 |
+- $(CXX) $(MMDB_CXXFLAGS) $(MMDB_LIBS) $? -o $@ |
651 |
++ $(CXX) $(MMDB_CFLAGS) $(MMDB_LIBS) $? -o $@ |
652 |
+Index: density-contour/Makefile.am |
653 |
+=================================================================== |
654 |
+--- density-contour/Makefile.am (revision 4651) |
655 |
++++ density-contour/Makefile.am (working copy) |
656 |
+@@ -20,7 +20,7 @@ |
657 |
+ |
658 |
+ COORD_INCLUDES = -I$(top_srcdir)/coords |
659 |
+ |
660 |
+-INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CXXFLAGS) |
661 |
++INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CFLAGS) |
662 |
+ |
663 |
+ lib_LTLIBRARIES = libcoot-isosurface.la |
664 |
+ |
665 |
+Index: geometry/Makefile.am |
666 |
+=================================================================== |
667 |
+--- geometry/Makefile.am (revision 4651) |
668 |
++++ geometry/Makefile.am (working copy) |
669 |
+@@ -29,7 +29,7 @@ |
670 |
+ -I$(top_srcdir)/mini-mol \ |
671 |
+ -I$(top_srcdir)/coot-utils \ |
672 |
+ -I$(top_srcdir)/compat \ |
673 |
+- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) |
674 |
++ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) |
675 |
+ |
676 |
+ AM_CXXFLAGS = \ |
677 |
+ -DDATADIR='"$(datadir)"' \ |
678 |
+Index: geometry/Makefile.simple |
679 |
+=================================================================== |
680 |
+--- geometry/Makefile.simple (revision 4651) |
681 |
++++ geometry/Makefile.simple (working copy) |
682 |
+@@ -46,7 +46,7 @@ |
683 |
+ |
684 |
+ |
685 |
+ CXX = g++ |
686 |
+-MMDB_CXXFLAGS = -I$(MMDB)/include |
687 |
++MMDB_CFLAGS = -I$(MMDB)/include |
688 |
+ FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw |
689 |
+ |
690 |
+ MMDB_LIBS = -L$(MMDB)/lib -lmmdb |
691 |
+@@ -55,9 +55,9 @@ |
692 |
+ -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS) |
693 |
+ |
694 |
+ MCCP4_CFLAGS = -I$(MCCP4)/include |
695 |
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include |
696 |
++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include |
697 |
+ |
698 |
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -I$(top_srcdir)/coords |
699 |
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/coords |
700 |
+ |
701 |
+ top_srcdir = .. |
702 |
+ |
703 |
+Index: high-res/Makefile.am |
704 |
+=================================================================== |
705 |
+--- high-res/Makefile.am (revision 4651) |
706 |
++++ high-res/Makefile.am (working copy) |
707 |
+@@ -36,8 +36,8 @@ |
708 |
+ -I$(top_srcdir)/coot-utils \ |
709 |
+ -I$(top_srcdir)/lidia-core \ |
710 |
+ -I$(top_srcdir)/compat \ |
711 |
+- $(MMDB_CXXFLAGS) \ |
712 |
+- $(CLIPPER_CXXFLAGS) |
713 |
++ $(MMDB_CFLAGS) \ |
714 |
++ $(CLIPPER_CFLAGS) |
715 |
+ |
716 |
+ libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \ |
717 |
+ sequence-assignment.cc |
718 |
+Index: ideal/Makefile.am |
719 |
+=================================================================== |
720 |
+--- ideal/Makefile.am (revision 4651) |
721 |
++++ ideal/Makefile.am (working copy) |
722 |
+@@ -37,11 +37,11 @@ |
723 |
+ -I$(top_srcdir)/coot-utils \ |
