Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/10.4-EOL/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv30581
Modified Files:
pymol-py.info pymol-py.patch
Log Message:
sync. w/ 10.!4/stable, validated on powerpc-darwin8
Index: pymol-py.info
===================================================================
RCS file:
/cvsroot/fink/dists/10.4/stable/main/finkinfo/10.4-EOL/sci/pymol-py.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- pymol-py.info 11 Jul 2011 04:08:34 -0000 1.1
+++ pymol-py.info 7 Dec 2011 23:34:20 -0000 1.2
@@ -1,12 +1,14 @@
Info2: <<
Package: pymol-py%type_pkg[python]
-Version: 1.2r2
-Revision: 2
+Version: 1.4
+Revision: 8
+UseMaxBuildJobs: false
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
-Type: python (2.5 2.6)
+Type: python (2.6 2.7)
+# 3962.
#Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
-Source-MD5: 3a6a8369d585178343f2c6d8fb8a4e0a
+Source-MD5: c520de57b1b3ad7fbc891057a4e32c3e
Source2: http://www.weizmann.ac.il/ISPC/eMovie.py
Source2-MD5: 832252d4cee1ba88d50a35681b5ecd4b
Source3: http://www.weizmann.ac.il/ISPC/eMovie_rigimol.inp
@@ -14,24 +16,33 @@
Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
PatchFile: pymol-py.patch
-PatchFile-MD5: 292ca189abe92c4d5bc2bac819aeb14e
+PatchFile-MD5: ee777e18ad893e1be061f0bd3abe05c3
+PatchFile2: pymol-scipy.patch
+PatchFile2-MD5: 09a486091a5cfe8c7e299a9f18446239
SourceDirectory: pymol-%v
-Depends: python%type_pkg[python], libpng3-shlibs, numeric-py%type_pkg[python],
tcltk, pmw-py%type_pkg[python] (>= 1.3.2-1000), freeglut-shlibs, blt-shlibs,
meschach-shlibs
-BuildDepends: libpng3, freeglut, db43-ssl (>= 4.3.29-1001)|db43 (>=
4.3.29-1001), readline (>= 4.3-1028), gdbm3, tcltk-dev, blt, x11-dev, swig,
meschach, fink (>= 0.24.12)
-Conflicts: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26
-Replaces: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26
+Depends: python%type_pkg[python], libpng15-shlibs, scipy-py%type_pkg[python],
tcltk, pmw-py%type_pkg[python] (>= 1.3.2-1000), freeglut-shlibs, glew-shlibs,
blt-shlibs, meschach-shlibs
+BuildDepends: libpng15, freeglut, glew, readline5, gdbm3, tcltk-dev, blt,
x11-dev, swig, meschach, fink (>= 0.30.0)
+Conflicts: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26,
pymol-py27
+Replaces: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26,
pymol-py27
PatchScript: <<
+#! /bin/sh -ex
+cd ..
sed 's|@FINKPREFIX@|%p|g' < %{PatchFile} | sed
's|python2.X|python%type_raw[python]|g' | sed
's|pymol-py2X|pymol-py%type_pkg[python]|g' | patch -p1
+cd pymol-%v
+patch -p1 < %{PatchFile2}
perl -pi -e 's|self.dialog.activate|\#self.dialog.activate|g'
modules/pmg_tk/startup/apbs_tools.py
<<
CompileScript: <<
#! /bin/sh -ex
(cd setup; cp Rules.osx-fink %b/Rules.delsci) || exit 1
case `uname -r` in
-10.*) perl -pi -e "s,-Wno-long-double,," ./Rules.delsci ;;
+10.*|11.*) perl -pi -e "s,-Wno-long-double,," ./Rules.delsci ;;
esac
make -f Makefile.delsci
cd %b/../pynmr_0.37f_src/pmg_tk/startup/pynmr
+perl -pi -e 's|Numeric import|numpy.oldnumeric import|g' *.py
+perl -pi -e 's|LinearAlgebra import|numpy.oldnumeric.linear_algebra import|g'
*.py
+perl -pi -e 's|import MLab|import numpy.oldnumeric.mlab as MLab|g' *.py
./run.macos
<<
InstallScript: <<
@@ -48,20 +59,17 @@
