#A* ------------------------------------------------------------------- #B* This file contains source code for the PyMOL computer program #C* Copyright (c) Schrodinger, LLC. #D* ------------------------------------------------------------------- #E* It is unlawful to modify or remove this copyright notice. #F* ------------------------------------------------------------------- #G* Please see the accompanying LICENSE file for further information. #H* ------------------------------------------------------------------- #I* Additional authors of this source file include: #-* Filipe Maia (slicing code) #-* #-* #Z* ------------------------------------------------------------------- from . import colorprinting if True: import sys import threading import pymol from . import selector import copy from . import parsing import re cmd = sys.modules["pymol.cmd"] from .cmd import _cmd, Shortcut, \ _feedback,fb_module,fb_mask, \ repres,repres_sc, is_string, is_list, \ repmasks,repmasks_sc, \ toggle_dict,toggle_sc,stereo_dict,stereo_sc, \ palette_dict, palette_sc, window_dict, window_sc, \ safe_list_eval, safe_alpha_list_eval, \ location_code, location_sc, boolean_dict, boolean_sc, \ DEFAULT_ERROR, DEFAULT_SUCCESS palette_colors_dict = { 'rainbow_cycle' : 'magenta blue cyan green yellow orange red magenta', 'rainbow_cycle_rev' : 'magenta red orange yellow green cyan blue magenta', 'rainbow' : 'blue cyan green yellow orange red', 'rainbow_rev' : 'red orange yellow green cyan blue', 'rainbow2' : 'blue cyan green yellow orange red', 'rainbow2_rev' : 'red orange yellow green cyan blue', 'gcbmry' : 'green cyan blue magenta red yellow', 'yrmbcg' : 'yellow red magenta blue cyan green', 'cbmr' : 'cyan blue magenta red', 'rmbc' : 'red magenta blue cyan', } rep_list = [ "lines", "sticks", "spheres", "dots", "surface", "mesh", "nonbonded", "nb_spheres", "cartoon", "ribbon", "labels", "slice", "ellipsoids", "volume" ] scene_action_sc = Shortcut(['store','recall','clear','insert_before', 'insert_after','next','previous', 'start', 'update','rename','delete', 'order', 'sort', 'first', 'append']) scene_action_dict = {} scene_action_dict_sc = Shortcut([]) view_sc = Shortcut(['store','recall','clear']) def zoom(selection="all", buffer=0.0, state=0, complete=0, animate=0, *, _self=cmd): ''' DESCRIPTION "zoom" scales and translates the window and the origin to cover the atom selection. USAGE zoom [ selection [, buffer [, state [, complete [, animate ]]]]] EXAMPLES zoom zoom complete=1 zoom 142/, animate=3 zoom (chain A) ARGUMENTS selection = string: selection-expression or name pattern {default: all} buffer = float: distance {default: 0} state = 0: uses all coordinate states {default} state = -1: uses only coordinates for the current state state > 0: uses coordinates for a specific state complete = 0 or 1: will insure no atoms centers are clipped animate < 0: uses the default animation duration animate = 0: no animation animate > 0: animates using the provided duration in seconds PYMOL API cmd.zoom(string selection, float buffer, int state, int complete, int animate) NOTES The zoom command normally tries to guess an optimal zoom level for visualization, balancing closeness against occasional clipping of atoms out of the field of view. You can change this behavior by setting the complete option to 1, which will guarantee that the atom positions for the entire selection will fit in the field of an orthoscopic view. To absolutely prevent clipping, you may also need to add an additional buffer (typically 2 A) to account for graphical representations which extend beyond the atom coordinates. SEE ALSO origin, orient, center ''' # preprocess selection selection = selector.process(selection) # with _self.lockcm: r = _cmd.zoom(_self._COb,str(selection),float(buffer), int(state)-1,int(complete),float(animate)) return r def center(selection="all", state=0, origin=1, animate=0, *, _self=cmd): ''' DESCRIPTION "center" translates the window, the clipping slab, and the origin to a point centered within the atom selection. USAGE center [ selection [, state [, origin [, animate ]]]] EXAMPLES center chain B center 145/ ARGUMENTS selection = string: selection-expression or name pattern (default: "all"). state = 0 (default) use all coordinate states state = -1 use only coordinates for the current state state > 0 use