724 |
+ -I$(top_srcdir)/mini-mol \ |
725 |
+ -I$(top_srcdir)/geometry \ |
726 |
+- $(CLIPPER_CXXFLAGS) \ |
727 |
+- $(MMDB_CXXFLAGS) |
728 |
++ $(CLIPPER_CFLAGS) \ |
729 |
++ $(MMDB_CFLAGS) |
730 |
+ |
731 |
+ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) $(COOT_WINDOWS_CFLAGS) \ |
732 |
+- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) $(COOT_GSL_FLAGS) |
733 |
++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) $(COOT_GSL_FLAGS) |
734 |
+ AM_LDFLAGS = $(GSL_LIBS) $(MMDB_LIBS) $(CLIPPER_LIBS) |
735 |
+ |
736 |
+ |
737 |
+Index: ideal/Makefile.simple |
738 |
+=================================================================== |
739 |
+--- ideal/Makefile.simple (revision 4651) |
740 |
++++ ideal/Makefile.simple (working copy) |
741 |
+@@ -44,7 +44,7 @@ |
742 |
+ |
743 |
+ |
744 |
+ CXX = g++ |
745 |
+-MMDB_CXXFLAGS = -I$(MMDB)/include |
746 |
++MMDB_CFLAGS = -I$(MMDB)/include |
747 |
+ FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw |
748 |
+ |
749 |
+ MMDB_LIBS = -L$(MMDB)/lib -lmmdb |
750 |
+@@ -53,9 +53,9 @@ |
751 |
+ -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS) |
752 |
+ |
753 |
+ MCCP4_CFLAGS = -I$(MCCP4)/include |
754 |
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include |
755 |
++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include |
756 |
+ |
757 |
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) \ |
758 |
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) \ |
759 |
+ -I$(top_srcdir)/coords \ |
760 |
+ -I$(top_srcdir)/geometry |
761 |
+ |
762 |
+Index: lbg/Makefile.am |
763 |
+=================================================================== |
764 |
+--- lbg/Makefile.am (revision 4651) |
765 |
++++ lbg/Makefile.am (working copy) |
766 |
+@@ -11,7 +11,7 @@ |
767 |
+ $(GSL_CFLAGS) \ |
768 |
+ $(GOOCANVAS_CFLAGS) \ |
769 |
+ $(GTK_CFLAGS) \ |
770 |
+- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \ |
771 |
++ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \ |
772 |
+ $(COOT_WINDOWS_CFLAGS) \ |
773 |
+ $(ENTERPRISE_TOOLS_CFLAGS) \ |
774 |
+ $(RDKIT_CXXFLAGS) \ |
775 |
+Index: lbg/Makefile.simple |
776 |
+=================================================================== |
777 |
+--- lbg/Makefile.simple (revision 4651) |
778 |
++++ lbg/Makefile.simple (working copy) |
779 |
+@@ -24,11 +24,11 @@ |
780 |
+ MMDB=$(CRYST) |
781 |
+ # MMDB=$(HOME)/test/mmdb |
782 |
+ |
783 |
+-MMDB_CXXFLAGS=-I$(MMDB)/include/mmdb |
784 |
++MMDB_CFLAGS=-I$(MMDB)/include/mmdb |
785 |
+ MMDB_LDFLAGS=$(MMDB)/lib/libmmdb.la |
786 |
+ |
787 |
+ CLIPPER=$(CRYST) |
788 |
+-CLIPPER_CXXFLAGS=-I$(CLIPPER)/include |
789 |
++CLIPPER_CFLAGS=-I$(CLIPPER)/include |
790 |
+ CLIPPER_LDFLAGS=$(CLIPPER)/lib/libclipper-core.la \ |
791 |
+ $(CLIPPER)/lib/librfftw.la \ |
792 |
+ $(CLIPPER)/lib/libfftw.la |
793 |
+@@ -40,7 +40,7 @@ |
794 |
+ LIDIA_CORE_LDFLAGS = $(COOT_INSTALLED)/lib/libcoot-lidia-core.la |
795 |
+ |
796 |
+ |
797 |
+-CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(LIDIA_CORE_CXXFLAGS) \ |
798 |
++CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(LIDIA_CORE_CXXFLAGS) \ |
799 |
+ -I$(top_srcdir)/compat |
800 |
+ |
801 |
+ lbg: lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o residue-circles.o |
802 |
+Index: lidia-core/Makefile.am |
803 |
+=================================================================== |
804 |
+--- lidia-core/Makefile.am (revision 4651) |
805 |
++++ lidia-core/Makefile.am (working copy) |
806 |
+@@ -22,7 +22,7 @@ |
807 |
+ |
808 |
+ # 20110408 I add a CResidue,dictionary_residue_restraints_t constructor to molfile_molecule_t |
809 |
+ # simple |
810 |
+-#INCLUDES = $(CLIPPER_CXXFLAGS) |
811 |
++#INCLUDES = $(CLIPPER_CFLAGS) |
812 |
+ # |
813 |
+ INCLUDES = \ |
814 |
+ -I$(top_srcdir)/geometry \ |
815 |
+@@ -31,7 +31,7 @@ |
816 |
+ -I$(top_srcdir)/utils \ |
817 |
+ $(ENTERPRISE_TOOLS_CFLAGS) \ |
818 |
+ $(RDKIT_CXXFLAGS) \ |
819 |
+- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) |
820 |
++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) |
821 |
+ |
822 |
+ libcoot_lidia_core_la_SOURCES = lbg-shared.cc lbg-molfile.cc lig-build.cc rdkit-interface.cc \ |
823 |
+ cod-types.cc |
824 |
+Index: ligand/Makefile.am |
825 |
+=================================================================== |
826 |
+--- ligand/Makefile.am (revision 4651) |
827 |
++++ ligand/Makefile.am (working copy) |
828 |
+@@ -36,7 +36,7 @@ |
829 |
+ -I$(top_srcdir)/db-main \ |
830 |
+ $(COOT_GSL_FLAGS) \ |
831 |
+ $(GSL_CFLAGS) \ |
832 |
+- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) |
833 |
++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) |
834 |
+ |
835 |
+ include_HEADERS = ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh \ |
836 |
+ chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh \ |
837 |
+Index: macros/clipper.m4 |
838 |
+=================================================================== |
839 |
+--- macros/clipper.m4 (revision 4651) |
840 |
++++ macros/clipper.m4 (working copy) |
841 |
+@@ -56,7 +56,7 @@ |
842 |
+ # |
843 |
+ # should use clipper-config --cflags |
844 |
+ # |
845 |
+- CLIPPER_CXXFLAGS="-I$clipper_prefix/include" |
846 |
++ CLIPPER_CFLAGS="-I$clipper_prefix/include" |
847 |
+ # -I$clipper_prefix/cctbx |
848 |
+ |
849 |
+ # yes, libmmtz.a is in -L$clipper_prefix/umtz! |
850 |
+@@ -75,7 +75,7 @@ |
851 |
+ # |
852 |
+ ccp4c=ccp4c |
853 |
+ |
854 |
+- CLIPPER_LDOPTS="-L$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${fftw_pre}fftw -lz -lm" |
855 |
++ CLIPPER_LIBS="-L$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${fftw_pre}fftw -lz -lm" |
856 |
+ # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx |
857 |
+ |
858 |
+ |
859 |
+@@ -102,8 +102,8 @@ |
860 |
+ # this needs to be 'configured' - typically either s or blank. |
861 |
+ fftw_pre= |
862 |
+ |
863 |
+- CLIPPER_CXXFLAGS="$CCP4_CFLAGS" |
864 |
+- 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${fftw_pre}fftw -lz -lm" |
865 |
++ CLIPPER_CFLAGS="$CCP4_CFLAGS" |
866 |
++ 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" |
867 |
+ fi |
868 |
+ |
869 |