cd pynmr
cp -r Crmsd.so *.py BIOPYTHON_LICENSE LICENSE README help images test_data
%i/lib/pymol-py%type_pkg[python]/modules/pmg_tk/startup/pynmr
rm
%i/lib/pymol-py%type_pkg[python]/modules/pmg_tk/startup/pynmr/test_data/.noe.tbl.swp
+# precompile python scripts
+%p/bin/python%type_raw[python] -O %p/lib/python%type_raw[python]/compileall.py
-f -d %p/lib/%n/modules %i/lib/%n/modules
<<
DocFiles: DEVELOPERS LICENSE README
PostInstScript: <<
update-alternatives --install %p/bin/pymol pymol
%p/lib/pymol-py%type_pkg[python]/bin/pymol %type_pkg[python]
-%p/bin/python%type_raw[python] -O %p/lib/python%type_raw[python]/compileall.py
-q %p/lib/%n/modules
<<
PreRmScript: <<
if [ $1 != "upgrade" ]; then
update-alternatives --remove pymol %p/lib/pymol-py%type_pkg[python]/bin/pymol
fi
-PACKAGE=%N
-dpkg --listfiles $PACKAGE |
- /usr/bin/awk '$0~/\.py$/ {print $0"c\n" $0"o"}' |
- xargs rm -f >&2
<<
Description: Molecular graphics system
DescDetail: <<
@@ -76,8 +84,8 @@
DescPackaging: <<
The tarball used for this version was created in accordance to the BSD
license of pymol using the following instructions...
- svn -r3881 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol
pymol-1.2r2
- tar --exclude=.svn -jcvf pymol-1.2r0-src.tar.bz2 pymol-1.2r0
+ svn -r3962 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol
pymol-1.4
+ tar --exclude=.svn -jcvf pymol-1.4-src.tar.bz2 pymol-1.4
Added eMovie.py plug-in manually. Commented out line that opens the window
for eMovie by
default every time pymol is started as this is annoying behavior. eMovie is
activated via
the plugin menu.
Index: pymol-py.patch
===================================================================
RCS file:
/cvsroot/fink/dists/10.4/stable/main/finkinfo/10.4-EOL/sci/pymol-py.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- pymol-py.patch 11 Jul 2011 04:08:34 -0000 1.1
+++ pymol-py.patch 7 Dec 2011 23:34:20 -0000 1.2
@@ -1,15 +1,6 @@
---- pymol/../pynmr_0.37f_src/pmg_tk/startup/pynmr/Crmsd.i.org 2009-08-17
22:47:39.000000000 -0400
-+++ pymol/../pynmr_0.37f_src/pmg_tk/startup/pynmr/Crmsd.i 2009-08-17
22:47:48.000000000 -0400
-@@ -4,6 +4,7 @@
- %array_functions(char *, charArray);
- %array_functions(int, intArray);
- %{
-+extern char * C_do_best_range(char*, char*, char*, char*, char*, double);
- %}
-
- extern char * C_do_best_range(char*, char*, char*, char*, char*, double);
---- pymol/../eMovie.py.org 2009-03-31 19:19:48.000000000 -0400
-+++ pymol/../eMovie.py 2009-03-31 19:20:35.000000000 -0400
+diff -uNr pymol-py26-1.4-1/eMovie.py pymol-py26-1.4-1.patched/eMovie.py
+--- pymol-py26-1.4-1/eMovie.py 2011-04-23 16:24:37.000000000 -0400
++++ pymol-py26-1.4-1.patched/eMovie.py 2011-04-23 16:06:47.000000000 -0400
@@ -188,7 +188,7 @@
cmd.extend('mvSet',mv_set) # adjust parameter over frame range
@@ -19,36 +10,32 @@
def open_eMovie():
---- pymol/../pynmr_0.37f_src/pmg_tk/startup/pynmr/run.macos.org
2006-04-06 10:10:45.000000000 -0400
-+++ pymol/../pynmr_0.37f_src/pmg_tk/startup/pynmr/run.macos 2009-04-03
21:04:39.000000000 -0400
-@@ -1,4 +1,4 @@
--/Users/leigh/pynmr/swig/swig -python -I/Users/leigh/pynmr/swig/Lib/
-I/Users/leigh/pynmr/swig/Lib/python Crmsd.i
-+@FINKPREFIX@/bin/swig -python Crmsd.i
-
- # now fix the error that swig produces...
