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.
| __init__.py (pymol-v1.8.6.0.tar.bz2) | : | __init__.py (pymol-v2.1.0.tar.bz2) |
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| | |
| skipping to change at line 15 | | skipping to change at line 15 |
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| License: BSD-2-Clause | | License: BSD-2-Clause |
| | |
| ''' | | ''' |
| | |
| from __future__ import print_function | | from __future__ import print_function |
| | |
| import os | | import os |
| import sys | | import sys |
| import pymol | | import pymol |
| from pymol import cmd | | from pymol import cmd |
|
| | from pymol import colorprinting |
| from .legacysupport import * | | from .legacysupport import * |
| | |
| # variables | | # variables |
| | |
| PYMOLPLUGINSRC = os.path.expanduser('~/.pymolpluginsrc.py') | | PYMOLPLUGINSRC = os.path.expanduser('~/.pymolpluginsrc.py') |
| | |
| preferences = { | | preferences = { |
| 'verbose': False, | | 'verbose': False, |
| 'instantsave': True, | | 'instantsave': True, |
| } | | } |
| | |
| autoload = {} | | autoload = {} |
| | |
| plugins = {} | | plugins = {} |
| | |
|
| | HAVE_QT = False |
| | |
| | # exception types |
| | |
| | class QtNotAvailableError(Exception): |
| | pass |
| | |
| | # plugins from PYMOL_DATA |
| | |
| | startup.__path__.append(cmd.exp_path('$PYMOL_DATA/startup')) |
| | N_NON_USER_PATHS = len(startup.__path__) |
| | |
| # API functions | | # API functions |
| | |
| def is_verbose(debug=0): | | def is_verbose(debug=0): |
| verbose = pref_get('verbose') | | verbose = pref_get('verbose') |
| if debug and verbose < 0: | | if debug and verbose < 0: |
| return True | | return True |
| return verbose and pymol.invocation.options.show_splash | | return verbose and pymol.invocation.options.show_splash |
| | |
| def get_startup_path(useronly=False): | | def get_startup_path(useronly=False): |
| if useronly: | | if useronly: |
| # assume last item is always from installation directory | | # assume last item is always from installation directory |
|
| return startup.__path__[:-1] | | return startup.__path__[:-N_NON_USER_PATHS] |
| return startup.__path__ | | return startup.__path__ |
| | |
| def set_startup_path(p, autosave=True): | | def set_startup_path(p, autosave=True): |
| if isinstance(p, list): | | if isinstance(p, list): |
|
| startup.__path__[:-1] = p | | startup.__path__[:-N_NON_USER_PATHS] = p |
| if autosave: | | if autosave: |
| set_pref_changed() | | set_pref_changed() |
| else: | | else: |
| print(' Error: set_startup_path failed') | | print(' Error: set_startup_path failed') |
| | |
| def pref_set(k, v): | | def pref_set(k, v): |
| preferences[k] = v | | preferences[k] = v |
| set_pref_changed() | | set_pref_changed() |
| | |
| def pref_get(k, d=None): | | def pref_get(k, d=None): |
| | |
| skipping to change at line 88 | | skipping to change at line 101 |
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| f.close() | | f.close() |
| | |
| if not int(quiet): | | if not int(quiet): |
| print(' Plugin settings saved!') | | print(' Plugin settings saved!') |
| | |
| def set_pref_changed(): | | def set_pref_changed(): |
| if pref_get('instantsave', True): | | if pref_get('instantsave', True): |
| verbose = pref_get('verbose', False) | | verbose = pref_get('verbose', False) |
| pref_save(quiet=not verbose) | | pref_save(quiet=not verbose) |
| | |
|
| | def addmenuitemqt(label, command=None, menuName='PluginQt'): |
| | ''' |
| | Adds plugin menu item to main 'Plugin' menu. |
| | Intended for plugins which open a PyQt window. |
| | ''' |
| | if not HAVE_QT: |
| | raise QtNotAvailableError() |
| | |
| | addmenuitem(label, command, menuName) |
| | |
| def addmenuitem(label, command=None, menuName='Plugin'): | | def addmenuitem(label, command=None, menuName='Plugin'): |
| ''' | | ''' |
| Generic replacement for MegaWidgets menu item adding | | Generic replacement for MegaWidgets menu item adding |
| ''' | | ''' |
| labels1 = [menuName] + label.split('|') | | labels1 = [menuName] + label.split('|') |
| labels2 = ['|'.join(labels1[0:i]) for i in range(1, len(labels1))] | | labels2 = ['|'.join(labels1[0:i]) for i in range(1, len(labels1))] |
| pmgapp = get_pmgapp() | | pmgapp = get_pmgapp() |
| if pmgapp is not None: | | if pmgapp is not None: |
| for i in range(1, len(labels2)): | | for i in range(1, len(labels2)): |
| try: | | try: |
| | |
| skipping to change at line 176 | | skipping to change at line 199 |
|---|
| | |
| @property | | @property |
| def is_temporary(self): | | def is_temporary(self): |
| return self.mod_name is None | | return self.mod_name is None |
| | |
| def get_metadata(self): | | def get_metadata(self): |
| ''' | | ''' |
| Parse plugin file for metadata (hash-commented block at beginning of fil
e). | | Parse plugin file for metadata (hash-commented block at beginning of fil
e). |
| ''' | | ''' |