coordinates for a specific state origin = 1 (default) move the origin origin = 0 leave the origin unchanged PYMOL API cmd.center(string selection, int state, int origin) SEE ALSO origin, orient, zoom ''' # preprocess selection selection = selector.process(selection) # with _self.lockcm: r = _cmd.center(_self._COb,str(selection),int(state)-1,int(origin),float(animate)) return r clip_action_sc = Shortcut([ 'near','far','move','slab','atoms', 'near_set', 'far_set' ]) def clip(mode, distance, selection=None, state=0, *, _self=cmd): ''' DESCRIPTION "clip" alters the positions of the clipping planes. USAGE clip mode, distance [, selection [, state ]] ARGUMENTS mode = near, far, move, slab, or atoms distance is a floating point value selection = atom selection (for mode=atoms only) EXAMPLES clip near, -5 # moves near plane away from you by 5 A clip far, 10 # moves far plane towards you by 10 A clip move, -5 # moves the slab away from you by 5 A clip slab, 20 # sets slab thickness to 20 A clip slab, 10, resi 11 # clip 10 A slab about residue 11 clip atoms, 5, pept # clip atoms in "pept" with a 5 A buffer # about their current camera positions PYMOL API cmd.clip(string mode, float distance, string selection, int state) SEE ALSO zoom, orient, reset ''' mode = clip_action_sc.auto_err(str(mode),'mode') if selection is not None: selection = selector.process(selection) else: selection = '' with _self.lockcm: r = _cmd.clip(_self._COb,str(mode),float(distance), str(selection),int(state)-1) return r def get_clip(quiet: int = 1, _self=cmd): ''' DESCRIPTION "get_clip" returns the positions of the clipping planes. USAGE get_clip ARGUMENTS EXAMPLES PYMOL API cmd.get_clip() SEE ALSO clip ''' with _self.lockcm: r = _cmd.get_clip(_self._COb) if not quiet: print(r) return r def origin(selection="(all)", object=None, position=None, state=0, *, _self=cmd): ''' DESCRIPTION "origin" sets the center of rotation about a selection. If an object name is specified, it can be used to set the center of rotation for the object (for use in animation and editing). USAGE origin [ selection [, object [,position, [, state ]]]] ARGUMENTS selection = string: selection-expression or name-list {default: (all)} state = 0 (default) use all coordinate states state = -1 use only coordinates for the current state state > 0 use coordinates for a specific state EXAMPLES origin chain A origin position=[1.0,2.0,3.0] PYMOL API cmd.origin(string object-or-selection) SEE ALSO zoom, orient, reset ''' #' # preprocess selection selection = selector.process(selection) # with _self.lockcm: if object is None: object='' if position is None: position=(0.0,0.0,0.0) else: if _self.is_string(position): position = safe_list_eval(position) selection = '' r = _cmd.origin(_self._COb,selection,str(object), (float(position[0]), float(position[1]), float(position[2]) ),int(state)-1) return r def orient(selection="(all)", state=0, animate=0, *, _self=cmd): ''' DESCRIPTION "orient" aligns the principal components of the atoms in the selection with the XYZ axes. USAGE orient [ selection [, state [, animate ]]] ARGUMENTS selection = a selection-expression or name-pattern {default: (all)} state = 0: use all coordinate states {default} state = -1: uses only coordinates for the current state state > 0: uses coordinates for a specific state EXAMPLES orient organic NOTES The function is similar to the orient command in X-PLOR. PYMOL API cmd.orient(string object-or-selection, int state, float animate) SEE ALSO zoom, origin, reset ''' # preprocess selection selection = selector.process(selection) with _self.lockcm: return _cmd.orient(_self._COb,"("+selection+")",int(state)-1,float(animate)) def move(axis, distance, *, _self=cmd): ''' DESCRIPTION "move" translates the camera about one of the three primary axes. USAGE move axis, distance EXAMPLES move x, 3 move y, -1 PYMOL API cmd.move(string axis, float distance) SEE ALSO turn, rotate, translate, zoom, center, clip ''' with _self.lockcm: return _cmd.move(_self._COb,str(axis),float(distance)) def enable(name='all', parents=0, *, _self=cmd): ''' DESCRIPTION "enable" turns on display of one or more objects and/or selections. USAGE enable name ARGUMENTS name = name-pattern or selection. NOTES If name matches a selection name, then selection indicator dots are shown for atoms in that selection. If name is a selection-expression, then all objects with atoms in that selection are enabled. For an object\'s content to be displayed in the 3D viewer, the object must be enabled AND at least one of the available representations must be shown. PYMOL API cmd.enable(string object-name) EXAMPLES enable target_protein # enables the target_protein object enable 1dn2.