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nomad-lab
pymolfile
Commits
c6feda88
Commit
c6feda88
authored
Oct 23, 2017
by
Berk Onat
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Added cmake installer for linmolfile+plugins.a
parent
d397d505
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213 changed files
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74870 additions
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219 deletions
+74870
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build/lib.macosx-10.12-x86_64-3.6/pymolfile/__init__.py
build/lib.macosx-10.12-x86_64-3.6/pymolfile/__init__.py
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build/lib.macosx-10.12-x86_64-3.6/pymolfile/molfile/__init__.py
...lib.macosx-10.12-x86_64-3.6/pymolfile/molfile/__init__.py
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build/lib.macosx-10.12-x86_64-3.6/pymolfile/molfile/_libpymolfile.cpython-36m-darwin.so
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build/lib.macosx-10.12-x86_64-3.6/pymolfile/molfile/libpymolfile.py
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build/lib.macosx-10.12-x86_64-3.6/pymolfile/plugin_list.py
build/lib.macosx-10.12-x86_64-3.6/pymolfile/plugin_list.py
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-0
build/lib.macosx-10.12-x86_64-3.6/pymolfile/pymolfile.py
build/lib.macosx-10.12-x86_64-3.6/pymolfile/pymolfile.py
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build/lib.macosx-10.12-x86_64-3.6/pymolfile/test_libpymolfile.py
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build/temp.macosx-10.12-x86_64-3.6/pymolfile/molfile/libpymolfile_wrap.o
...sx-10.12-x86_64-3.6/pymolfile/molfile/libpymolfile_wrap.o
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build/temp.macosx-10.12-x86_64-3.6/pymolfile/molfile/pymolfile.o
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pymolfile/molfile/external/CMakeLists.txt
pymolfile/molfile/external/CMakeLists.txt
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pymolfile/molfile/include/pymolfile.h
pymolfile/molfile/include/pymolfile.h
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pymolfile/molfile/molfile_plugins/CMakeLists.txt
pymolfile/molfile/molfile_plugins/CMakeLists.txt
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pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/CMakeLists.txt
...olfile/molfile_plugins/vmd_molfile_plugins/CMakeLists.txt
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pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/LICENSE
...lfile/molfile/molfile_plugins/vmd_molfile_plugins/LICENSE
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pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/Make-arch
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pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/Makefile
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pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/README
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/README
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pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/create_static_header.sh
...lfile_plugins/vmd_molfile_plugins/create_static_header.sh
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pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/LICENSE
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pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/Makefile
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...gins/vmd_molfile_plugins/molfile_plugin/src/CVS/mmCIF.C,t
+0
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/Gromacs.h
..._plugins/vmd_molfile_plugins/molfile_plugin/src/Gromacs.h
+1967
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ReadPARM.h
...plugins/vmd_molfile_plugins/molfile_plugin/src/ReadPARM.h
+976
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ReadPARM7.h
...lugins/vmd_molfile_plugins/molfile_plugin/src/ReadPARM7.h
+462
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/abinitplugin.c
...ins/vmd_molfile_plugins/molfile_plugin/src/abinitplugin.c
+1930
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/avsplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/avsplugin.C
+579
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/babelplugin.c
...gins/vmd_molfile_plugins/molfile_plugin/src/babelplugin.c
+725
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/basissetplugin.c
...s/vmd_molfile_plugins/molfile_plugin/src/basissetplugin.c
+739
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/bgfplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/bgfplugin.C
+668
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/binposplugin.c
...ins/vmd_molfile_plugins/molfile_plugin/src/binposplugin.c
+251
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/biomoccaplugin.C
...s/vmd_molfile_plugins/molfile_plugin/src/biomoccaplugin.C
+193
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/brixplugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/brixplugin.C
+314
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/carplugin.c
...lugins/vmd_molfile_plugins/molfile_plugin/src/carplugin.c
+415
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ccp4plugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/ccp4plugin.C
+706
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/corplugin.c
...lugins/vmd_molfile_plugins/molfile_plugin/src/corplugin.c
+392
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/cpmdlogplugin.c
...ns/vmd_molfile_plugins/molfile_plugin/src/cpmdlogplugin.c
+1666
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/cpmdplugin.c