+ # BL: workaround needed for new MinGW |
870 |
+@@ -113,17 +113,17 @@ |
871 |
+ case $ac_cv_build_alias in |
872 |
+ # BL says:: same as for cygwin in mingw |
873 |
+ MINGW*|Mingw*|*mingw*|Cygwin*|CYGWIN*|*cygwin*) |
874 |
+- CLIPPER_LDOPTS=$CLIPPER_LDOPTS |
875 |
++ CLIPPER_LIBS=$CLIPPER_LIBS |
876 |
+ ;; |
877 |
+ *) |
878 |
+- CLIPPER_LDOPTS=$CLIPPER_LDOPTS" -lpthread" |
879 |
++ CLIPPER_LIBS=$CLIPPER_LIBS" -lpthread" |
880 |
+ ;; |
881 |
+ esac |
882 |
+ |
883 |
+ AC_MSG_CHECKING([for Clipper]) |
884 |
+ |
885 |
+- LIBS="$save_LIBS $CLIPPER_LDOPTS" |
886 |
+- CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS" |
887 |
++ LIBS="$save_LIBS $CLIPPER_LIBS" |
888 |
++ CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS" |
889 |
+ # AC_TRY_LINK uses the c compiler, so we will temporarily |
890 |
+ # reassign $CC to the c++ compiler. |
891 |
+ # |
892 |
+@@ -140,7 +140,7 @@ |
893 |
+ |
894 |
+ LIBS="$saved_LIBS" |
895 |
+ CFLAGS="$saved_CFLAGS" |
896 |
+- CLIPPER_LIBS="$CLIPPER_LDOPTS" |
897 |
++ CLIPPER_LIBS="$CLIPPER_LIBS" |
898 |
+ ifelse([$1], , :, [$1]) |
899 |
+ |
900 |
+ else |
901 |
+@@ -148,12 +148,12 @@ |
902 |
+ LIBS="$saved_LIBS" |
903 |
+ CFLAGS="$saved_CFLAGS" |
904 |
+ CLIPPER_LIBS="" |
905 |
+- CLIPPER_CXXFLAGS="" |
906 |
++ CLIPPER_CFLAGS="" |
907 |
+ ifelse([$2], , :, [$2]) |
908 |
+ |
909 |
+ fi |
910 |
+ |
911 |
+-AC_SUBST(CLIPPER_CXXFLAGS) |
912 |
++AC_SUBST(CLIPPER_CFLAGS) |
913 |
+ AC_SUBST(CLIPPER_LIBS) |
914 |
+ |
915 |
+ ]) |
916 |
+Index: macros/clipper.m4.old |
917 |
+=================================================================== |
918 |
+--- macros/clipper.m4.old (revision 4651) |
919 |
++++ macros/clipper.m4.old (working copy) |
920 |
+@@ -34,7 +34,7 @@ |
921 |
+ # should ideally be CLIPPER_CFLAGS="-I$clipper_prefix/include", and the like |
922 |
+ # when clipper and dependencies get installed. |
923 |
+ # |
924 |
+- CLIPPER_CXXFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include" |
925 |
++ CLIPPER_CFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include" |
926 |
+ # -I$clipper_prefix/cctbx |
927 |
+ |
928 |
+ # yes, libmmtz.a is in -L$clipper_prefix/umtz! |
929 |
+@@ -45,20 +45,20 @@ |
930 |
+ # HACK! FIXME |
931 |
+ # added lz, we should have proper autoconf check for this. |
932 |
+ # |
933 |
+- 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" |
934 |
++ 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" |
935 |
+ # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx |
936 |
+ else |
937 |
+ # the compiler looks in the "standard" places for clipper. In real life, |
938 |
+ # it would be quite unlikely that clipper would be installed in /usr/include, |
939 |
+ # /usr/lib etc. so this code will not usually find the right dependencies. |
940 |
+- CLIPPER_CXXFLAGS="" |
941 |
+- CLIPPER_LDOPTS="" |
942 |
++ CLIPPER_CFLAGS="" |
943 |
++ CLIPPER_LIBS="" |
944 |
+ fi |
945 |
+ |
946 |
+ AC_MSG_CHECKING([for Clipper]) |
947 |
+ |
948 |
+- LIBS="$save_LIBS $CLIPPER_LDOPTS" |
949 |
+- CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS" |