* # enables all entities starting with 1dn2. enable *lig # enables all entities ending with lig SEE ALSO show, hide, disable ''' if name[0]=='(': selection = selector.process(name) with _self.lockcm: r = _cmd.onoff_by_sele(_self._COb,selection,1) else: with _self.lockcm: r = _cmd.onoff(_self._COb,str(name),1,int(parents)); return r def disable(name='all', *, _self=cmd): ''' DESCRIPTION "disable" turns off display of one or more objects and/or selections. USAGE disable name ARGUMENTS name = name-pattern or selection. PYMOL API cmd.disable(string name) SEE ALSO show, hide, enable ''' if name[0]=='(': selection = selector.process(name) with _self.lockcm: r = _cmd.onoff_by_sele(_self._COb,selection,0) else: with _self.lockcm: r = _cmd.onoff(_self._COb,str(name),0,0); return r def _rep_to_repmask(rep): repn = 0 for rep in rep.split(): rep = repmasks_sc.auto_err(rep, 'representation') repn |= repmasks[rep] return repn def toggle(representation="lines", selection="all", *, _self=cmd): ''' DESCRIPTION "toggle" toggles the visibility of a representation within a selection. USAGE toggle [ representation [, selection ]] ARGUMENTS representation = string: named representation {default: lines} selection = string: atom selection {default: all} NOTES If the representation is enabled for any atom in the selection, it will be turned off. PYMOL API cmd.toggle(string representation, string selection) SEE ALSO show, hide ''' with _self.lockcm: if representation == 'object': repn = -2 else: repn = _rep_to_repmask(representation) # preprocess selection selection = selector.process(selection) r = _cmd.toggle(_self._COb,str(selection),int(repn)); return r def _showhide(rep, selection, value, _self): if not selection and (rep in ("", "all") or '(' in rep or '/' in rep): # rep looks like a selection selection = rep rep = "wire" if value else "everything" selection = selector.process(selection) or "all" repn = _rep_to_repmask(rep) with _self.lockcm: r = _cmd.showhide(_self._COb, str(selection), int(repn), value) return r def show(representation="wire", selection="", *, _self=cmd): ''' DESCRIPTION "show" turns on representations for objects and selections. USAGE show [ representation [, selection ]] ARGUMENTS representation = lines, spheres, mesh, ribbon, cartoon, sticks, dots, surface, labels, extent, nonbonded, nb_spheres, slice, extent, slice, dashes, angles, dihedrals, cgo, cell, callback, or everything selection = string: a selection-expression or name-pattern NOTES With no arguments, "show" alone turns on lines for all bonds and nonbonded for all atoms in all molecular objects. EXAMPLES show show ribbon show lines, (name CA+C+N) SEE ALSO hide, enable, disable ''' return _showhide(representation, selection, 1, _self) def show_as(representation="wire", selection="", *, _self=cmd): ''' DESCRIPTION "as" turns on and off atom and bond representations. USAGE as representation [, selection ] ARGUMENTS representation = lines, spheres, mesh, ribbon, cartoon, sticks, dots, surface, labels, extent, nonbonded, nb_spheres, slice, extent, slice, dashes, angles, dihedrals, cgo, cell, callback, volume or everything selection = string {default: all} EXAMPLES as lines, name CA+C+N as ribbon PYMOL API cmd.show_as(string representation, string selection) NOTES "selection" can be an object name "as" alone will turn on lines and nonbonded and hide everything else. SEE ALSO show, hide, enable, disable ''' return _showhide(representation, selection, 2, _self) def hide(representation="everything", selection="", *, _self=cmd): ''' DESCRIPTION "hide" turns off atom and bond representations. USAGE hide [ representation [, selection ]] ARGUMENTS representation = lines, spheres, mesh, ribbon, cartoon, sticks, dots, surface, labels, extent, nonbonded, nb_spheres, slice, extent, slice, dashes, angles, dihedrals, cgo, cell, callback, or everything selection = string: a selection-expression or name-pattern EXAMPLES hide lines, all hide ribbon PYMOL API cmd.hide(string