...ugins/vmd_molfile_plugins/molfile_plugin/src/cpmdplugin.c
+201
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/crdplugin.c
...lugins/vmd_molfile_plugins/molfile_plugin/src/crdplugin.c
+217
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/cubeplugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/cubeplugin.C
+665
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dcdplugin.c
...lugins/vmd_molfile_plugins/molfile_plugin/src/dcdplugin.c
+1244
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dlpolyplugin.c
...ins/vmd_molfile_plugins/molfile_plugin/src/dlpolyplugin.c
+777
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dmsplugin.cxx
...gins/vmd_molfile_plugins/molfile_plugin/src/dmsplugin.cxx
+919
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dsn6plugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/dsn6plugin.C
+316
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.cxx
...gins/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.cxx
+2380
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.hxx
...gins/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.hxx
+342
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/dxplugin.C
...plugins/vmd_molfile_plugins/molfile_plugin/src/dxplugin.C
+486
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/edmplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/edmplugin.C
+571
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/endianswap.h
...ugins/vmd_molfile_plugins/molfile_plugin/src/endianswap.h
+173
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/fastio.h
...e_plugins/vmd_molfile_plugins/molfile_plugin/src/fastio.h
+613
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/fortread.h
...plugins/vmd_molfile_plugins/molfile_plugin/src/fortread.h
+152
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/fs4plugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/fs4plugin.C
+374
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gamessplugin.c
...ins/vmd_molfile_plugins/molfile_plugin/src/gamessplugin.c
+4885
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.c
...s/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.c
+2262
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.h
...s/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.h
+339
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/graspplugin.C
...gins/vmd_molfile_plugins/molfile_plugin/src/graspplugin.C
+520
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/grdplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/grdplugin.C
+271
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gridplugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/gridplugin.C
+234
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/gromacsplugin.C
...ns/vmd_molfile_plugins/molfile_plugin/src/gromacsplugin.C
+808
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/hash.c
...ile_plugins/vmd_molfile_plugins/molfile_plugin/src/hash.c
+291
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/hash.h
...ile_plugins/vmd_molfile_plugins/molfile_plugin/src/hash.h
+73
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/hoomdplugin.c
...gins/vmd_molfile_plugins/molfile_plugin/src/hoomdplugin.c
+2504
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/inthash.c
..._plugins/vmd_molfile_plugins/molfile_plugin/src/inthash.c
+288
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/inthash.h
..._plugins/vmd_molfile_plugins/molfile_plugin/src/inthash.h
+76
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/jsplugin.c
...plugins/vmd_molfile_plugins/molfile_plugin/src/jsplugin.c
+2157
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/lammpsplugin.c
...ins/vmd_molfile_plugins/molfile_plugin/src/lammpsplugin.c
+1689
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/largefiles.h
...ugins/vmd_molfile_plugins/molfile_plugin/src/largefiles.h
+36
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/maeffplugin.cxx
...ns/vmd_molfile_plugins/molfile_plugin/src/maeffplugin.cxx
+2107
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/main.c
...ile_plugins/vmd_molfile_plugins/molfile_plugin/src/main.c
+163
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mapplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/mapplugin.C
+225
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mdfplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/mdfplugin.C
+417
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mmcif.C
...le_plugins/vmd_molfile_plugins/molfile_plugin/src/mmcif.C
+177
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/mol2plugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/mol2plugin.C
+609
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/moldenplugin.c
...ins/vmd_molfile_plugins/molfile_plugin/src/moldenplugin.c
+1332
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/molemeshplugin.C
...s/vmd_molfile_plugins/molfile_plugin/src/molemeshplugin.C
+331
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/msmsplugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/msmsplugin.C
+251
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/namdbinplugin.c
...ns/vmd_molfile_plugins/molfile_plugin/src/namdbinplugin.c
+289
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/netcdfplugin.c
...ins/vmd_molfile_plugins/molfile_plugin/src/netcdfplugin.c
+1140
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/offplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/offplugin.C
+315
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/parm7plugin.C
...gins/vmd_molfile_plugins/molfile_plugin/src/parm7plugin.C
+174
