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.
| cmd2.py (pymol-v1.8.6.0.tar.bz2) | : | cmd2.py (pymol-v2.1.0.tar.bz2) |
|---|
| from pymol import cmd as global_cmd | | from pymol import cmd as global_cmd |
| import pymol | | import pymol |
| import inspect | | import inspect |
|
| | import itertools |
| | import weakref |
| | |
| #most recently created Cmd (for now) | | #most recently created Cmd (for now) |
| cmd = None | | cmd = None |
| | |
| class Cmd: | | class Cmd: |
| ''' | | ''' |
| Proxy for the pymol.cmd module for multiple instances support. | | Proxy for the pymol.cmd module for multiple instances support. |
| ''' | | ''' |
| | |
| def __init__(self, _pymol, _COb): | | def __init__(self, _pymol, _COb): |
| global cmd | | global cmd |
|
| cmd = self | | cmd = weakref.proxy(self) |
| | self._weakref = weakref.ref(self) |
| | self._weakrefproxy = weakref.proxy(self) |
| | |
| # store parent | | # store parent |
| | |
|
| self._pymol = _pymol | | self._pymol = weakref.proxy(_pymol) |
| | |
| # store C object for easy access | | # store C object for easy access |
| | |
| self._COb = _COb | | self._COb = _COb |
| | |
| # private data | | # private data |
| | |
| self.color_sc = None | | self.color_sc = None |
| self.reaper = None | | self.reaper = None |
| | |
|
| # CONSTANTS (pymol/constants.py) | | |
| | |
| self.fb_debug = global_cmd.fb_debug # this cannot be right... | | |
| | | |
| # deferred initiailization | | # deferred initiailization |
| | |
| global_cmd._deferred_init_pymol_internals(_pymol) | | global_cmd._deferred_init_pymol_internals(_pymol) |
| | |
| # PRIVATE FUNCTIONS (requiring '_self' as a keyword argument) | | # PRIVATE FUNCTIONS (requiring '_self' as a keyword argument) |
| | |
| # locking.py | | # locking.py |
| | |
| self.reaper = None | | self.reaper = None |
| | |
| | |
| skipping to change at line 66 | | skipping to change at line 67 |
|---|
| self.lock_api_status = global_cmd._pymol.lock_api_status | | self.lock_api_status = global_cmd._pymol.lock_api_status |
| | |
| self.lock_api_allow_flush = 1 | | self.lock_api_allow_flush = 1 |
| self.lockcm = global_cmd.LockCM(self) | | self.lockcm = global_cmd.LockCM(self) |
| | |
| # now we create the command langauge | | # now we create the command langauge |
| | |
| from pymol import keywords | | from pymol import keywords |
| | |
| self.keyword = keywords.get_command_keywords() | | self.keyword = keywords.get_command_keywords() |
|
| self.kw_list = self.keyword.keys() | | self.kw_list = list(self.keyword) |
| | |
| keywords.fix_list(self.kw_list) | | keywords.fix_list(self.kw_list) |
| self.kwhash = self.Shortcut(self.kw_list) | | self.kwhash = self.Shortcut(self.kw_list) |
| keywords.fix_dict(self.keyword) | | keywords.fix_dict(self.keyword) |
| | |
| self.help_only = keywords.get_help_only_keywords() | | self.help_only = keywords.get_help_only_keywords() |
|
| self.help_sc = self.Shortcut(self.keyword.keys()+self.help_only.keys()) | | self.help_sc = self.Shortcut( |
| | itertools.chain(self.keyword, self.help_only)) |
| | |
| self.selection_sc = lambda sc=self.Shortcut,gn=self.get_names:sc(gn('pub
lic')+['all']) | | self.selection_sc = lambda sc=self.Shortcut,gn=self.get_names:sc(gn('pub
lic')+['all']) |
| self.object_sc = lambda sc=self.Shortcut,gn=self.get_names:sc(gn('object
s')) | | self.object_sc = lambda sc=self.Shortcut,gn=self.get_names:sc(gn('object
s')) |
| self.map_sc = lambda sc=self.Shortcut,gnot=self.get_names_of_type:sc(gno
t('object:map')) | | self.map_sc = lambda sc=self.Shortcut,gnot=self.get_names_of_type:sc(gno
t('object:map')) |
| self.contour_sc = lambda sc=self.Shortcut,gnot=self.get_names_of_type:s
c(gnot('object:mesh')+gnot('object:surface')) | | self.contour_sc = lambda sc=self.Shortcut,gnot=self.get_names_of_type:s
c(gnot('object:mesh')+gnot('object:surface')) |
| self.group_sc = lambda sc=self.Shortcut,gnot=self.get_names_of_type:sc(g
not('object:group')) | | self.group_sc = lambda sc=self.Shortcut,gnot=self.get_names_of_type:sc(g
not('object:group')) |
| | |
| self.fb_action_sc = pymol.feedingback.fb_action_sc | | self.fb_action_sc = pymol.feedingback.fb_action_sc |
| self.fb_module_sc = pymol.feedingback.fb_module_sc | | self.fb_module_sc = pymol.feedingback.fb_module_sc |
| self.fb_mask_sc = pymol.feedingback.fb_mask_sc | | self.fb_mask_sc = pymol.feedingback.fb_mask_sc |
| | |
| skipping to change at line 103 | | skipping to change at line 105 |
|---|
| | |
| # PUBLIC API METHODS which expect "self" as the first argument | | # PUBLIC API METHODS which expect "self" as the first argument |
| | |
| def __getattr__(self, key): | | def __getattr__(self, key): |
| v = getattr(global_cmd, key) | | v = getattr(global_cmd, key) |
| try: | | try: |
| i = inspect.getargspec(v).args.index('_self') | | i = inspect.getargspec(v).args.index('_self') |
| except: | | except: |
| setattr(self, key, v) | | setattr(self, key, v) |
| return v | | return v |
|
| | # don't bind a circular reference into the wrapper |
| | # namespace, use a weak reference instead |
| | cmdref = self._weakref |
| def wrapper(*a, **k): | | def wrapper(*a, **k): |
| if len(a) <= i: | | if len(a) <= i: |
|
| k['_self'] = self | | k['_self'] = cmdref() |
| return v(*a, **k) | | return v(*a, **k) |
| wrapper.__name__ = key | | wrapper.__name__ = key |
| setattr(self, key, wrapper) | | setattr(self, key, wrapper) |
| return wrapper | | return wrapper |
| | | |
| End of changes. 8 change blocks. |
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| 9 lines changed or deleted | | 14 lines changed or added |
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