- sed -e '/SWIG_init/s/init_/init/' -e '/SWIG_name/s/_Crmsd/Crmsd/ '
Crmsd_wrap.c > Crmsd_wrap2.c
-@@ -8,8 +8,8 @@
- #gcc -c Crmsd.c Crmsd_wrap.c -I../../../meschach -I/usr/include/python2.3 -lm
- #gcc -shared Crmsd.o Crmsd_wrap.o meschach.a -o Crmsd.so
-
--gcc -fno-common -c Crmsd.c Crmsd_wrap.c -I/Users/leigh/pynmr/meschach
-I/usr/include/python2.3 -D_POSIX_C_SOURCE
--gcc -bundle -flat_namespace -L/usr/include/python2.3 Crmsd.o Crmsd_wrap.o
/Users/leigh/pynmr/meschach/meschach.a -lPython -o Crmsd.so
-+gcc -O3 -fno-common -c Crmsd.c Crmsd_wrap.c -I@FINKPREFIX@/include/meschach
-I@FINKPREFIX@/include/python2.X -D_POSIX_C_SOURCE
-+gcc -O3 -bundle -bundle_loader @FINKPREFIX@/bin/python2.X -flat_namespace
-undefined suppress Crmsd.o Crmsd_wrap.o -L@FINKPREFIX@/lib -lmeschach -o
Crmsd.so
-
-
+diff -uNr pymol-py26-1.4-1/pymol-1.4/Makefile.delsci
pymol-py26-1.4-1.patched/pymol-1.4/Makefile.delsci
+--- pymol-py26-1.4-1/pymol-1.4/Makefile.delsci 2010-06-13 20:46:59.000000000
-0400
++++ pymol-py26-1.4-1.patched/pymol-1.4/Makefile.delsci 2011-04-23
16:06:47.000000000 -0400
+@@ -61,15 +61,15 @@
+ /bin/rm -f .update .includes
+ cd contrib;$(MAKE) -f Makefile.delsci
+ cd contrib/uiuc/plugins/molfile_plugin/src;$(MAKE) -f Makefile.delsci
+- cd modules/cealign/src; g++ -c ccealignmodule.cpp -o ccealignmodule.o
-Itnt -I. $(PYTHON_INC_DIR) -I$(PYMOL_PATH)/layer0 -I$(PYMOL_PATH)/ov/src
+- $(CC) $(BUILD) $(DEST) */*.o ov/src/*.o
contrib/uiuc/plugins/molfile_plugin/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS)
++ cd modules/cealign/src; g++ -c ccealignmodule.cpp -o ccealignmodule.o
-Itnt -I. $(PYTHON_INC_DIR) -I../../../layer0 -I../../../ov/src
++ $(CC) $(BUILD) $(DEST) */*.o ov/src/*.o
contrib/uiuc/plugins/molfile_plugin/src/*.o modules/cealign/src/*.o $(CFLAGS)
$(LIB_DIRS) $(LIBS)
---- pymol/../pynmr_0.37f_src/pmg_tk/startup/pynmr/test_data/test.script.org
2009-04-04 00:49:35.000000000 -0400
-+++ pymol/../pynmr_0.37f_src/pmg_tk/startup/pynmr/test_data/test.script
2009-04-04 00:52:04.000000000 -0400
-@@ -6,5 +6,5 @@
- pairfit=0)
- nmr_cmd.C_do_best_range('test_1', 'C N CA', \
- "test_1 test_2 test_3", "all", \
-- "/home2/leigh/Proj/pynmr/pmg_tk/startup/pynmr/test_data/", 1.0)
-+ "@FINKPREFIX@/lib/pymol-py2X/modules/pmg_tk/startup/pynmr/test_data",
1.0)
+ semistatic: .includes .depends .update
+ /bin/rm -f .update .includes
+ cd contrib;$(MAKE) -f Makefile.delsci static
+ cd contrib/uiuc/plugins/molfile_plugin/src;$(MAKE) -f Makefile.delsci
+- cd modules/cealign/src; g++ -c ccealignmodule.cpp -o ccealignmodule.o
-Itnt -I. $(PYTHON_INC_DIR) -I$(PYMOL_PATH)/layer0 -I$(PYMOL_PATH)/ov/src
+- g++ $(BUILD) $(DEST) */*.o ov/src/*.o
contrib/uiuc/plugins/molfile_plugin/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS)
++ cd modules/cealign/src; g++ -c ccealignmodule.cpp -o ccealignmodule.o