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/parmplugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/parmplugin.C
+147
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pbeqplugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/pbeqplugin.C
+328
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pdbplugin.c
...lugins/vmd_molfile_plugins/molfile_plugin/src/pdbplugin.c
+604
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pdbxplugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/pdbxplugin.C
+1555
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/periodic_table.h
...s/vmd_molfile_plugins/molfile_plugin/src/periodic_table.h
+205
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/phiplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/phiplugin.C
+261
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pltplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/pltplugin.C
+187
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/plugintest.x
...ugins/vmd_molfile_plugins/molfile_plugin/src/plugintest.x
+0
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ply.c
...file_plugins/vmd_molfile_plugins/molfile_plugin/src/ply.c
+3316
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/ply.h
...file_plugins/vmd_molfile_plugins/molfile_plugin/src/ply.h
+233
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/plyplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/plyplugin.C
+308
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/pqrplugin.c
...lugins/vmd_molfile_plugins/molfile_plugin/src/pqrplugin.c
+455
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/psfplugin.c
...lugins/vmd_molfile_plugins/molfile_plugin/src/psfplugin.c
+1113
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/qmplugin.h
...plugins/vmd_molfile_plugins/molfile_plugin/src/qmplugin.h
+1116
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/raster3dplugin.C
...s/vmd_molfile_plugins/molfile_plugin/src/raster3dplugin.C
+519
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/readpdb.h
..._plugins/vmd_molfile_plugins/molfile_plugin/src/readpdb.h
+403
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/rst7plugin.c
...ugins/vmd_molfile_plugins/molfile_plugin/src/rst7plugin.c
+306
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/situsplugin.C
...gins/vmd_molfile_plugins/molfile_plugin/src/situsplugin.C
+379
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/spiderplugin.C
...ins/vmd_molfile_plugins/molfile_plugin/src/spiderplugin.C
+328
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/stlplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/stlplugin.C
+260
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/tinkerplugin.c
...ins/vmd_molfile_plugins/molfile_plugin/src/tinkerplugin.c
+220
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/tngplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/tngplugin.C
+629
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/uhbdplugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/uhbdplugin.C
+346
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/unit_conversion.h
.../vmd_molfile_plugins/molfile_plugin/src/unit_conversion.h
+35
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vasp5xdatcarplugin.c
...d_molfile_plugins/molfile_plugin/src/vasp5xdatcarplugin.c
+279
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspchgcarplugin.c
...vmd_molfile_plugins/molfile_plugin/src/vaspchgcarplugin.c
+337
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspoutcarplugin.c
...vmd_molfile_plugins/molfile_plugin/src/vaspoutcarplugin.c
+289
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspparchgplugin.c
...vmd_molfile_plugins/molfile_plugin/src/vaspparchgplugin.c
+319
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspplugin.h
...ugins/vmd_molfile_plugins/molfile_plugin/src/vaspplugin.h
+124
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspposcarplugin.c
...vmd_molfile_plugins/molfile_plugin/src/vaspposcarplugin.c
+415
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspxdatcarplugin.c
...md_molfile_plugins/molfile_plugin/src/vaspxdatcarplugin.c
+323
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vaspxmlplugin.c
...ns/vmd_molfile_plugins/molfile_plugin/src/vaspxmlplugin.c
+258
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vmddir.h
...e_plugins/vmd_molfile_plugins/molfile_plugin/src/vmddir.h
+161
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vtfplugin.c
...lugins/vmd_molfile_plugins/molfile_plugin/src/vtfplugin.c
+1356
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/vtkplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/vtkplugin.C
+445
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/webpdbplugin.c
...ins/vmd_molfile_plugins/molfile_plugin/src/webpdbplugin.c
+458
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/xbgfplugin.C
...ugins/vmd_molfile_plugins/molfile_plugin/src/xbgfplugin.C
+706
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/xsfplugin.C
...lugins/vmd_molfile_plugins/molfile_plugin/src/xsfplugin.C
+1023
-0
pymolfile/molfile/molfile_plugins/vmd_molfile_plugins/molfile_plugin/src/xyzplugin.c
...lugins/vmd_molfile_plugins/molfile_plugin/src/xyzplugin.c
+321
-0
pymolfile/molfile/vmd_molfile_plugins/CMakeLists.txt
pymolfile/molfile/vmd_molfile_plugins/CMakeLists.txt
+0
-12
No files found.
build/lib.macosx-10.12-x86_64-3.6/pymolfile/__init__.py
0 → 100644
View file @
c6feda88
from
__future__
import
absolute_import
import
warnings
try
:
from
.molfile
import
libpymolfile
except
ImportError
:
warnings
.
warn
(
"libpymolfile package not available, pymolfile does not work without its library!"