950 |
++ LIBS="$save_LIBS $CLIPPER_LIBS" |
951 |
++ CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS" |
952 |
+ # AC_TRY_LINK uses the c compiler, so we will temporarily |
953 |
+ # reassign $CC to the c++ compiler. |
954 |
+ # |
955 |
+@@ -72,7 +72,7 @@ |
956 |
+ |
957 |
+ LIBS="$saved_LIBS" |
958 |
+ CFLAGS="$saved_CFLAGS" |
959 |
+- CLIPPER_LIBS="$CLIPPER_LDOPTS" |
960 |
++ CLIPPER_LIBS="$CLIPPER_LIBS" |
961 |
+ ifelse([$1], , :, [$1]) |
962 |
+ |
963 |
+ else |
964 |
+@@ -80,12 +80,12 @@ |
965 |
+ LIBS="$saved_LIBS" |
966 |
+ CFLAGS="$saved_CFLAGS" |
967 |
+ CLIPPER_LIBS="" |
968 |
+- CLIPPER_CXXFLAGS="" |
969 |
++ CLIPPER_CFLAGS="" |
970 |
+ ifelse([$2], , :, [$2]) |
971 |
+ |
972 |
+ fi |
973 |
+ |
974 |
+-AC_SUBST(CLIPPER_CXXFLAGS) |
975 |
++AC_SUBST(CLIPPER_CFLAGS) |
976 |
+ AC_SUBST(CLIPPER_LIBS) |
977 |
+ |
978 |
+ ]) |
979 |
+Index: macros/goo-canvas.m4 |
980 |
+=================================================================== |
981 |
+--- macros/goo-canvas.m4 (revision 4651) |
982 |
++++ macros/goo-canvas.m4 (working copy) |
983 |
+@@ -36,9 +36,9 @@ |
984 |
+ # GCC c++ does not. |
985 |
+ # |
986 |
+ if test -e $goocanvas_prefix/lib/libgoocanvas.la ; then |
987 |
+- GOOCANVAS_LDOPTS="$goocanvas_prefix/lib/libgoocanvas.la" |
988 |
++ GOOCANVAS_LIBS="$goocanvas_prefix/lib/libgoocanvas.la" |
989 |
+ else |
990 |
+- GOOCANVAS_LDOPTS="-L$goocanvas_prefix/lib -lgoocanvas" |
991 |
++ GOOCANVAS_LIBS="-L$goocanvas_prefix/lib -lgoocanvas" |
992 |
+ fi |
993 |
+ else |
994 |
+ # the compiler looks in the "standard" places for GOOCANVAS. (or uses pkgconfig) |
995 |
+@@ -57,19 +57,19 @@ |
996 |
+ break;; |
997 |
+ esac |
998 |
+ if test -e /usr/lib/libgoocanvas.la ; then |
999 |
+- GOOCANVAS_LDOPTS="libgoocanvas.la" |
1000 |
++ GOOCANVAS_LIBS="libgoocanvas.la" |
1001 |
+ else |
1002 |
+ if test -z "${PKG_CONFIG}"; then |
1003 |
+- GOOCANVAS_LDOPTS="-lgoocanvas" |
1004 |
++ GOOCANVAS_LIBS="-lgoocanvas" |
1005 |
+ else |
1006 |
+- GOOCANVAS_LDOPTS=`$PKG_CONFIG goocanvas --libs` |
1007 |
++ GOOCANVAS_LIBS=`$PKG_CONFIG goocanvas --libs` |
1008 |
+ fi |
1009 |
+ fi |
1010 |
+ fi |
1011 |
+ |
1012 |
+ AC_MSG_CHECKING([for Goocanvas]) |
1013 |
+ |
1014 |
+-LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS" |
1015 |
++LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS" |
1016 |
+ CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS" |
1017 |
+ # |
1018 |
+ # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will |
1019 |
+@@ -95,7 +95,7 @@ |
1020 |
+ if test x$have_goocanvas = xyes; then |
1021 |
+ |
1022 |
+ GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS" |
1023 |
+- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS" |
1024 |
++ GOOCANVAS_LIBS="$GOOCANVAS_LIBS" |
1025 |
+ |
1026 |
+ ifelse([$1], , :, [$1]) |
1027 |
+ |
1028 |
+Index: macros/mmdb-ssm.m4 |
1029 |
+=================================================================== |
1030 |
+--- macros/mmdb-ssm.m4 (revision 4651) |
1031 |
++++ macros/mmdb-ssm.m4 (working copy) |
1032 |
+@@ -32,7 +32,7 @@ |
1033 |
