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.
| creating.py (pymol-v1.8.6.0.tar.bz2) | : | creating.py (pymol-v2.1.0.tar.bz2) |
|---|
| | |
| skipping to change at line 506 | | skipping to change at line 506 |
|---|
| EXAMPLES | | EXAMPLES |
| | |
| ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue] | | ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue] |
| ramp_update e_pot_color, range=[-15,0,15] | | ramp_update e_pot_color, range=[-15,0,15] |
| ramp_update e_pot_color, color=[green,white,orange] | | ramp_update e_pot_color, color=[green,white,orange] |
| | |
| SEE ALSO | | SEE ALSO |
| | |
| ramp_new | | ramp_new |
| ''' | | ''' |
|
| return ramp_new(name, '', range, color, quiet=quiet, _self=cmd) | | return _self.ramp_new(name, '', range, color, quiet=quiet) |
| | |
| def isomesh(name, map, level=1.0, selection='', buffer=0.0, | | def isomesh(name, map, level=1.0, selection='', buffer=0.0, |
| state=1, carve=None, source_state=0, quiet=1, _self=cmd): | | state=1, carve=None, source_state=0, quiet=1, _self=cmd): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
| | |
| "isomesh" creates a mesh isosurface object from a map object. | | "isomesh" creates a mesh isosurface object from a map object. |
| | |
| USAGE | | USAGE |
| | |
| | |
| skipping to change at line 968 | | skipping to change at line 968 |
|---|
| | |
| fragment name | | fragment name |
| | |
| ''' | | ''' |
| r = DEFAULT_ERROR | | r = DEFAULT_ERROR |
| try: | | try: |
| if object==None: | | if object==None: |
| object=name | | object=name |
| model = fragments.get(str(name)) | | model = fragments.get(str(name)) |
| la = len(model.atom) | | la = len(model.atom) |
|
| if la: | | if la and int(origin): |
| position = _self.get_position() | | position = _self.get_position() |
| for c in range(0,3): | | for c in range(0,3): |
| mean_c = sum([a.coord[c] for a in model.atom]) / la | | mean_c = sum([a.coord[c] for a in model.atom]) / la |
| mean_c = position[c] - mean_c | | mean_c = position[c] - mean_c |
| for a in model.atom: | | for a in model.atom: |
|
| _self._adjust_coord(a, c, mean_c) | | a.coord[c] += mean_c |
| r = _self.load_model(model,str(object),quiet=quiet,zoom=zoom, _self=
_self) | | r = _self.load_model(model,str(object),quiet=quiet,zoom=zoom, _self=
_self) |
| except IOError: | | except IOError: |
|
| print("Error: unable to load fragment '%s'." % name) | | raise pymol.CmdException("unable to load fragment '%s'." % name) |
| except: | | |
| traceback.print_exc() | | |
| print("Error: unable to load fragment '%s'." % name) | | |
| if _self._raising(r,_self): raise pymol.CmdException | | if _self._raising(r,_self): raise pymol.CmdException |
| return r | | return r |
| | |
| def create(name, selection, source_state=0, | | def create(name, selection, source_state=0, |
| target_state=0, discrete=0, zoom=-1, quiet=1, | | target_state=0, discrete=0, zoom=-1, quiet=1, |
| singletons=0, extract=None, copy_properties=False, _self=cmd): | | singletons=0, extract=None, copy_properties=False, _self=cmd): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
| | |
| "create" creates a new molecule object from a selection. It can | | "create" creates a new molecule object from a selection. It can |
| | |
| skipping to change at line 1030 | | skipping to change at line 1027 |
|---|
| load, copy, extract | | load, copy, extract |
| ''' | | ''' |
| r = DEFAULT_ERROR | | r = DEFAULT_ERROR |
| target_state = int(target_state) | | target_state = int(target_state) |
| if target_state == -1: | | if target_state == -1: |
| target_state = _self.count_states('?' + name) + 1 | | target_state = _self.count_states('?' + name) + 1 |
| if copy_properties: | | if copy_properties: |
