is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| invocation.py (pymol-open-source-2.2.0) | : | invocation.py (pymol-open-source-2.3.0) |
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| skipping to change at line 32 | | skipping to change at line 32 |
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| helptext1 = '''Copyright (C) Schrodinger, LLC | | helptext1 = '''Copyright (C) Schrodinger, LLC |
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| Usage: pymol [OPTIONS]... [FILES]... [-- CUSTOM SCRIPT ARGUMENTS] | | Usage: pymol [OPTIONS]... [FILES]... [-- CUSTOM SCRIPT ARGUMENTS] |
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| Options | | Options |
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| --help display this help and exit | | --help display this help and exit |
| --version display PyMOL version and exit | | --version display PyMOL version and exit |
| --retina use retina resolution (MacPyMOL) and set display_scale_factor=2 | | --retina use retina resolution (MacPyMOL) and set display_scale_factor=2 |
| --gldebug use glDebugMessageCallback for GL debugging | | --gldebug use glDebugMessageCallback for GL debugging |
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| | --testing run pymol testing |
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| -1 config_mouse one_button | | -1 config_mouse one_button |
| -2 config_mouse two_button | | -2 config_mouse two_button |
| -a N alias for -A | | -a N alias for -A |
| -A N application configuration: | | -A N application configuration: |
| -A1 simple viewer window (-qxiF -X 68 -Y 100) | | -A1 simple viewer window (-qxiF -X 68 -Y 100) |
| -A3 internal GUI only, no splash (-qx -X 68 -Y 100) | | -A3 internal GUI only, no splash (-qx -X 68 -Y 100) |
| -A4 used by PYMOLVIEWER (-X 68 -Y 100) | | -A4 used by PYMOLVIEWER (-X 68 -Y 100) |
| -A5 helper application (-QxiICUF -X 68 -Y 100) | | -A5 helper application (-QxiICUF -X 68 -Y 100) |
| -A6 full screen presentation (-qxieICUPF) | | -A6 full screen presentation (-qxieICUPF) |
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| skipping to change at line 113 | | skipping to change at line 114 |
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| psw implies -A6 (PyMOL Show File) | | psw implies -A6 (PyMOL Show File) |
| pwg PyMOL web GUI | | pwg PyMOL web GUI |
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| Active "pymolrc" Files | | Active "pymolrc" Files |
| ''' | | ''' |
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| helptext2 = ''' | | helptext2 = ''' |
| Mail bug reports to https://lists.sourceforge.net/lists/listinfo/pymol-users | | Mail bug reports to https://lists.sourceforge.net/lists/listinfo/pymol-users |
| ''' | | ''' |
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|
| if __name__=='pymol.invocation': | | if True: |
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| import copy | | import copy |
| import re | | import re |
| import os | | import os |
| import glob | | import glob |
| import sys | | import sys |
| import traceback | | import traceback |
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| pymolrc_pat1 = '.pymolrc*' | | pymolrc_pat1 = '.pymolrc*' |
| pymolrc_pat2 = 'pymolrc*' | | pymolrc_pat2 = 'pymolrc*' |
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| skipping to change at line 173 | | skipping to change at line 174 |
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| options.stereo_mode = 0 | | options.stereo_mode = 0 |
| options.zoom_mode = -1 | | options.zoom_mode = -1 |
| options.no_quit = 0 | | options.no_quit = 0 |
| options.plugins = 2 | | options.plugins = 2 |
| options.exit_on_error = 0 | | options.exit_on_error = 0 |
| options.pymolrc = None | | options.pymolrc = None |
| options.retina = 0 | | options.retina = 0 |
| options.no_spacenav = 0 | | options.no_spacenav = 0 |
| options.launch_status = 0 | | options.launch_status = 0 |
| options.gldebug = 0 | | options.gldebug = 0 |
|
| | options.testing = 0 |
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| options.win_py = { 'irix':240, | | options.win_py = { 'irix':240, |
| 'darwin': 214, # hmm...need to set to 192 for Leopard?... | | 'darwin': 214, # hmm...need to set to 192 for Leopard?... |
| 'linux2': 220, | | 'linux2': 220, |
| 'win32' : 230}.get(sys.platform,200) | | 'win32' : 230}.get(sys.platform,200) |
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| options.ext_y = 168 # external gui height (eg. for Tcl/Tk top bar) | | options.ext_y = 168 # external gui height (eg. for Tcl/Tk top bar) |
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| options.blue_line = 0 | | options.blue_line = 0 |
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| skipping to change at line 284 | | skipping to change at line 286 |
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| else: | | else: |
| print(' (no pymolrc file found)') | | print(' (no pymolrc file found)') |
| print(helptext2) | | print(helptext2) |
| sys.exit() | | sys.exit() |
| elif a == "--retina": | | elif a == "--retina": |
| options.retina = 1 | | options.retina = 1 |
| elif a == "--nospnav": | | elif a == "--nospnav": |
| print(' Warning: --nospnav not available in Open-Source
PyMOL') | | print(' Warning: --nospnav not available in Open-Source
PyMOL') |
| elif a == "--gldebug": | | elif a == "--gldebug": |
| options.gldebug = 1 | | options.gldebug = 1 |
|
| | elif a == "--testing": |
| | options.testing = 1 |
| else: | | else: |
| # double hypen signals end of PyMOL arguments | | # double hypen signals end of PyMOL arguments |
| if python_script == None: | | if python_script == None: |
| python_script = argv[0] | | python_script = argv[0] |
| rev_av = copy.deepcopy(av) | | rev_av = copy.deepcopy(av) |
| rev_av.reverse() | | rev_av.reverse() |
| if len(a)>2: | | if len(a)>2: |
| sys.argv = [python_script] + [a] + rev_av | | sys.argv = [python_script] + [a] + rev_av |
| else: | | else: |
| sys.argv = [python_script] + rev_av | | sys.argv = [python_script] + rev_av |
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| End of changes. 4 change blocks. |
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| 1 lines changed or deleted | | 5 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 