-Itnt -I. $(PYTHON_INC_DIR) -I../../../layer0 -I../../../ov/src
++ g++ $(BUILD) $(DEST) */*.o ov/src/*.o
contrib/uiuc/plugins/molfile_plugin/src/*.o modules/cealign/src/*.o $(CFLAGS)
$(LIB_DIRS) $(LIBS)
---- pymol-1.1b3/contrib/modules/Makefile.pre.in.src.org 2008-05-09
19:09:50.000000000 -0400
-+++ pymol-1.1b3/contrib/modules/Makefile.pre.in.src 2008-05-09
19:11:25.000000000 -0400
+ free:
+ /bin/rm -rf freemol
+diff -uNr pymol-py26-1.4-1/pymol-1.4/contrib/modules/Makefile.pre.in.src
pymol-py26-1.4-1.patched/pymol-1.4/contrib/modules/Makefile.pre.in.src
+--- pymol-py26-1.4-1/pymol-1.4/contrib/modules/Makefile.pre.in.src
2009-02-24 22:30:40.000000000 -0500
++++ pymol-py26-1.4-1.patched/pymol-1.4/contrib/modules/Makefile.pre.in.src
2011-04-23 16:06:47.000000000 -0400
@@ -88,10 +88,10 @@
# === Variables that you may want to customize (rarely) ===
@@ -86,9 +73,49 @@
SYSLIBS= $(LIBM) $(LIBC)
-diff -uNr pymol-0.95.org/setup/Rules.osx-fink pymol-0.95/setup/Rules.osx-fink
---- pymol-0.95.org/setup/Rules.osx-fink Sat Apr 3 04:05:01 2004
-+++ pymol-0.95/setup/Rules.osx-fink Mon Apr 5 18:11:02 2004
+diff -uNr pymol-py26-1.4-1/pymol-1.4/layer3/Makefile.delsci
pymol-py26-1.4-1.patched/pymol-1.4/layer3/Makefile.delsci
+--- pymol-py26-1.4-1/pymol-1.4/layer3/Makefile.delsci 2009-02-24
22:30:34.000000000 -0500
++++ pymol-py26-1.4-1.patched/pymol-1.4/layer3/Makefile.delsci 2011-04-23
16:14:56.000000000 -0400
+@@ -3,7 +3,7 @@
+
+ include ../Rules.delsci
+
+-CFLAGS = $(PYMOL_INC_DIRS) $(C_FLAGS) -I../ov/src
++CFLAGS = $(PYMOL_INC_DIRS) $(C_FLAGS) -I../ov/src -I../modules/cealign/src
+
+ all: layer
+
+diff -uNr pymol-py26-1.4-1/pymol-1.4/layer4/Makefile.delsci
pymol-py26-1.4-1.patched/pymol-1.4/layer4/Makefile.delsci
+--- pymol-py26-1.4-1/pymol-1.4/layer4/Makefile.delsci 2010-06-13
20:47:00.000000000 -0400
++++ pymol-py26-1.4-1.patched/pymol-1.4/layer4/Makefile.delsci 2011-04-23
16:06:47.000000000 -0400
+@@ -3,7 +3,7 @@
+
+ include ../Rules.delsci
+
+-CFLAGS = $(PYMOL_INC_DIRS) $(C_FLAGS) -I../ov/src
++CFLAGS = $(PYMOL_INC_DIRS) $(C_FLAGS) -I../ov/src -I../modules/cealign/src
+
+ all: layer
+
+diff -uNr pymol-py26-1.4-1/pymol-1.4/modules/pmg_tk/startup/apbs_tools.py
pymol-py26-1.4-1.patched/pymol-1.4/modules/pmg_tk/startup/apbs_tools.py
+--- pymol-py26-1.4-1/pymol-1.4/modules/pmg_tk/startup/apbs_tools.py
2011-04-21 07:40:48.000000000 -0400
++++ pymol-py26-1.4-1.patched/pymol-1.4/modules/pmg_tk/startup/apbs_tools.py
2011-04-23 16:06:47.000000000 -0400
+@@ -220,6 +220,12 @@
+ # correctly. /sw/bin/pdb2pqr just calls through to this.
+ searchDirs.append(os.path.join("/sw", "share", "pdb2pqr"))
+
++ # This must come before @FINKPREFIX@/bin (which may also be in PATH) in
++ # order for our pdb2pqr importing to work
++ # correctly. @FINKPREFIX@/bin/pdb2pqr just calls through to this.