)
from
.
import
plugin_list
from
.
import
pymolfile
__all__
=
[
"pymolfile"
]
from
.pymolfile
import
OpenMolfile
,
list_plugins
build/lib.macosx-10.12-x86_64-3.6/pymolfile/molfile/__init__.py
0 → 100644
View file @
c6feda88
# Stand-alone python bindings for libpymolfile
# Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
# Published under the UIUC OpenSource LICENSE
"""libpymolfile library.
"""
build/lib.macosx-10.12-x86_64-3.6/pymolfile/molfile/_libpymolfile.cpython-36m-darwin.so
0 → 100755
View file @
c6feda88
File added
build/lib.macosx-10.12-x86_64-3.6/pymolfile/molfile/libpymolfile.py
0 → 100644
View file @
c6feda88
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 3.0.12
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.
"""
:Author: Berk Onat <b.onat@warwick.ac.uk>
:Year: 2017
:Licence: UIUC LICENSE
"""
from
sys
import
version_info
as
_swig_python_version_info
if
_swig_python_version_info
>=
(
2
,
7
,
0
):
def
swig_import_helper
():
import
importlib
pkg
=
__name__
.
rpartition
(
'.'
)[
0
]
mname
=
'.'
.
join
((
pkg
,
'_libpymolfile'
)).
lstrip
(
'.'
)
try
:
return
importlib
.
import_module
(
mname
)
except
ImportError
:
return
importlib
.
import_module
(
'_libpymolfile'
)
_libpymolfile
=
swig_import_helper
()
del
swig_import_helper
elif
_swig_python_version_info
>=
(
2
,
6
,
0
):
def
swig_import_helper
():
from
os.path
import
dirname
import
imp
fp
=
None
try
:
fp
,
pathname
,
description
=
imp
.
find_module
(
'_libpymolfile'
,
[
dirname
(
__file__
)])
except
ImportError
:
import
_libpymolfile
return
_libpymolfile
try
:
_mod
=
imp
.
load_module
(
'_libpymolfile'
,
fp
,
pathname
,
description
)
finally
:
if
fp
is
not
None
:
fp
.
close
()
return
_mod
_libpymolfile
=
swig_import_helper
()
del
swig_import_helper
else
:
import
_libpymolfile
del
_swig_python_version_info
try
:
_swig_property
=
property
except
NameError
:
pass
# Python < 2.2 doesn't have 'property'.
try
:
import
builtins
as
__builtin__
except
ImportError
:
import
__builtin__
def
_swig_setattr_nondynamic
(
self
,
class_type
,
name
,
value
,
static
=
1
):
if
(
name
==
"thisown"
):
return
self
.
this
.
own
(
value
)
if
(
name
==
"this"
):
if
type
(
value
).
__name__
==
'SwigPyObject'
:
self
.
__dict__
[
name
]
=
value
return
method
=
class_type
.
__swig_setmethods__
.
get
(
name
,
None
)
if
method
:
return
method
(
self
,
value
)
if
(
not
static
):
if
_newclass
:
object
.
__setattr__
(
self
,
name
,
value
)
else
:
self
.
__dict__
[
name
]
=
value
else
:
raise
AttributeError
(
"You cannot add attributes to %s"
%
self
)
def
_swig_setattr
(
self
,
class_type
,
name
,
value
):
return
_swig_setattr_nondynamic
(
self
,
class_type
,
name
,
value
,
0
)
def
_swig_getattr
(
self
,
class_type
,
name
):
if
(
name
==
"thisown"
):
return
self
.
this
.
own
()
method
=
class_type
.
__swig_getmethods__
.
get
(
name
,
None
)
if
method
:
return
method
(
self
)
raise
AttributeError
(
"'%s' object has no attribute '%s'"
%
(
class_type
.
__name__
,
name
))
def
_swig_repr
(
self
):
try
:
strthis
=
"proxy of "
+
self
.
this
.