+ |
1034 |
+ if test x$with_ssmlib_prefix != x; then |
1035 |
+ |
1036 |
+- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB" |
1037 |
++ MMDBSSM_CFLAGS="-DHAVE_SSMLIB" |
1038 |
+ MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm" |
1039 |
+ |
1040 |
+ ac_mmdb_dirs=' |
1041 |
+@@ -47,16 +47,16 @@ |
1042 |
+ |
1043 |
+ for ac_dir in $ac_mmdb_dirs; do |
1044 |
+ if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then |
1045 |
+- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir" |
1046 |
++ ac_MMDBSSM_CFLAGS="-I$with_ssmlib_prefix/$ac_dir" |
1047 |
+ break |
1048 |
+ fi |
1049 |
+ done |
1050 |
+ |
1051 |
+- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS" |
1052 |
++ MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS" |
1053 |
+ |
1054 |
+ else |
1055 |
+ |
1056 |
+- MMDBSSM_CXXFLAGS="" |
1057 |
++ MMDBSSM_CFLAGS="" |
1058 |
+ MMDBSSM_LIBS="" |
1059 |
+ with_ssmlib_prefix=no |
1060 |
+ |
1061 |
+@@ -64,6 +64,6 @@ |
1062 |
+ |
1063 |
+ AC_MSG_RESULT([$with_ssmlib_prefix]) |
1064 |
+ |
1065 |
+-AC_SUBST(MMDBSSM_CXXFLAGS) |
1066 |
++AC_SUBST(MMDBSSM_CFLAGS) |
1067 |
+ AC_SUBST(MMDBSSM_LIBS) |
1068 |
+ ]) |
1069 |
+Index: macros/mmdb.m4 |
1070 |
+=================================================================== |
1071 |
+--- macros/mmdb.m4 (revision 4651) |
1072 |
++++ macros/mmdb.m4 (working copy) |
1073 |
+@@ -55,7 +55,7 @@ |
1074 |
+ # --with-mmdb=/some/thing |
1075 |
+ # |
1076 |
+ |
1077 |
+- # should ideally be MMDB_CXXFLAGS="-I$MMDB_prefix/include", and the like |
1078 |
++ # should ideally be MMDB_CFLAGS="-I$MMDB_prefix/include", and the like |
1079 |
+ # when MMDB and dependencies get installed - we infact, include both |
1080 |
+ # directories. |
1081 |
+ # |
1082 |
+@@ -69,7 +69,7 @@ |
1083 |
+ lib/src/mmdb' |
1084 |
+ for ac_dir in $ac_mmdb_dirs; do |
1085 |
+ if test -r "$mmdb_prefix/$ac_dir/mmdb/mmdb_manager.h"; then |
1086 |
+- ac_MMDB_CXXFLAGS="-I$mmdb_prefix/$ac_dir" |
1087 |
++ ac_MMDB_CFLAGS="-I$mmdb_prefix/$ac_dir" |
1088 |
+ break |
1089 |
+ fi |
1090 |
+ done |
1091 |
+@@ -82,14 +82,14 @@ |
1092 |
+ # the compiler looks in the "standard" places for MMDB. In real life, |
1093 |
+ # it would be quite unlikely that MMDB would be installed in /usr/include, |
1094 |
+ # /usr/lib etc. so this code will not usually find the right dependencies. |
1095 |
+- ac_MMDB_CXXFLAGS="" |
1096 |
++ ac_MMDB_CFLAGS="" |
1097 |
+ ac_MMDB_LDOPTS="-lmmdb -lm" |
1098 |
+ fi |
1099 |
+ |
1100 |
+ AC_MSG_CHECKING([for MMDB]) |
1101 |
+ |
1102 |
+ LIBS="$save_LIBS $ac_MMDB_LDOPTS" |
1103 |
+- CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS" |
1104 |
++ CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CFLAGS" |
1105 |
+ # |
1106 |
+ # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will |
1107 |
+ # temporarily reassign $CC to the c++ compiler. |
1108 |
+@@ -118,7 +118,7 @@ |
1109 |
+ CLINKR_FLAG=-DMMDB_WITHOUT_LINKR |
1110 |
+ fi |
1111 |
+ CXXFLAGS="$saved_CXXFLAGS" |
1112 |
+- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG" |
1113 |