| metadata = dict() | | metadata = dict() |
|
| f = open(self.filename) | | f = open(self.filename, 'rU') |
| for line in f: | | for line in f: |
| if line.strip() == '': | | if line.strip() == '': |
| continue | | continue |
| if not line.startswith('#'): | | if not line.startswith('#'): |
| break | | break |
| if ':' in line: | | if ':' in line: |
| key, value = line[1:].split(':', 1) | | key, value = line[1:].split(':', 1) |
| metadata[key.strip()] = value.strip() | | metadata[key.strip()] = value.strip() |
| f.close() | | f.close() |
| self.get_metadata = lambda: metadata | | self.get_metadata = lambda: metadata |
| | |
| skipping to change at line 216 | | skipping to change at line 239 |
|---|
| | |
| def get_docstring(self): | | def get_docstring(self): |
| ''' | | ''' |
| Get docstring either from loaded module, or try to parse first python | | Get docstring either from loaded module, or try to parse first python |
| statement from file, without executing any code. | | statement from file, without executing any code. |
| ''' | | ''' |
| if self.loaded: | | if self.loaded: |
| return self.module.__doc__ | | return self.module.__doc__ |
| | |
| try: | | try: |
|
| c = compile(''.join(open(self.filename)), 'x', 'single') | | c = compile(''.join(open(self.filename)), 'x', 'exec', dont_inherit=
True) |
| s = c.co_consts[0] | | s = c.co_consts[0] |
| if cmd.is_string(s): | | if cmd.is_string(s): |
| return s | | return s |
|
| | except SyntaxError as e: |
| | if sys.version_info[0] > 2: |
| | return 'WARNING: Plugin not Python 3.x compatible: ' + str(e) |
| except: | | except: |
| pass | | pass |
| | |
| def load(self, pmgapp=None, force=0): | | def load(self, pmgapp=None, force=0): |
| ''' | | ''' |
| Load and initialize plugin. | | Load and initialize plugin. |
| | |
| If pmgapp == -1, do not initialize. | | If pmgapp == -1, do not initialize. |
| ''' | | ''' |
| import time | | import time |
| | |
| skipping to change at line 249 | | skipping to change at line 275 |
|---|
| try: | | try: |
| # overload cmd.extend to register commands | | # overload cmd.extend to register commands |
| extend_orig = cmd.extend | | extend_orig = cmd.extend |
| def extend_overload(a, b=None): | | def extend_overload(a, b=None): |
| self.commands.append(a if b else a.__name__) | | self.commands.append(a if b else a.__name__) |
| return extend_orig(a, b) | | return extend_orig(a, b) |
| cmd.extend = extend_overload | | cmd.extend = extend_overload |
| | |
| # do not use self.loaded here | | # do not use self.loaded here |
| if force and self.module is not None: | | if force and self.module is not None: |
|
| | if sys.version_info[0] > 2: |
| | from importlib import reload |
| | else: |
| | from __builtin__ import reload |
| reload(self.module) | | reload(self.module) |
| else: | | else: |
| __import__(self.mod_name, level=0) | | __import__(self.mod_name, level=0) |
| | |
| if pmgapp != -1: | | if pmgapp != -1: |
| self.legacyinit(pmgapp) | | self.legacyinit(pmgapp) |
| | |
| cmd.extend = extend_orig | | cmd.extend = extend_orig |
| | |
| self.loadtime = time.time() - starttime | | self.loadtime = time.time() - starttime |
| if verbose and pymol.invocation.options.show_splash: | | if verbose and pymol.invocation.options.show_splash: |
| print(' Plugin "%s" loaded in %.2f seconds' % (self.name, self.l
oadtime)) | | print(' Plugin "%s" loaded in %.2f seconds' % (self.name, self.l
oadtime)) |
|
| | except QtNotAvailableError: |
| | colorprinting.warning("Plugin '%s' only available with PyQt GUI." % |
| | (self.name,)) |
| except: | | except: |
|
| | e = sys.exc_info()[1] |
| if verbose: | | if verbose: |
|
| import traceback | | colorprinting.print_exc([__file__]) |
| traceback.print_exc() | | elif 'libX11' in str(e) and sys.platform == 'darwin': |
| | colorprinting.error('Please install XQuartz (https://www.xquartz |
| | .org/)') |
| else: | | else: |
|
| print(sys.exc_info()[1]) | | colorprinting.error(e) |
| print("Unable to initialize plugin '%s' (%s)." % (self.name, self.mo | | colorprinting.warning("Unable to initialize plugin '%s' (%s)." % (se |
| d_name)) | | lf.name, self.mod_name)) |
| return False | | return False |
| | |
| return True | | return True |
| | |
| def legacyinit(self, pmgapp): | | def legacyinit(self, pmgapp): |
| ''' | | ''' |
| Call the __init__ or __init_plugin__ function which takes the PMGApp | | Call the __init__ or __init_plugin__ function which takes the PMGApp |
| instance as argument (usually adds menu items). | | instance as argument (usually adds menu items). |
| | |
| This must be called after loading and after launching of the external | | This must be called after loading and after launching of the external |
| | | |
| End of changes. 13 change blocks. |
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| 9 lines changed or deleted | | 45 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 