__repr__
()
except
__builtin__
.
Exception
:
strthis
=
""
return
"<%s.%s; %s >"
%
(
self
.
__class__
.
__module__
,
self
.
__class__
.
__name__
,
strthis
,)
try
:
_object
=
object
_newclass
=
1
except
__builtin__
.
Exception
:
class
_object
:
pass
_newclass
=
0
def
molfile_plugin_list
(
maxsize
:
'int'
)
->
"PyObject *"
:
"""molfile_plugin_list(maxsize) -> PyObject *"""
return
_libpymolfile
.
molfile_plugin_list
(
maxsize
)
def
molfile_init
()
->
"int"
:
"""molfile_init() -> int"""
return
_libpymolfile
.
molfile_init
()
def
molfile_finish
()
->
"int"
:
"""molfile_finish() -> int"""
return
_libpymolfile
.
molfile_finish
()
def
get_plugin
(
molcapsule
:
'PyObject *'
,
plug_no
:
'int'
)
->
"PyObject *"
:
"""get_plugin(molcapsule, plug_no) -> PyObject *"""
return
_libpymolfile
.
get_plugin
(
molcapsule
,
plug_no
)
def
molfile_plugin_info
(
molcapsule
:
'PyObject *'
,
plugin_no
:
'int'
)
->
"PyObject *"
:
"""molfile_plugin_info(molcapsule, plugin_no) -> PyObject *"""
return
_libpymolfile
.
molfile_plugin_info
(
molcapsule
,
plugin_no
)
def
open_file_read
(
molcapsule
:
'PyObject *'
,
fname
:
'char *'
,
ftype
:
'char *'
,
natoms
:
'int'
)
->
"PyObject *"
:
"""open_file_read(molcapsule, fname, ftype, natoms) -> PyObject *"""
return
_libpymolfile
.
open_file_read
(
molcapsule
,
fname
,
ftype
,
natoms
)
def
close_file_read
(
molpack
:
'PyObject *'
)
->
"PyObject *"
:
"""close_file_read(molpack) -> PyObject *"""
return
_libpymolfile
.
close_file_read
(
molpack
)
def
read_fill_structure
(
molpack
:
'PyObject *'
,
prototype
:
'PyObject *'
)
->
"PyObject *"
:
"""read_fill_structure(molpack, prototype) -> PyObject *"""
return
_libpymolfile
.
read_fill_structure
(
molpack
,
prototype
)
def
read_fill_bonds
(
molpack
:
'PyObject *'
)
->
"PyObject *"
:
"""read_fill_bonds(molpack) -> PyObject *"""
return
_libpymolfile
.
read_fill_bonds
(
molpack
)
def
read_fill_angles
(
molpack
:
'PyObject *'
)
->
"PyObject *"
:
"""read_fill_angles(molpack) -> PyObject *"""
return
_libpymolfile
.
read_fill_angles
(
molpack
)
def
read_fill_next_timestep
(
molpack
:
'PyObject *'
)
->
"PyObject *"
:
"""read_fill_next_timestep(molpack) -> PyObject *"""
return
_libpymolfile
.
read_fill_next_timestep
(
molpack
)
def
are_plugins_same
(
molpack_a
:
'PyObject *'
,
molpack_b
:
'PyObject *'
)
->
"PyObject *"
:
"""are_plugins_same(molpack_a, molpack_b) -> PyObject *"""
return
_libpymolfile
.
are_plugins_same
(
molpack_a
,
molpack_b
)
def
are_filehandles_same
(
molpack_a
:
'PyObject *'
,
molpack_b
:
'PyObject *'
)
->
"PyObject *"
:
"""are_filehandles_same(molpack_a, molpack_b) -> PyObject *"""
return
_libpymolfile
.
are_filehandles_same
(
molpack_a
,
molpack_b
)
# This file is compatible with both classic and new-style classes.
build/lib.macosx-10.12-x86_64-3.6/pymolfile/plugin_list.py
0 → 100644
View file @
c6feda88
import
warnings
import
sys
from
.molfile
import
libpymolfile
try
:
from
.molfile
import
libpymolfile
except
ImportError
:
warnings
.
warn
(
"libpymolfile package not available, pymolfile does not work without its library!"
