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-v2.1.0.tar.bz2) | : | invocation.py (pymol-open-source-2.2.0) |
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| skipping to change at line 30 | | skipping to change at line 30 |
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| # | | # |
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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 |
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| --retina use retina resolution (Experimental, MacPyMOL only) | | --retina use retina resolution (MacPyMOL) and set display_scale_factor=2 |
| | --gldebug use glDebugMessageCallback for GL debugging |
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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 67 | | skipping to change at line 68 |
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| -j side-by-side stereo (stereo_mode=4) | | -j side-by-side stereo (stereo_mode=4) |
| -J cd to user's home directory | | -J cd to user's home directory |
| -k don't load pymolrc or plugins | | -k don't load pymolrc or plugins |
| -K keep alive: when running without a GUI, don't quit after the input | | -K keep alive: when running without a GUI, don't quit after the input |
| is exhausted | | is exhausted |
| -l file run python script in thread (spawn) | | -l file run python script in thread (spawn) |
| -L file load file after everything else (only if something was loaded before
) | | -L file load file after everything else (only if something was loaded before
) |
| -m INTERNAL - do not use (mac external GUI) | | -m INTERNAL - do not use (mac external GUI) |
| -M force mono | | -M force mono |
| -n INTERNAL - do not use (incentive_product=1) | | -n INTERNAL - do not use (incentive_product=1) |
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| -N name UNSUPPORTED - external gui type (default: pmg_tk) (same as -w) | | -N name UNSUPPORTED - external gui type (pmg_qt or pmg_tk) (same as -w) |
| -o disable security protections | | -o disable security protections |
| -O N sphere_mode=N | | -O N sphere_mode=N |
| -p read commands from STDIN | | -p read commands from STDIN |
| -P handle scenes as if the session were opened in presentation mode | | -P handle scenes as if the session were opened in presentation mode |
| -q supress startup message | | -q supress startup message |
| -Q quiet, suppress all text output | | -Q quiet, suppress all text output |
| -r file run python script | | -r file run python script |
| -R launch RPC Server | | -R launch RPC Server |
| -s file log to file | | -s file log to file |
| -S force stereo | | -S force stereo |
| -t N stereo_mode=N | | -t N stereo_mode=N |
| -T name UNSUPPORTED - Tcl/Tk GUI skin | | -T name UNSUPPORTED - Tcl/Tk GUI skin |
| -u file resume log file (execute existing content and append new log output) | | -u file resume log file (execute existing content and append new log output) |
| -U UNSUPPORTED reuse the helper application | | -U UNSUPPORTED reuse the helper application |
| -v UNUSED | | -v UNUSED |
| -V N external GUI window height in pixels | | -V N external GUI window height in pixels |
|
| -w name UNSUPPORTED - external gui type (default: pmg_tk) (same as -N) | | -w name UNSUPPORTED - external gui type (pmg_qt or pmg_tk) (same as -N) |
| -W N window width in pixels | | -W N window width in pixels |
| -x no external gui | | -x no external gui |
| -X N window x position on screen | | -X N window x position on screen |
| -y exit on error | | -y exit on error |
| -Y N window y position on screen | | -Y N window y position on screen |
| -z N window_visible=N | | -z N window_visible=N |
| -Z N zoom_mode=N | | -Z N zoom_mode=N |
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| File Extensions | | File Extensions |
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| skipping to change at line 168 | | skipping to change at line 169 |
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| options.defer_builds_mode = 0 | | options.defer_builds_mode = 0 |
| options.full_screen = 0 | | options.full_screen = 0 |
| options.sphere_mode = -1 | | options.sphere_mode = -1 |
| options.stereo_capable = 0 | | options.stereo_capable = 0 |
| 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.no_spacenav = 0 |
| | options.launch_status = 0 |
| | options.gldebug = 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 273 | | skipping to change at line 278 |
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| print(pymol.get_version_message()) | | print(pymol.get_version_message()) |
| if a == '--help': | | if a == '--help': |
| print(helptext1) | | print(helptext1) |
| if pymolrc: | | if pymolrc: |
| for filename in pymolrc: | | for filename in pymolrc: |
| print(' ' + filename) | | print(' ' + filename) |
| else: | | else: |
| print(' (no pymolrc file found)') | | print(' (no pymolrc file found)') |
| print(helptext2) | | print(helptext2) |
| sys.exit() | | sys.exit() |
|
| | elif a == "--retina": |
| | options.retina = 1 |
| | elif a == "--nospnav": |
| | print(' Warning: --nospnav not available in Open-Source |
| | PyMOL') |
| | elif a == "--gldebug": |
| | options.gldebug = 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. 5 change blocks. |
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| 3 lines changed or deleted | | 15 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 