representation, string selection) SEE ALSO show, enable, disable ''' return _showhide(representation, selection, 0, _self) def get_view(output=1, quiet=1, *, _self=cmd): ''' DESCRIPTION "get_view" returns and optionally prints out the current view information in a format which can be embedded into a command script and can be used in subsequent calls to "set_view". If a log file is currently open, get_view will not write the view matrix to the screen unless the "output" parameter is 2. USAGE get_view [output] ARGUMENTS output = 0: output matrix to screen output = 1: do not Output matrix to screen output = 2: force output to screen even if log file is open output = 3: return formatted string instead of a list NOTES Contents of the view matrix: * 0 - 8: column-major 3x3 matrix which rotates model space to camera space * 9 - 11: origin of rotation relative to camera (in camera space) * 12 - 14: origin of rotation (in model space) * 15: front plane distance from the camera * 16: rear plane distance from the camera * 17: orthoscopic flag (+/-) and field of view (if abs(value) > 1) The camera always looks down -Z with its +X left and its +Y down. Therefore, in the default view, model +X is to the observer\'s right, +Y is upward, and +Z points toward the observer. PYMOL API cmd.get_view(output=1, quiet=1) SEE ALSO set_view ''' with _self.lockcm: r = _cmd.get_view(_self._COb) if True: output = int(output) if True: if (_self.get_setting_int("logging") != 0) and (output<3): if not quiet: print(" get_view: matrix written to log file.") _self.log("_ set_view (\\\n","cmd.set_view((\\\n") _self.log("_ %14.9f, %14.9f, %14.9f,\\\n"%r[0:3] , " %14.9f, %14.9f, %14.9f,\\\n"%r[0:3]) _self.log("_ %14.9f, %14.9f, %14.9f,\\\n"%r[4:7] , " %14.9f, %14.9f, %14.9f,\\\n"%r[4:7]) _self.log("_ %14.9f, %14.9f, %14.9f,\\\n"%r[8:11] , " %14.9f, %14.9f, %14.9f,\\\n"%r[8:11]) _self.log("_ %14.9f, %14.9f, %14.9f,\\\n"%r[16:19], " %14.9f, %14.9f, %14.9f,\\\n"%r[16:19]) _self.log("_ %14.9f, %14.9f, %14.9f,\\\n"%r[19:22], " %14.9f, %14.9f, %14.9f,\\\n"%r[19:22]) _self.log("_ %14.9f, %14.9f, %14.9f )\n"%r[22:25] , " %14.9f, %14.9f, %14.9f ))\n"%r[22:25]) if output<2: # suppress if we have a log file open output=0 if output and (not quiet) and (output<3): print("### cut below here and paste into script ###") print("set_view (\\") print(" %14.9f, %14.9f, %14.9f,\\"%r[0:3]) print(" %14.9f, %14.9f, %14.9f,\\"%r[4:7]) print(" %14.9f, %14.9f, %14.9f,\\"%r[8:11]) print(" %14.9f, %14.9f, %14.9f,\\"%r[16:19]) print(" %14.9f, %14.9f, %14.9f,\\"%r[19:22]) print(" %14.9f, %14.9f, %14.9f )"%r[22:25]) print("### cut above here and paste into script ###") if output==3: return ("set_view (\\\n"+ " %14.9f, %14.9f, %14.9f,\\\n"%r[0:3] + " %14.9f, %14.9f, %14.9f,\\\n"%r[4:7] + " %14.9f, %14.9f, %14.9f,\\\n"%r[8:11] + " %14.9f, %14.9f, %14.9f,\\\n"%r[16:19] + " %14.9f, %14.9f, %14.9f,\\\n"%r[19:22] + " %14.9f, %14.9f, %14.9f )\n"%r[22:25]) r = r[0:3]+r[4:7]+r[8:11]+r[16:25] return r def set_view(view,animate=0,quiet=1,hand=1, *, _self=cmd): r''' DESCRIPTION "set_view" sets viewing information for the current scene, including the rotation matrix, position, origin of rotation, clipping planes, and the orthoscopic flag. USAGE set_view [ view ] EXAMPLE set_view (\ 0.999876618, -0.000452542, -0.015699286,\ 0.000446742, 0.999999821, -0.000372844,\ 0.015699454, 0.000365782, 0.999876678,\ 0.000000000, 0.000000000, -150.258514404,\ 11.842411041, 20.648729324, 8.775371552,\ 118.464958191, 182.052062988, 0.000000000 ) PYMOL API cmd.set_view(string-or-sequence view) SEE ALSO get_view ''' if isinstance(view, (str, bytes)): view = safe_list_eval(view) if len(view)!=18: raise pymol.CmdException( "bad view argument; should be a sequence of 18 floats") with _self.lockcm: r = _cmd.set_view(_self._COb,( float(view[ 0]),float(view[ 1]),float(view[ 2]),0.0, float(view[ 3]),float(view[ 4]),float(view[ 5]),0.0, float(view[ 6]),float(view[ 7]),float(view[ 8]),0.0, 0.0,0.0,0.0,1.0, float(view[ 9]),float(view[10]),float(view[11]), float(view[12]),float(view[13]),float(view[14]), float(view[15]),float(view[16]),float(view[17])), int(quiet),float(animate),int(hand)) return r def view(key, action='recall', animate=-1, *, _self=cmd): ''' DESCRIPTION "view" saves and restore camera views. USAGE view key [, action [, animate]] ARGUMENTS key = string