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-v1.8.6.0.tar.bz2) | : | invocation.py (pymol-v2.1.0.tar.bz2) |
|---|
| | |
| skipping to change at line 105 | | skipping to change at line 105 |
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| pdb,sdf,... molecular structure files | | pdb,sdf,... molecular structure files |
| ccp4,dx,... map files | | ccp4,dx,... map files |
| | |
| py,pym,pyc python script | | py,pym,pyc python script |
| pml PyMOL command script | | pml PyMOL command script |
| | |
| p5m implies -A5 (PDB File) | | p5m implies -A5 (PDB File) |
| psw implies -A6 (PyMOL Show File) | | psw implies -A6 (PyMOL Show File) |
| pwg PyMOL web GUI | | pwg PyMOL web GUI |
| | |
|
| Any unrecognized file extension will be treated as PDB format. | | |
| | | |
| Active "pymolrc" Files | | Active "pymolrc" Files |
| ''' | | ''' |
| | |
| 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 |
| ''' | | ''' |
| | |
| if __name__=='pymol.invocation': | | if __name__=='pymol.invocation': |
| | |
| import copy | | import copy |
| | |
| skipping to change at line 140 | | skipping to change at line 138 |
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| | |
| global_options = generic(); | | global_options = generic(); |
| | |
| options = global_options | | options = global_options |
| | |
| options.deferred = [] | | options.deferred = [] |
| options.no_gui = 0 | | options.no_gui = 0 |
| options.internal_gui = 1 | | options.internal_gui = 1 |
| options.internal_feedback = 1 | | options.internal_feedback = 1 |
| options.external_gui = 1 | | options.external_gui = 1 |
|
| options.force_stereo = 0 | | options.force_stereo = -1 if sys.platform == 'darwin' else 0 |
| options.game_mode = 0 | | options.game_mode = 0 |
|
| options.gui = 'pmg_tk' | | options.gui = 'pmg_qt' |
| options.skin = 'normal' | | options.skin = 'normal' |
| options.show_splash = 1 | | options.show_splash = 1 |
| options.read_stdin = 0 | | options.read_stdin = 0 |
| options.win_x = 640 | | options.win_x = 640 |
| options.win_y = 480 | | options.win_y = 480 |
|
| | options.win_xy_set = False |
| options.win_px = 4 | | options.win_px = 4 |
| options.sigint_handler = 1 # terminate on Ctrl-C? | | options.sigint_handler = 1 # terminate on Ctrl-C? |
| options.reuse_helper = 0 | | options.reuse_helper = 0 |
| options.auto_reinitialize = 0 | | options.auto_reinitialize = 0 |
| options.keep_thread_alive = 0 | | options.keep_thread_alive = 0 |
| options.after_load_script = "" | | options.after_load_script = "" |
| options.quiet = 0 | | options.quiet = 0 |
| options.multisample = 0 | | options.multisample = 0 |
| options.incentive_product = 0 | | options.incentive_product = 0 |
| options.window_visible = 1 | | options.window_visible = 1 |
| | |
| skipping to change at line 188 | | skipping to change at line 187 |
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| | |
| # Greg Landrum | | # Greg Landrum |
| options.rpcServer = 0 | | options.rpcServer = 0 |
| # end | | # end |
| options.security = 1 | | options.security = 1 |
| | |
| script_re = re.compile(r"pymolrc$|\.pml$|\.PML$|\.p1m$|\.P1M$") | | script_re = re.compile(r"pymolrc$|\.pml$|\.PML$|\.p1m$|\.P1M$") |
| py_re = re.compile(r"\.py$|\.pym$|\.PY$|\.PYM$") | | py_re = re.compile(r"\.py$|\.pym$|\.PY$|\.PYM$") |
| | |
| def get_pwg_options(filename): | | def get_pwg_options(filename): |
|
| for line in open(filename): | | for line in open(filename, 'rU'): |
| a = line.split() | | a = line.split() |
| if not a or a[0].startswith('#'): | | if not a or a[0].startswith('#'): |
| continue | | continue |
| if a[0].lower() == 'options': | | if a[0].lower() == 'options': |
| return a[1:] | | return a[1:] |
| return [] | | return [] |
| | |
| def get_personal_folder(): | | def get_personal_folder(): |
| if sys.platform.startswith('win'): | | if sys.platform.startswith('win'): |
| try: | | try: |
| | |
| skipping to change at line 350 | | skipping to change at line 349 |
|---|
| if "F" in a: | | if "F" in a: |
| options.internal_feedback = 0 | | options.internal_feedback = 0 |
| if "B" in a: | | if "B" in a: |
| options.blue_line = 1 | | options.blue_line = 1 |
| if "E" in a: | | if "E" in a: |
| options.multisample = int(av.pop()) | | options.multisample = int(av.pop()) |
| if "P" in a: | | if "P" in a: |
| options.presentation = 1 | | options.presentation = 1 |
| if "W" in a: | | if "W" in a: |
| options.win_x = int(av.pop()) | | options.win_x = int(av.pop()) |
|
| | options.win_xy_set = True |
| if "H" in a: | | if "H" in a: |
| options.win_y = int(av.pop()) | | options.win_y = int(av.pop()) |
|
| | options.win_xy_set = True |
| if "X" in a: | | if "X" in a: |
| options.win_px = int(av.pop()) | | options.win_px = int(av.pop()) |
| if "y" in a: | | if "y" in a: |
| options.exit_on_error = 1 | | options.exit_on_error = 1 |
| if "Y" in a: | | if "Y" in a: |
| options.win_py = int(av.pop()) | | options.win_py = int(av.pop()) |
| if "D" in a: | | if "D" in a: |
| options.defer_builds_mode = int(av.pop()) | | options.defer_builds_mode = int(av.pop()) |