| print(' Warning: properties are not supported in Open-Source PyMOL') | | print(' Warning: properties are not supported in Open-Source PyMOL') |
| # preprocess selection | | # preprocess selection |
| selection = selector.process(selection) | | selection = selector.process(selection) |
|
| # | | |
| | # TODO is this too much convenience? 'extract' should be a simple boolea |
| | n |
| | if extract in (None, 0, '0', ''): |
| | extract = '' |
| | elif extract in (1, '1'): |
| | extract = selection |
| | else: |
| | print(' Warning: non-boolean extract values are deprecated!') |
| | extract = selector.process(extract) |
| | |
| | if extract: |
| | extract_sele = _self.get_unused_name('_extract') |
| | _self.select(extract_sele, extract, 0) |
| | |
| try: | | try: |
| _self.lock(_self) | | _self.lock(_self) |
|
| if name==None: | | if not name: |
| name = _self.get_unused_name("obj") | | name = _self.get_unused_name("obj") |
| r = _cmd.create(_self._COb,str(name),"("+str(selection)+")", | | r = _cmd.create(_self._COb,str(name),"("+str(selection)+")", |
| int(source_state)-1,int(target_state)-1, | | int(source_state)-1,int(target_state)-1, |
| int(discrete),int(zoom),int(quiet),int(singletons)) | | int(discrete),int(zoom),int(quiet),int(singletons)) |
| finally: | | finally: |
| _self.unlock(r,_self) | | _self.unlock(r,_self) |
|
| if not is_error(r): # temporary inefficient implementation | | |
| if extract not in (None, 0, '0'): | | if extract: |
| if extract not in (1, '1'): | | if not is_error(r): |
| extract = selector.process(extract) | | _self.remove(extract_sele) |
| else: | | _self.delete(extract_sele) |
| extract = selection | | |
| _self.remove("(("+extract+") in (%s)) and not (%s)"%(name,name)) | | |
| if _self._raising(r,_self): raise pymol.CmdException | | if _self._raising(r,_self): raise pymol.CmdException |
| return r | | return r |
| | |
| def extract(*arg,**kw): | | def extract(*arg,**kw): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
| | |
| "extract" is simply a shorthand way calling the "create" command | | "extract" is simply a shorthand way calling the "create" command |
| with the extract argument activated, so that atoms in the new | | with the extract argument activated, so that atoms in the new |
| object are removed from the source object. | | object are removed from the source object. |
| | |
| skipping to change at line 1083 | | skipping to change at line 1092 |
|---|
| "extent" : 1, | | "extent" : 1, |
| "rms" : 2, | | "rms" : 2, |
| # "ellipse" : 2, for anisotropic b-factors? | | # "ellipse" : 2, for anisotropic b-factors? |
| } | | } |
| | |
| pseudoatom_mode_sc = Shortcut(pseudoatom_mode_dict.keys()) | | pseudoatom_mode_sc = Shortcut(pseudoatom_mode_dict.keys()) |
| | |
| unquote_re = re.compile(r"r?('.*'|\".*\")$") | | unquote_re = re.compile(r"r?('.*'|\".*\")$") |
| | |
| def unquote(s): | | def unquote(s): |
|
| | if sys.version_info[0] > 2 and isinstance(s, bytes): |
| | s = s.decode('utf-8', 'replace') |
| | |
| s = str(s) | | s = str(s) |
| if unquote_re.match(s): | | if unquote_re.match(s): |
| try: | | try: |
| return cmd.safe_eval(s) | | return cmd.safe_eval(s) |
| except SyntaxError: | | except SyntaxError: |
| print(" Warning: unquote failed for", repr(s)) | | print(" Warning: unquote failed for", repr(s)) |
| return s | | return s |
| | |
| def pseudoatom(object='', selection='', name='PS1', resn='PSD', resi='1', ch
ain='P', | | def pseudoatom(object='', selection='', name='PS1', resn='PSD', resi='1', ch
ain='P', |
| segi='PSDO', elem='PS', vdw=-1.0, hetatm=1, b=0.0, q=0.0, col
or='', | | segi='PSDO', elem='PS', vdw=-1.0, hetatm=1, b=0.0, q=0.0, col
or='', |
| | | |
| End of changes. 8 change blocks. |
|---|
| 16 lines changed or deleted | | 29 lines changed or added |
|---|
"Fossies" - the Fresh Open Source Software Archive 