or * action = store, recall, clear: {default: recall} NOTES Views F1 through F12 are automatically bound to function keys provided that "set_key" has not been used to redefine the behaviour of the respective key, and that a "scene" has not been defined for that key. EXAMPLES view 0, store view 0 PYMOL API cmd.view(string key, string action) SEE ALSO scene, set_view, get_view ''' pymol=_self._pymol if key=='*': action = view_sc.auto_err(action,'action') if action=='clear': pymol._view_dict = {} pymol._view_dict_sc = Shortcut(pymol._view_dict.keys()) else: print(" view: stored views:") lst = list(pymol._view_dict.keys()) lst.sort() parsing.dump_str_list(lst) else: action = view_sc.auto_err(action,'action') if action=='recall': key = pymol._view_dict_sc.auto_err(key,'view') _self.set_view(pymol._view_dict[key],animate=animate) if _feedback(fb_module.scene,fb_mask.actions,_self): # redundant print(" view: \"%s\" recalled."%key) elif (action=='store') or (action=='update'): pymol._view_dict_sc.append(key) pymol._view_dict[key]=_self.get_view(0) if _feedback(fb_module.scene,fb_mask.actions,_self): print(" view: view "+action+"d as \"%s\"."%key) elif action=='clear': key = pymol._view_dict_sc.auto_err(key,'view') if key in pymol._view_dict: del pymol._view_dict[key] pymol._view_dict_sc = Shortcut(pymol._view_dict.keys()) if _feedback(fb_module.scene,fb_mask.actions,_self): # redundant print(" view: '%s' deleted."%key) def get_viewport(output=1, quiet=1, *, _self=cmd): ''' DESCRIPTION "get_viewport" returns and optionally prints out the screen viewport size USAGE get_viewport [output] ARGUMENTS output = 0: do not print to screen output = 1 {default}: print to screen if not logging and not quiet output = 2: force output to screen even if log file is open PYMOL API cmd.get_viewport(output=1, quiet=1) ''' output = int(output) with _self.lockcm: r = _cmd.get_viewport(_self._COb) if _self.get_setting_int("logging") and output < 3: _self.log(f"_ viewport {r[0]}, {r[1]}\n", f"cmd.viewport{r}\n") if not quiet: print(" get_viewport: data written to log file.") if output < 2: # suppress if we have a log file open output = 0 if (0 < output < 3) and not quiet: print("### cut below here and paste into script ###") print("viewport %4d, %4d" % r) print("### cut above here and paste into script ###") if output == 3: colorprinting.warning(" Warning: get_viewport(3) is deprecated") return "viewport ( %4d, %4d )\n" % r return r def get_vis(_self=cmd): with _self.lockcm: return _cmd.get_vis(_self._COb) def set_vis(dict, *, _self=cmd): with _self.lockcm: return _cmd.set_vis(_self._COb, dict) def get_colorection(key, *, _self=cmd): with _self.lockcm: return _cmd.get_colorection(_self._COb, key) def set_colorection(dict,key, *, _self=cmd): with _self.lockcm: return _cmd.set_colorection(_self._COb, dict, key) def del_colorection(dict,key, *, _self=cmd): with _self.lockcm: return _cmd.del_colorection(_self._COb, dict, key) def get_scene_list(_self=cmd): with _self.lockcm: return _cmd.get_scene_order(_self._COb) def get_scene_thumbnail(name, _self=cmd): with _self.lockcm: return _cmd.get_scene_thumbnail(_self._COb, name) def get_scene_message(name, _self=cmd): with _self.lockcm: return _cmd.get_scene_message(_self._COb, name) def set_scene_message(name, message, _self=cmd): with _self.lockcm: return _cmd.set_scene_message(_self._COb, name, message) def chain_session(_self=cmd): import os # assumes locked interpreter r = 0 session_file = str(_self.get("session_file")) re_pat = re.compile(r"[0-9]+\.") if len(session_file): # find next session file, if it exists mo = re_pat.search(session_file) if mo is not None: pat = mo.group(0) if len(pat): file_no = int(float(pat)) + 1 new_form = r"%0"+str(len(pat)-1)+"d." for new_num in range(file_no, file_no+11): new_pat = new_form % new_num new_file = re_pat.sub(new_pat, session_file) # try both PSE and PSW if not os.path.exists(new_file): new_file = re.sub(r"\.pse$",".psw",new_file,re.I) if not os.path.exists(new_file): new_file = re.sub(r"\.psw$",".pse",new_file,re.I) if os.path.exists(new_file): _self.do("_ cmd.load(r'''"+new_file+"''',format='psw')") return 1 return 0 def scene_order(names,sort=0,location='current',quiet=1, *, _self=cmd): ''' DESCRIPTION "scene_order" changes the ordering of scenes. USAGE scene_order names, sort, location ARGUMENTS names = string: a space-separated list of names sort = yes or no {default: no} location = top, current, or bottom {default: current} EXAMPLES scene_order *,yes scene_order F6 F4 F3 scene_order 003 006 004, location=top # if names have spaces cmd.scene_order(["name 1", "name 2"]) PYMOL API cmd.scene_order(names: Union[list, str], sort: str, location: str) SEE ALSO scene ''' location = location_sc.auto_err(location,'location') if is_string(sort): sort=boolean_dict[boolean_sc.auto_err(sort,'sort option')] if isinstance(names, str): names = names.split() with _self.lockcm: return _cmd.scene_order(_self._COb, names, sort, location) def _scene_get_current_message(_self=cmd): wiz = _self.get_wizard() return '\n'.join(wiz.message) if (wiz is not None and wiz.__class__.__name__ == 'Message' and hasattr(wiz, 'from_scene')) else None def scene_recall_message(message, *, _self=cmd): ''' INTERNAL, DO NOT USE. Display a scene message. ''' wiz = _self.get_wizard() replace_flag = (wiz is not None and wiz.__class__.__name__ == 'Message' and hasattr(wiz, 'from_scene')) if message: if is_string(message): message = message.splitlines() elif not is_list(message): raise TypeError("message %s" % (type(message))) wizard_func = _self.replace_wizard if replace_flag else _self.wizard wizard_func("message", *message) _self.get_wizard().from_scene = 1 elif replace_flag: _self.wizard() def scene(key='auto', action='recall', message=None, view=1, color=1, active=1, rep=1, frame=1, animate=-1, new_key=None, hand=1, quiet=1, sele="all", *, _self=cmd): ''' DESCRIPTION "scene" saves and restores scenes. A scene consists of the camera view, all object activity information, all atom-wise visibilities, all atom-wise colors, all representations, the global frame index, and may contain a text message to display on playback. USAGE scene [key [,action [, message, [ new_key=new-key-value ]]]] ARGUMENTS key = string, new, auto, or *: use new for an automatically numbered new scene, use auto for the current scene (if one exists), and use * for all scenes (clear and recall actions only). action = store, recall, insert_after, insert_before, next, previous, update, rename, or clear: (default = recall). If rename, then a new_key argument must be explicitly defined. message = string: a text message to display with the scene. new_key = string: the new name for the scene EXAMPLES scene * scene F1, store scene F2, store, Please note the critical hydrogen bond shown in yellow. scene F1 scene F2 scene F1, rename, new_key=F5 NOTES Scenes F1 through F12 are automatically bound to function keys provided that "set_key" has not been used to redefine the behaviour of the respective key. SEE ALSO view, set_view, get_view ''' action = scene_action_sc.auto_err(action, 'action') if is_list(message): message = '\n'.join(message) # default when called with no arguments if key == 'auto': if action == 'recall': action = 'next' # preserve message on update if action == 'update': if message is None: message = _scene_get_current_message(_self) # aliases (DEPRECATED) if action == 'clear': action = 'delete' elif action == 'append' or action == 'update': action = 'store' # presentation auto quit if (pymol._scene_quit_on_action == action and action in ('next', 'previous') and _self.get_setting_boolean("presentation") and _self.get_setting_boolean("presentation_auto_quit") and _self.get("scene_current_name") == ""): if not chain_session(_self): _self.quit() # call C function def func(): with _self.lockcm: return _cmd.scene(_self._COb, key, action, message, int(view), int(color), int(active), int(rep), int(frame), float(animate), new_key, int(hand), int(quiet), sele) r = _self._call_with_opengl_context(func) # for presentation auto quit pymol._scene_quit_on_action = action return r def _legacy_scene(key='auto', action='recall', message=None, view=1, color=1, active=1, rep=1, frame=1, animate=-1, new_key=None, hand=1, quiet=1, *, _self=cmd): ''' FOR INTERNAL USE ONLY. Stores and deletes <=1.7.4 compatible scenes. ''' pymol=_self._pymol view = int(view) rep = int(rep) color = int(color) active = int(active) frame = int(frame) quiet = int(quiet) animate = 0 with _self.lockcm: if key=='*': if action=='clear': for key in pymol._scene_dict: # free selections scene_list = pymol._scene_dict[key] if len(scene_list)>3: colorection = scene_list[3] if