++ MMDB_CFLAGS="$ac_MMDB_CFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG" |
1114 |
+ MMDB_LIBS="$ac_MMDB_LDOPTS" |
1115 |
+ ifelse([$1], , :, [$1]) |
1116 |
+ |
1117 |
+@@ -134,12 +134,12 @@ |
1118 |
+ LIBS="$saved_LIBS" |
1119 |
+ CXXFLAGS="$saved_CXXFLAGS" |
1120 |
+ MMDB_LIBS="" |
1121 |
+- MMDB_CXXFLAGS="" |
1122 |
++ MMDB_CFLAGS="" |
1123 |
+ ifelse([$2], , :, [$2]) |
1124 |
+ |
1125 |
+ fi |
1126 |
+ |
1127 |
+-AC_SUBST(MMDB_CXXFLAGS) |
1128 |
++AC_SUBST(MMDB_CFLAGS) |
1129 |
+ AC_SUBST(MMDB_LIBS) |
1130 |
+ |
1131 |
+ ]) |
1132 |
+Index: mini-mol/Makefile.am |
1133 |
+=================================================================== |
1134 |
+--- mini-mol/Makefile.am (revision 4651) |
1135 |
++++ mini-mol/Makefile.am (working copy) |
1136 |
+@@ -25,8 +25,8 @@ |
1137 |
+ INCLUDES = \ |
1138 |
+ -I$(top_srcdir)/coot-utils \ |
1139 |
+ -I$(top_srcdir)/compat \ |
1140 |
+- $(CLIPPER_CXXFLAGS) \ |
1141 |
+- $(MMDB_CXXFLAGS) |
1142 |
++ $(CLIPPER_CFLAGS) \ |
1143 |
++ $(MMDB_CFLAGS) |
1144 |
+ |
1145 |
+ AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS) |
1146 |
+ |
1147 |
+Index: protein_db/Makefile.am |
1148 |
+=================================================================== |
1149 |
+--- protein_db/Makefile.am (revision 4651) |
1150 |
++++ protein_db/Makefile.am (working copy) |
1151 |
+@@ -19,7 +19,7 @@ |
1152 |
+ |
1153 |
+ lib_LTLIBRARIES=libcoot-protein-db.la |
1154 |
+ |
1155 |
+-INCLUDES= $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) |
1156 |
++INCLUDES= $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) |
1157 |
+ |
1158 |
+ include_HEADERS=protein_db.h protein_db_utils.h rna_db.h |
1159 |
+ |
1160 |
+Index: sequence-view/Makefile.am |
1161 |
+=================================================================== |
1162 |
+--- sequence-view/Makefile.am (revision 4651) |
1163 |
++++ sequence-view/Makefile.am (working copy) |
1164 |
+@@ -55,9 +55,9 @@ |
1165 |
+ -I$(top_srcdir)/analysis \ |
1166 |
+ -I$(top_srcdir)/cootaneer \ |
1167 |
+ -I$(top_srcdir)/src \ |
1168 |
+- $(CLIPPER_CXXFLAGS) \ |
1169 |
+- $(MMDB_CXXFLAGS) \ |
1170 |
+- $(MMDBSSM_CXXFLAGS) \ |
1171 |
++ $(CLIPPER_CFLAGS) \ |
1172 |
++ $(MMDB_CFLAGS) \ |
1173 |
++ $(MMDBSSM_CFLAGS) \ |
1174 |
+ $(GLUT_CFLAGS) \ |
1175 |
+ $(CANVAS_CFLAGS) \ |
1176 |
+ $(GTKGL_CONTEXT_CFLAGS) \ |
1177 |
+Index: skeleton/Makefile.am |
1178 |
+=================================================================== |
1179 |
+--- skeleton/Makefile.am (revision 4651) |
1180 |
++++ skeleton/Makefile.am (working copy) |
1181 |
+@@ -28,7 +28,7 @@ |
1182 |
+ -I$(top_srcdir)/angles \ |
1183 |
+ -I$(top_srcdir)/coot-utils \ |
1184 |
+ -I$(top_srcdir)/compat \ |
1185 |
+- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) |
1186 |
++ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) |
1187 |
+ |
1188 |
+ AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS) |
1189 |
+ |
1190 |
+Index: src/Makefile.am |
1191 |
+=================================================================== |
1192 |
+--- src/Makefile.am (revision 4651) |