)
MAX_NUM_PLUGINS
=
200
C_MOLFILE_PLUGINS
=
libpymolfile
.
molfile_plugin_list
(
MAX_NUM_PLUGINS
)
def
byte_str_decode
(
data
,
dectype
=
None
):
try
:
return
data
.
decode
(
dectype
).
replace
(
'
\x00
'
,
''
)
except
AttributeError
:
return
data
def
plugins
():
""" Information on the available molfile plugins
Example tuple: ('psf', 'psf', 1, 1, 1, 0, 1, 1, 1, 0,
'CHARMM,NAMD,XPLOR PSF', 'mol file reader',
'Justin Gullingsrud, John Stone', 1, 9, 17, 1)
The fields in the tuple represent info in ordered as follows:
1: format extension
2: format name
3: read_structure is avaliable if 1
4: read_bonds is avaliable if 1
5: read_angles is avaliable if 1
6: read_next_timestep is avaliable if 1
7: write_structure is avaliable if 1
8: write_bonds is avaliable if 1
9: write_angles is avaliable if 1
10: write_timestep is avaliable if 1
11: long name of the plugin
12: type of plugin
13: authors of the plugin
14: major version of the plugin
15: minor version of the plugin
16: ABI version of the plugin
17: 1 if is reentrant (returns is_reentrant)
Returns: A list of tuples that includes the information and
capabilities of each molfile plugin. The information is
extracted from molfile_plugin_t.
"""
global
C_MOLFILE_PLUGINS
numlist
=
libpymolfile
.
molfile_init
()
if
sys
.
version_info
>
(
3
,):
basestring
=
str
plugins_list
=
[
[
byte_str_decode
(
item
,
dectype
=
"unicode_escape"
)
for
item
in
libpymolfile
.
molfile_plugin_info
(
C_MOLFILE_PLUGINS
,
i
)
]
for
i
in
range
(
numlist
)
]
libpymolfile
.
molfile_finish
()
return
plugins_list
MOLFILE_PLUGINS
=
plugins
()
build/lib.macosx-10.12-x86_64-3.6/pymolfile/pymolfile.py
0 → 100644
View file @
c6feda88
This diff is collapsed.
Click to expand it.
build/lib.macosx-10.12-x86_64-3.6/pymolfile/test_libpymolfile.py
0 → 100644
View file @
c6feda88
import
numpy
import
molfile.libpymolfile
as
pym
mylist
=
pym
.
molfile_plugin_list
(
200
)
print
(
mylist
)
numlist
=
pym
.
molfile_init
()
print
(
numlist
)
for
i
in
range
(
numlist
):
testplugin
=
pym
.
molfile_plugin_info
(
mylist
,
i
)
print
(
i
,
testplugin
)
#splugin = pym.get_plugin(mylist, 99) #pdb
#cplugin = pym.get_plugin(mylist, 83) #trr
#cplugin = pym.get_plugin(mylist, 85) #xtc
splugin
=
pym
.
get_plugin
(
mylist
,
105
)
#psf
#splugin = pym.get_plugin(mylist, 81) #gro
cplugin
=
pym
.
get_plugin
(
mylist
,
69
)
#dcd
#cplugin = pym.get_plugin(mylist, 126) #nc
print
(
splugin
)
print
(
cplugin
)
natoms
=
0
#sfname="../test/DPDP.pdb"
#cfname="../test/DPDP.nc"
#sfname="../test/ala3.pdb"
sfname
=
"../test/ala3.psf"
cfname
=
"../test/ala3.dcd"
#sfname="../test/md.gro"
#cfname="../test/md.trr"
#cfname="../test/md.xtc"
#sfname="../test/md_1u19.gro"
#cfname="../test/md_1u19.xtc"
#sftype="pdb"
#cftype="trr"
#cftype="xtc"
sftype
=
"psf"
#sftype="gro"
cftype
=
"dcd"
#cftype="nc"
print
(
"Structure plugin:"
)
spluginhandle
=
pym
.
open_file_read
(
splugin
,
sfname
,
sftype
,
natoms
)
print
(
"Coordinate plugin:"
)
cpluginhandle
=
pym
.
open_file_read
(
cplugin
,
cfname
,
cftype
,
natoms
)
print
(
cpluginhandle
)
print
(
cpluginhandle
.
natoms
)
print
(
spluginhandle
)
print
(
spluginhandle
.
natoms
)
if
cpluginhandle
.
natoms
!=
spluginhandle
.
natoms
:
print
(
"Number of atoms do not match in structure and coordinate files."