| if "V" in a: | | if "V" in a: |
| options.ext_y = int(av.pop()) | | options.ext_y = int(av.pop()) |
| | |
| skipping to change at line 403 | | skipping to change at line 404 |
|---|
| options.win_py = 184 | | options.win_py = 184 |
| | |
| if "e" in a: | | if "e" in a: |
| options.full_screen = 1 | | options.full_screen = 1 |
| if "G" in a: # Game mode (reqd for Mac stereo) | | if "G" in a: # Game mode (reqd for Mac stereo) |
| options.game_mode = 1 | | options.game_mode = 1 |
| options.win_x = 1024 | | options.win_x = 1024 |
| options.win_y = 768 | | options.win_y = 768 |
| if "S" in a: # Force stereo context on stereo-capable hardwa
re | | if "S" in a: # Force stereo context on stereo-capable hardwa
re |
| options.force_stereo = 1 | | options.force_stereo = 1 |
|
| | if options.stereo_mode == 0: |
| | options.stereo_mode = 1 # quadbuffer |
| if sys.platform=='darwin': | | if sys.platform=='darwin': |
| options.deferred.append( | | options.deferred.append( |
| "_do__ set stereo_double_pump_mono,1,quiet=1") | | "_do__ set stereo_double_pump_mono,1,quiet=1") |
| if "M" in a: # Force mono on stereo hardware (all) | | if "M" in a: # Force mono on stereo hardware (all) |
| options.force_stereo = -1 | | options.force_stereo = -1 |
| if "j" in a: # Geowall: two side-by-side images | | if "j" in a: # Geowall: two side-by-side images |
| options.stereo_mode = 4 | | options.stereo_mode = 4 |
| options.deferred.append("_do__ stereo on") | | options.deferred.append("_do__ stereo on") |
| if ("d" in a): | | if ("d" in a): |
| options.deferred.append( | | options.deferred.append( |
| | |
| skipping to change at line 477 | | skipping to change at line 480 |
|---|
| if "Q" in a: | | if "Q" in a: |
| options.quiet = 1 | | options.quiet = 1 |
| options.show_splash = 0 | | options.show_splash = 0 |
| if "I" in a: | | if "I" in a: |
| options.auto_reinitialize = 1 | | options.auto_reinitialize = 1 |
| if "h" in a: # generic helper application | | if "h" in a: # generic helper application |
| options.internal_gui = 0 | | options.internal_gui = 0 |
| options.external_gui = 0 | | options.external_gui = 0 |
| options.internal_feedback = 0 | | options.internal_feedback = 0 |
| options.show_splash = 1 | | options.show_splash = 1 |
|
| | elif a in ('+1', '+2', '+3', '+4'): |
| | print('ignoring PyMOLWin.exe argument', a) |
| elif not restricted: | | elif not restricted: |
| suffix = a[-4:].lower().split('.')[-1] | | suffix = a[-4:].lower().split('.')[-1] |
| if suffix == "p5m": | | if suffix == "p5m": |
| # mode 5 helper application | | # mode 5 helper application |
| av.append("-A5") | | av.append("-A5") |
| elif suffix == "psw": | | elif suffix == "psw": |
| # presentation mode | | # presentation mode |
| av.append("-A6") | | av.append("-A6") |
| elif suffix in [ 'pym' ,'py', 'pyc' ]: | | elif suffix in [ 'pym' ,'py', 'pyc' ]: |
| python_script = a | | python_script = a |
| | |
| skipping to change at line 500 | | skipping to change at line 505 |
|---|
| if pwg_options: | | if pwg_options: |
| parse_args(['pymol'] + pwg_options, _pymol, options,
1) | | parse_args(['pymol'] + pwg_options, _pymol, options,
1) |
| except: | | except: |
| traceback.print_exc() | | traceback.print_exc() |
| options.deferred.append(a) | | options.deferred.append(a) |
| loaded_something = 1 | | loaded_something = 1 |
| if pymolrc != None: | | if pymolrc != None: |
| options.deferred = [('_do__ @' + a) if script_re.search(a) else a | | options.deferred = [('_do__ @' + a) if script_re.search(a) else a |
| for a in pymolrc] + options.deferred | | for a in pymolrc] + options.deferred |
| options.pymolrc = pymolrc | | options.pymolrc = pymolrc |
|
| | if options.rpcServer: |
| | options.deferred.append('_do__ /import pymol.rpc;pymol.rpc.launch_XM |
| | LRPC()') |
| if options.plugins == 1: | | if options.plugins == 1: |
| # Load plugins independent of PMGApp (will not add menu items) | | # Load plugins independent of PMGApp (will not add menu items) |
| options.deferred.append('_do__ /import pymol.plugins;pymol.plugins.i
nitialize(-1)') | | options.deferred.append('_do__ /import pymol.plugins;pymol.plugins.i
nitialize(-1)') |
| if loaded_something and (options.after_load_script!=""): | | if loaded_something and (options.after_load_script!=""): |
| options.deferred.append(options.after_load_script) | | options.deferred.append(options.after_load_script) |
| options.deferred.extend(final_actions) | | options.deferred.extend(final_actions) |
| if options.show_splash and not options.no_gui and not restricted: | | if options.show_splash and not options.no_gui and not restricted: |
| options.deferred.insert(0,"_do__ cmd.splash(1)") | | options.deferred.insert(0,"_do__ cmd.splash(1)") |
| if options.full_screen: | | if options.full_screen: |
| options.deferred.append("_do__ full_screen on") | | options.deferred.append("_do__ full_screen on") |
| | | |
| End of changes. 10 change blocks. |
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| 5 lines changed or deleted | | 13 lines changed or added |
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