colorection is not None: _self.del_colorection(colorection,key) name = "_scene_"+key+"_*" _self.delete(name) else: raise ValueError('action=' + action) else: if action == 'store': if key in ('new', 'auto'): raise ValueError('key=' + key) if key in pymol._scene_dict: raise RuntimeError('update not supported') if rep: for rep_name in rep_list: name = "_scene_"+key+"_"+rep_name _self.select(name,"rep "+rep_name) if is_string(message): if message: if (message[0:1] in [ '"',"'"] and message[-1:] in [ '"',"'"]): message=message[1:-1] else: message = message.splitlines() pymol._scene_dict[key] = [ _self.get_view(0) if view else None, _self.get_vis() if active else None, _self.get_frame() if frame else None, _self.get_colorection(key) if color else None, 1 if rep else None, message, ] else: raise ValueError('action=' + action) def session_save_views(session, *, _self=cmd): pymol=_self._pymol session['view_dict']=copy.deepcopy(pymol._view_dict) return 1 def session_restore_views(session, *, _self=cmd): pymol=_self._pymol if 'view_dict' in session: pymol._view_dict=copy.deepcopy(session['view_dict']) pymol._view_dict_sc.rebuild(list(pymol._view_dict.keys())) return 1 def session_restore_scenes(session, *, _self=cmd): # Restore scenes from old session files (<= 1.7.4) if 'scene_dict' in session: _self.scene('*', 'clear') # save initial scene tempname = '_initial_scene' while tempname in session['scene_dict']: tempname += '_' _self.scene(tempname, 'store') frame = 0 if _self.get_movie_playing(): _self.mstop() frame = _self.get_frame() for key, data in list(session['scene_dict'].items()): _convert_legacy_scene(key, data, _self) if frame: _self.frame(frame) _self.mplay() # restore initial scene _self.scene(tempname, 'recall', animate=0) _self.scene(tempname, 'clear') if 'scene_order' in session: _self.scene_order(' '.join(session['scene_order'])) return 1 def _convert_legacy_scene(key, scene_list, _self=cmd): # Create a scene from the given legacy scene list and finally delete # the colorection and rep selections. scene_list += [None] * 5 view, active, frame, color, rep = [(0 if x is None else 1) for x in scene_list[:5]] if frame: _self.frame(scene_list[2]) if view: _self.set_view(scene_list[0], 0.0) if active: _self.disable() _self.deselect() _self.set_vis(scene_list[1]) if color: _self.set_colorection(scene_list[3], key) _self.del_colorection(scene_list[3], key) if rep: # only atomic representations _self.hide('everything', '(*)') sele_prefix = _self.get_legal_name('_scene_' + key + '_') for rep_name in rep_list: _self.show(rep_name, "?" + sele_prefix + rep_name) _self.delete(sele_prefix + "*") _self.scene(key, 'store', scene_list[5], view, color, active, rep, frame) def stereo(toggle='on', quiet=1, *, _self=cmd): ''' DESCRIPTION "stereo" activates or deactives stereo mode. USAGE stereo [toggle] ARGUMENTS toggle = on, off, crosseye, walleye, quadbuffer, sidebyside, geowall, or openvr EXAMPLES stereo on stereo off stereo crosseye NOTES "quadbuffer" is the default stereo mode if hardware stereo is available. otherwise, "crosseye" is the default. PYMOL API cmd.stereo(string toggle) ''' toggle = stereo_dict[stereo_sc.auto_err(str(toggle),'toggle')] with _self.lockcm: return _cmd.stereo(_self._COb, toggle) def turn(axis, angle, *, _self=cmd): ''' DESCRIPTION "turn" rotates the camera about one of the three primary axes, centered at the origin. USAGE turn axis, angle EXAMPLES turn x, 90 turn y, 45 PYMOL API cmd.turn(string axis, float angle) SEE ALSO move, rotate, translate, zoom, center, clip ''' with _self.lockcm: r = _cmd.turn(_self._COb,str(axis),float(angle)) return r def full_screen(toggle=-1, *, _self=cmd): ''' DESCRIPTION "full_screen" enables or disables full screen mode. USAGE full_screen [toggle] EXAMPLES full_screen full_screen on full_screen off NOTES This does not work correctly on all platforms. If you encounter trouble, try using the maximize button on the viewer window instead. ''' toggle = toggle_dict[toggle_sc.auto_err(str(toggle),'toggle')] with _self.lockcm: if _self.is_gui_thread(): return _cmd.full_screen(_self._COb,int(toggle)) return _self._do("full_screen %s" % (toggle), echo=0) def rock(mode=-1, *, _self=cmd): ''' DESCRIPTION "rock" toggles Y axis rocking. USAGE rock PYMOL API cmd.rock() ''' with _self.lockcm: r = _cmd.rock(_self._COb,int(mode)) return r def