)
if
pym
.
is_plugin_same
(
spluginhandle
,
cpluginhandle
):
pym
.
close_file_read
(
cpluginhandle
)
cpluginhandle
=
spluginhandle
#if 0 && vmdplugin_ABIVERSION > 17
# /* The new PDB file formats allows for much larger structures, */
# /* which can therefore require longer chain ID strings. The */
# /* new PDBx/mmCIF file formats do not have length limits on */
# /* fields, so PDB chains could be arbitrarily long strings */
# /* in such files. At present, we know we need at least 3-char */
# /* chains for existing PDBx/mmCIF files. */
# char chain[4]; /**< required chain name, or "" */
#else
# char chain[2]; /**< required chain name, or "" */
#endif
# Change 'chain', 'S4' to S2 for PDB
if
'pdb'
in
[
sftype
,
cftype
]:
print
(
"file chain is set to S2"
)
chain_size
=
'S2'
else
:
chain_size
=
'S4'
x
=
numpy
.
array
([
(
'C1'
,
'C'
,
'ACE'
,
0
,
''
,
''
,
''
,
''
,
1.0
,
1.0
,
1.0
,
1.0
,
1.0
,
6
),
(
'C2'
,
'C'
,
'ACE'
,
0
,
''
,
''
,
''
,
''
,
1.0
,
1.0
,
1.0
,
1.0
,
1.0
,
6
)
],
dtype
=
[
(
'name'
,
'S16'
),
(
'type'
,
'S16'
),
(
'resname'
,
'S8'
),
(
'resid'
,
'i4'
),
(
'segid'
,
'S8'
),
(
'chain'
,
chain_size
),
(
'altloc'
,
'S2'
),
(
'insertion'
,
'S2'
),
(
'occupancy'
,
'f4'
),
(
'bfactor'
,
'f4'
),
(
'mass'
,
'f4'
),
(
'charge'
,
'f4'
),
(
'radius'
,
'f4'
),
(
'atomicnumber'
,
'i4'
)
]
)
y
=
pym
.
read_fill_structure
(
spluginhandle
,
x
)
if
y
is
not
None
:
print
(
y
)
print
(
len
(
y
))
try
:
z
=
pym
.
read_fill_bonds
(
spluginhandle
)
if
z
is
not
None
:
print
(
z
)
print
(
len
(
z
))
except
(
AttributeError
,
SystemError
):
pass
try
:
a
=
pym
.
read_fill_angles
(
spluginhandle
)
if
a
is
not
None
:
print
(
a
)
print
(
len
(
a
))
except
(
AttributeError
,
SystemError
):
pass
if
pym
.
is_plugin_same
(
spluginhandle
,
cpluginhandle
):
pass
else
:
pym
.
close_file_read
(
spluginhandle
)
step
=
0
while
True
:
#while False:
try
:
c
=
pym
.
read_fill_next_timestep
(
cpluginhandle
)
if
c
is
None
:
break
step
=
step
+
1
print
(
"Step:"
,
step
)
print
(
c
)
if
c
[
"coords"
]
is
not
None
:
print
(
len
(
c
[
"coords"
]))
except
(
AttributeError
,
OSError
):
pass
pym
.
close_file_read
(
cpluginhandle
)
pym
.