1193 |
++++ src/Makefile.am (working copy) |
1194 |
+@@ -220,11 +220,11 @@ |
1195 |
+ $(GOOCANVAS_CFLAGS) \ |
1196 |
+ @GTK_CFLAGS@ \ |
1197 |
+ $(GLUT_CFLAGS) \ |
1198 |
+- $(MMDBSSM_CXXFLAGS) \ |
1199 |
+- $(MMDB_CXXFLAGS) \ |
1200 |
++ $(MMDBSSM_CFLAGS) \ |
1201 |
++ $(MMDB_CFLAGS) \ |
1202 |
+ $(CCP4SRS_CXXFLAGS) \ |
1203 |
+ $(GSL_CFLAGS) \ |
1204 |
+- $(CLIPPER_CXXFLAGS) \ |
1205 |
++ $(CLIPPER_CFLAGS) \ |
1206 |
+ $(PYGTK_CFLAGS) \ |
1207 |
+ $(GLOB_CFLAGS) \ |
1208 |
+ $(CURL_CFLAGS) |
1209 |
+Index: surface/Makefile.am |
1210 |
+=================================================================== |
1211 |
+--- surface/Makefile.am (revision 4651) |
1212 |
++++ surface/Makefile.am (working copy) |
1213 |
+@@ -1,5 +1,5 @@ |
1214 |
+ |
1215 |
+-INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(FFTW_CXXFLAGS) |
1216 |
++INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(FFTW_CXXFLAGS) |
1217 |
+ |
1218 |
+ AM_CXXFLAGS = $(OPENMP_CFLAGS) |
1219 |
+ |
1220 |
|
1221 |
diff --git a/sci-chemistry/coot/files/9999-ssm.patch b/sci-chemistry/coot/files/9999-ssm.patch |
1222 |
deleted file mode 100644 |
1223 |
index c801da7..0000000 |
1224 |
--- a/sci-chemistry/coot/files/9999-ssm.patch |
1225 |
+++ /dev/null |
1226 |
@@ -1,56 +0,0 @@ |
1227 |
- macros/mmdb-ssm.m4 | 42 +----------------------------------------- |
1228 |
- 1 files changed, 1 insertions(+), 41 deletions(-) |
1229 |
- |
1230 |
-diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4 |
1231 |
-index 1937a16..6ef547c 100644 |
1232 |
---- a/macros/mmdb-ssm.m4 |
1233 |
-+++ b/macros/mmdb-ssm.m4 |
1234 |
-@@ -22,47 +22,7 @@ |
1235 |
- AC_DEFUN([AM_WITH_MMDBSSM], |
1236 |
- [AC_PROVIDE([AM_USE_MMDBSSM]) |
1237 |
- |
1238 |
-- |
1239 |
--AC_ARG_WITH(ssmlib-prefix, |
1240 |
-- AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ), |
1241 |
-- [ with_ssmlib_prefix="$withval" ], |
1242 |
-- with_ssmlib_prefix="") |
1243 |
-- |
1244 |
--AC_MSG_CHECKING([for SSMLib]) |
1245 |
-- |
1246 |
--if test x$with_ssmlib_prefix != x; then |
1247 |
-- |
1248 |
-- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB" |
1249 |
-- MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm" |
1250 |
-- |
1251 |
--ac_mmdb_dirs=' |
1252 |
--. |
1253 |
--include |
1254 |
--include/ssm |
1255 |
--include/mmdb |
1256 |
--lib |
1257 |
--src |
1258 |
--lib/src |
1259 |
--lib/src/mmdb' |
1260 |
-- |
1261 |
-- for ac_dir in $ac_mmdb_dirs; do |
1262 |
-- if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then |
1263 |
-- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir" |
1264 |
-- break |
1265 |
-- fi |
1266 |
-- done |
1267 |
-- |
1268 |
-- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS" |
1269 |
-- |
1270 |
--else |
1271 |
-- |
1272 |
-- MMDBSSM_CXXFLAGS="" |
1273 |
-- MMDBSSM_LIBS="" |
1274 |
-- with_ssmlib_prefix=no |
1275 |
-- |
1276 |
--fi |
1277 |
-- |
1278 |
--AC_MSG_RESULT([$with_ssmlib_prefix]) |
1279 |
-+PKG_CHECK_MODULES([MMDBSSM],[ssm]) |
1280 |
- |
1281 |
- AC_SUBST(MMDBSSM_CXXFLAGS) |
1282 |
- AC_SUBST(MMDBSSM_LIBS) |