++ searchDirs.append(os.path.join("@FINKPREFIX@", "share", "pdb2pqr"))
++ searchDirs.append(os.path.join("@FINKPREFIX@", "share", "apbs", "tools",
"manip"))
++
+ searchDirs.extend(string.split(os.environ["PATH"], ":"))
+ searchDirs.append(os.path.join("/usr", "local", "bin"))
+ searchDirs.append(os.path.join("/opt", "local", "bin"))
+diff -uNr pymol-py26-1.4-1/pymol-1.4/setup/Rules.osx-fink
pymol-py26-1.4-1.patched/pymol-1.4/setup/Rules.osx-fink
+--- pymol-py26-1.4-1/pymol-1.4/setup/Rules.osx-fink 2009-02-24
22:30:35.000000000 -0500
++++ pymol-py26-1.4-1.patched/pymol-1.4/setup/Rules.osx-fink 2011-04-23
16:24:00.000000000 -0400
@@ -6,7 +6,7 @@
#
#- Building ----------------------------------------------------------
@@ -98,7 +125,7 @@
#---------------------------------------------------------------------
#
#- Dependencies ------------------------------------------------------
-@@ -14,14 +14,14 @@
+@@ -14,29 +14,29 @@
XLIB_DIR = -L/usr/X11R6/lib
XINC_DIR = -I/usr/X11R6/include
#--- Python
@@ -118,18 +145,28 @@
#---------------------------------------------------------------------
#
#- Build for LINUX as an importable module ---------------------------
-@@ -30,7 +30,7 @@
+ #--- System libraries
+-LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -lpng $(ZLIB) -lm -lX11 -lXext
++LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -lGLEW -lpng $(ZLIB) -lm -lX11 -lXext
#--- PyMOL configuration
- DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY -D_PYMOL_FINK
+-DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY -D_PYMOL_FINK
++DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY -D_PYMOL_FINK -D_PYMOL_INLINE
-D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS
#--- How we build shared libraries
-BUILD = -bundle -bundle_loader /sw/bin/python2.3 -flat_namespace -undefined
suppress
+BUILD = -bundle -bundle_loader @FINKPREFIX@/bin/python2.X -flat_namespace
-undefined suppress
#--- What are we trying to build?
DEST = -o modules/pymol/_cmd.so
#--- Gcc Options for Linux
-diff -uNr pymol-0.99beta33/setup/pymol.com.osx-fink.orig
pymol-0.99beta33/setup/pymol.com.osx-fink
---- pymol-0.99beta33/setup/pymol.com.osx-fink.orig 2005-11-19
12:46:39.000000000 -0500
-+++ pymol-0.99beta33/setup/pymol.com.osx-fink 2006-01-09 20:24:01.000000000
-0500
+ CCOPT1 = -no-cpp-precomp -Wmissing-prototypes -Wno-long-double
+ #--- libraries for PyOpenGL
+-PYOGL_LIB = -lglut -lGL -lGLU -lXmu -lXi
++PYOGL_LIB = -lglut -lGL -lGLU -lGLEW -lXmu -lXi
+ #---------------------------------------------------------------------
+ #
+ #- Choose One --------------------------------------------------------
+diff -uNr pymol-py26-1.4-1/pymol-1.4/setup/pymol.com.osx-fink
pymol-py26-1.4-1.patched/pymol-1.4/setup/pymol.com.osx-fink
+--- pymol-py26-1.4-1/pymol-1.4/setup/pymol.com.osx-fink 2009-02-24
22:30:35.000000000 -0500
++++ pymol-py26-1.4-1.patched/pymol-1.4/setup/pymol.com.osx-fink
2011-04-23 16:06:47.000000000 -0400
@@ -5,7 +5,7 @@
# ==============================================================
# Set PYMOL_PATH to point at the correct location on your system
@@ -139,7 +176,7 @@