molfile_finish
()
build/temp.macosx-10.12-x86_64-3.6/pymolfile/molfile/libpymolfile_wrap.o
0 → 100644
View file @
c6feda88
File added
build/temp.macosx-10.12-x86_64-3.6/pymolfile/molfile/pymolfile.o
0 → 100644
View file @
c6feda88
File added
pymolfile/molfile/external/CMakeLists.txt
0 → 100644
View file @
c6feda88
cmake_minimum_required
(
VERSION 2.8.12
)
project
(
TNGBuilder
)
include
(
ExternalProject
)
set
(
TNG_PREFIX
"
${
CMAKE_CURRENT_BINARY_DIR
}
/tng"
)
set
(
TNG_INSTALL_DIR
"
${
CMAKE_CURRENT_BINARY_DIR
}
/tng"
)
set
(
TNG_CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=
${
TNG_INSTALL_DIR
}
)
message
(
"TNG_PREFIX='
${
TNG_PREFIX
}
'"
)
message
(
"TNG_INSTALL_DIR='
${
TNG_INSTALL_DIR
}
'"
)
message
(
"TNG_CMAKE_ARGS='
${
TNG_CMAKE_ARGS
}
'"
)
message
(
"GIT_EXECUTABLE='
${
GIT_EXECUTABLE
}
'"
)
ExternalProject_Add
(
tng
PREFIX
${
TNG_PREFIX
}
GIT_REPOSITORY https://github.com/gromacs/tng.git
INSTALL_DIR
${
TNG_INSTALL_DIR
}
CMAKE_ARGS
${
TNG_CMAKE_ARGS
}
)
pymolfile/molfile/include/pymolfile.h
deleted
100644 → 0
View file @
d397d505
/* Hey emacs this is -*- C -*- and this is my editor vim.
*
* molfile.c : C and Fortran interfaces for molfile_plugins
* Copyright (c) Berk Onat <b.onat@warwick.ac.uk> 2017
*
* This program is under BSD LICENSE
*/
/*
* The code is written following the plugin test
* context of f77_molfile.c by Axel Kohlmeyer and
* in molfile_plugin/src/f77 and catdcd.c by
* Justin Gullingsrud of VMD plugins.
*/
#ifndef _MOLFILE_H_
#define _MOLFILE_H_
#ifdef __cplusplus
extern
"C"
{
#endif
#include "molfile_plugin.h"
#include "libmolfile_plugin.h"
#include "vmdplugin.h"
#include "Python.h"
#include "structmember.h"
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
enum
{
pluginOK
,
pluginNOINIT
,
pluginCLOSE
,
pluginNOMEM
,
pluginENDOFFILE
,
pluginFILENOTFOUND
,
pluginFORMATERROR
};
#ifndef MAXPLUGINS
#define MAXPLUGINS 200
#endif
struct
MolObject
{
PyObject_HEAD
molfile_plugin_t
*
plugin
;
void
*
file_handle
;
int
natoms
;
MolObject
(
void
)
{}
};
static
void
MolObject_dealloc
(
MolObject
*
self
)
{
Py_XDECREF
(
self
->
plugin
);
Py_XDECREF
(
self
->
file_handle
);
Py_TYPE
(
self
)
->
tp_free
((
PyObject
*
)
self
);
}
static
PyObject
*
MolObject_new
(
PyTypeObject
*
type
,
PyObject
*
args
,
PyObject
*
kwds
)
{
MolObject
*
self
;
self
=
(
MolObject
*
)
type
->
tp_alloc
(
type
,
0
);
if
(
self
!=
NULL
)
{
self
->
plugin
=
NULL
;
self
->
file_handle
=
NULL
;
self
->
natoms
=
0
;
}
return
(
PyObject
*
)
self
;
}
static
int
MolObject_init
(
MolObject
*
self
,
PyObject
*
args
,
PyObject
*
kwds
)
{
molfile_plugin_t
*
plugin
=
NULL
;
void
*
file_handle
=
NULL
;
molfile_plugin_t
*
tmp1
=
NULL
;
void
*
tmp2
=
NULL
;
static
char
*
kwlist
[]
=
{
"plugin"
,
"file_handle"
,
"natoms"
,
NULL
};
if
(
!
PyArg_ParseTupleAndKeywords
(
args
,
kwds
,
"|OOi"
,
kwlist
,
&
plugin
,
&
file_handle
,
&
self
->
natoms
))
return
-
1
;
if
(
plugin
)
{
tmp1
=
self
->
plugin
;
Py_INCREF
(
plugin
);
self
->
plugin
=
plugin
;
Py_XDECREF
(
tmp1
);
}
if
(
file_handle
)
{
tmp2
=
self
->
file_handle
;
Py_INCREF
(
file_handle
);
self
->
file_handle
=
file_handle
;
Py_XDECREF
(
tmp2
);
}
return
0
;
}
static
molfile_plugin_t
*
MolObject_plugin
(
MolObject
*
self
)
{
return
self
->
plugin
;