| 1 | --- Makefile.delsci.orig 2010-07-02 17:29:57.000000000 -0400 |
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| 2 | +++ Makefile.delsci 2010-07-02 17:35:04.000000000 -0400 |
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| 3 | @@ -61,15 +61,15 @@ |
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| 4 | /bin/rm -f .update .includes |
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| 5 | cd contrib;$(MAKE) -f Makefile.delsci |
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| 6 | cd contrib/uiuc/plugins/molfile_plugin/src;$(MAKE) -f Makefile.delsci |
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| 7 | - 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 |
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| 8 | - $(CC) $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS) |
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| 9 | + cd modules/cealign/src; $(CXX) -c ccealignmodule.cpp -o ccealignmodule.o -Itnt -I. $(PYTHON_INC_DIR) -I../../../layer0 -I../../../ov/src |
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| 10 | + $(CC) $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o modules/cealign/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS) |
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| 11 | |
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| 12 | semistatic: .includes .depends .update |
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| 13 | /bin/rm -f .update .includes |
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| 14 | cd contrib;$(MAKE) -f Makefile.delsci static |
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| 15 | cd contrib/uiuc/plugins/molfile_plugin/src;$(MAKE) -f Makefile.delsci |
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| 16 | - 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 |
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| 17 | - g++ $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS) |
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| 18 | + cd modules/cealign/src; $(CXX) -c ccealignmodule.cpp -o ccealignmodule.o -Itnt -I. $(PYTHON_INC_DIR) -I../../../layer0 -I../../../ov/src |
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| 19 | + $(CXX) $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o modules/cealign/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS) |
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| 20 | |
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| 21 | free: |
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| 22 | /bin/rm -rf freemol |
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| 23 | --- layer4/Makefile.delsci.orig 2010-07-02 17:37:56.000000000 -0400 |
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| 24 | +++ layer4/Makefile.delsci 2010-07-02 17:38:17.000000000 -0400 |
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| 25 | @@ -3,7 +3,7 @@ |
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| 26 | |
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| 27 | include ../Rules.delsci |
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| 28 | |
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| 29 | -CFLAGS = $(PYMOL_INC_DIRS) $(C_FLAGS) -I../ov/src |
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| 30 | +CFLAGS = $(PYMOL_INC_DIRS) $(C_FLAGS) -I../ov/src -I../modules/cealign/src |
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| 31 | |
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| 32 | all: layer |
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| 33 | |
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| 34 | --- modules/pmg_tk/startup/apbs_tools.py.orig 2010-07-02 18:40:05.000000000 -0400 |
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| 35 | +++ modules/pmg_tk/startup/apbs_tools.py 2010-07-02 18:41:40.000000000 -0400 |
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| 36 | @@ -183,6 +183,11 @@ |
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| 37 | searchDirs.append("/tmp") |
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| 38 | searchDirs.append(".") |
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| 39 | |
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| 40 | + # This must come before /opt/local/bin (which may also be in PATH) in |
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| 41 | + # order for our pdb2pqr importing to work |
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| 42 | + # correctly. /opt/local/bin/pdb2pqr just calls through to this. |
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| 43 | + searchDirs.append(os.path.join("/opt", "local", "share", "pdb2pqr")) |
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| 44 | + |
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| 45 | searchDirs.extend(string.split(os.environ["PATH"], ":")) |
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| 46 | searchDirs.append(os.path.join("/usr", "local", "bin")) |
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| 47 | searchDirs.append(os.path.join("/opt", "local", "bin")) |
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| 48 | @@ -787,7 +792,7 @@ |
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| 49 | label_pyclass = FileDialogButtonClassFactory.get(self.setPsizeLocation), |
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| 50 | validate = {'validator':quickFileValidation,}, |
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| 51 | #value = '/usr/local/apbs-0.3.1/tools/manip/psize.py', |
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| 52 | - value = get_default_location('psize.py'), |
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| 53 | + value = get_default_location('apbs-psize.py'), |
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| 54 | label_text = 'APBS psize.py location:', |
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| 55 | ) |
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| 56 | self.psize.pack(fill = 'x', padx = 20, pady = 10) |
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