export PYMOL_PATH
#
# ==============================================================
-@@ -20,6 +20,9 @@
+@@ -20,5 +20,8 @@
fi
export PYTHONPATH
#
@@ -148,3 +185,45 @@
+export APBS_PSIZE
+#
+exec @FINKPREFIX@/bin/python2.X $PYMOL_PATH/modules/pymol/__init__.py -d "_
set stereo_double_pump_mono,quiet=1" "$@"
+
+diff -uNr pymol-py26-1.4-1/pynmr_0.37f_src/pmg_tk/startup/pynmr/Crmsd.i
pymol-py26-1.4-1.patched/pynmr_0.37f_src/pmg_tk/startup/pynmr/Crmsd.i
+--- pymol-py26-1.4-1/pynmr_0.37f_src/pmg_tk/startup/pynmr/Crmsd.i
2006-04-06 08:47:42.000000000 -0400
++++ pymol-py26-1.4-1.patched/pynmr_0.37f_src/pmg_tk/startup/pynmr/Crmsd.i
2011-04-23 16:06:47.000000000 -0400
+@@ -4,6 +4,7 @@
+ %array_functions(char *, charArray);
+ %array_functions(int, intArray);
+ %{
++extern char * C_do_best_range(char*, char*, char*, char*, char*, double);
+ %}
+
+ extern char * C_do_best_range(char*, char*, char*, char*, char*, double);
+diff -uNr pymol-py26-1.4-1/pynmr_0.37f_src/pmg_tk/startup/pynmr/run.macos
pymol-py26-1.4-1.patched/pynmr_0.37f_src/pmg_tk/startup/pynmr/run.macos
+--- pymol-py26-1.4-1/pynmr_0.37f_src/pmg_tk/startup/pynmr/run.macos
2006-04-06 10:10:45.000000000 -0400
++++ pymol-py26-1.4-1.patched/pynmr_0.37f_src/pmg_tk/startup/pynmr/run.macos
2011-04-23 16:06:47.000000000 -0400
+@@ -1,4 +1,4 @@
+-/Users/leigh/pynmr/swig/swig -python -I/Users/leigh/pynmr/swig/Lib/
-I/Users/leigh/pynmr/swig/Lib/python Crmsd.i
++@FINKPREFIX@/bin/swig -python Crmsd.i
+
+ # now fix the error that swig produces...
+ sed -e '/SWIG_init/s/init_/init/' -e '/SWIG_name/s/_Crmsd/Crmsd/ '
Crmsd_wrap.c > Crmsd_wrap2.c
+@@ -8,8 +8,8 @@
+ #gcc -c Crmsd.c Crmsd_wrap.c -I../../../meschach -I/usr/include/python2.3 -lm
+ #gcc -shared Crmsd.o Crmsd_wrap.o meschach.a -o Crmsd.so
+
+-gcc -fno-common -c Crmsd.c Crmsd_wrap.c -I/Users/leigh/pynmr/meschach
-I/usr/include/python2.3 -D_POSIX_C_SOURCE
+-gcc -bundle -flat_namespace -L/usr/include/python2.3 Crmsd.o Crmsd_wrap.o
/Users/leigh/pynmr/meschach/meschach.a -lPython -o Crmsd.so
++gcc -O3 -fno-common -c Crmsd.c Crmsd_wrap.c -I@FINKPREFIX@/include/meschach
-I@FINKPREFIX@/include/python2.X -D_POSIX_C_SOURCE
++gcc -O3 -bundle -bundle_loader @FINKPREFIX@/bin/python2.X -flat_namespace
-undefined suppress Crmsd.o Crmsd_wrap.o -L@FINKPREFIX@/lib -lmeschach -o
Crmsd.so
+
+
+
+diff -uNr
pymol-py26-1.4-1/pynmr_0.37f_src/pmg_tk/startup/pynmr/test_data/test.script
pymol-py26-1.4-1.patched/pynmr_0.37f_src/pmg_tk/startup/pynmr/test_data/test.script
+---
pymol-py26-1.4-1/pynmr_0.37f_src/pmg_tk/startup/pynmr/test_data/test.script
2006-04-06 08:47:49.000000000 -0400
++++
pymol-py26-1.4-1.patched/pynmr_0.37f_src/pmg_tk/startup/pynmr/test_data/test.script
2011-04-23 16:06:47.000000000 -0400
+@@ -6,5 +6,5 @@
+ pairfit=0)
+ nmr_cmd.C_do_best_range('test_1', 'C N CA', \
+ "test_1 test_2 test_3", "all", \
+- "/home2/leigh/Proj/pynmr/pmg_tk/startup/pynmr/test_data/", 1.0)
++ "@FINKPREFIX@/lib/pymol-py2X/modules/pmg_tk/startup/pynmr/test_data",
1.0)
+
------------------------------------------------------------------------------
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