label(selection="(all)", expression="", quiet=1, *, _self=cmd): ''' DESCRIPTION "label" labels one or more atoms in a selection by evaluating an Python expression referencing properties for each atom. USAGE label [ selection [, expression ]] ARGUMENTS selection = string: a selection-expression expression = string: a Python expression that can be converted to a string EXAMPLES label chain A, chain label name CA,"%s-%s" % (resn,resi) label resi 200,"%1.3f" % partial_charge NOTES The symbols defined in the label name space for each atom are: name, resi, resn, resv, chain, segi, model, alt, q, b, type, index, rank, ID, ss, vdw, elec_radius, label, elem, geom, flags, color, cartoon, valence, formal_charge, partial_charge, numeric_type, text_type, stereo All strings in the expression must be explicitly quoted. This operation typically takes several seconds per thousand atoms labelled. To clear labels, simply omit the expression or set it to ''. ''' # preprocess selection selection = selector.process(selection) # with _self.lockcm: return _cmd.label(_self._COb, selection, expression, quiet) def label2(selection="(all)", expression="", quiet=1, *, _self=cmd): # preprocess selection selection = selector.process(selection) # with _self.lockcm: return _cmd.label2(_self._COb, selection, expression, quiet) def window(action='show', x=0, y=0, width=0, height=0, *, _self=cmd): ''' DESCRIPTION "window" controls the visibility of PyMOL\'s output window USAGE window [ action [, x [, y [, width [, height ]]]]] PYMOL API cmd.window(string action, int x, int y, int width, int height) ''' action = window_sc.auto_err(action,'action') action = window_dict[str(action)] with _self.lockcm: from pymol.gui import get_qtwindow as getPyMOLWindow qt_window = getPyMOLWindow() if qt_window: r = DEFAULT_SUCCESS qt_window.window_cmd(action, int(x),int(y),int(width),int(height)) else: r = _cmd.window(_self._COb,action,int(x),int(y),int(width),int(height)) return r def viewport(width=-1,height=-1, *, _self=cmd): ''' DESCRIPTION "viewport" changes the size of the graphics display area. USAGE viewport width, height PYMOL API cmd.viewport(int width, int height) ''' if cmd.is_string(width) and height == -1: width = _self.safe_eval(width) if _self.is_sequence(width): colorprinting.warning(" Warning: Tuple-syntax (parentheses) " "for viewport is deprecated") width, height = width if not cmd.is_gui_thread(): _self.do("viewport %d,%d"%(int(width),int(height)),0) return None with _self.lockcm: return _cmd.viewport(_self._COb, int(width), int(height)) def bg_color(color="black", *, _self=cmd): ''' DESCRIPTION "bg_color" sets the background color. USAGE bg_color [ color ] ARGUMENTS color = string: color name or number {default: black} EXAMPLES bg_color grey30 bg_color NOTES To obtain a transparent background, "unset opaque_background", and then use "ray". SEE ALSO set_color, ray PYMOL API cmd.bg_color(string color) ''' color = _self._interpret_color(_self,color) with _self.lockcm: r = _cmd.bg_color(_self._COb,str(color)) return r cartoon_dict = { 'skip' : -1, 'automatic' : 0, 'loop' : 1, 'rectangle' : 2, 'oval' : 3, 'tube' : 4, 'arrow' : 5, 'dumbbell' : 6, 'putty' : 7, 'dash' : 8, 'cylinder' : 9, } cartoon_sc = Shortcut(cartoon_dict.keys()) def cartoon(type, selection="(all)", *, _self=cmd): ''' DESCRIPTION "cartoon" changes the default cartoon representation for a set of atoms. USAGE cartoon type, selection ARGUMENTS type = automatic, skip, loop, rectangle, oval, tube, arrow, dumbbell PYMOL API cmd.cartoon(string type, string selection) EXAMPLES cartoon rectangle, chain A cartoon skip, resi 145-156 NOTES This command is rarely required since the default "automatic" mode chooses cartoons according to the information in the PDB HELIX and SHEET records. ''' # preprocess selection selection = selector.process(selection) # type = cartoon_dict[cartoon_sc.auto_err(str(type),'type')]; with _self.lockcm: return _cmd.cartoon(_self._COb, selection, int(type)) def _ray(width,height,antialias,angle,shift,renderer,quiet,_self=cmd): r = DEFAULT_ERROR try: _self.lock_without_glut() try: _cmd.set_busy(_self._COb,1) r = _cmd.render(_self._COb,int(width),int(height), int(antialias), float(angle), float(shift),int(renderer), int(quiet)) finally: _cmd.set_busy(_self._COb,0) finally: _self.unlock(r) return r def capture(quiet=1, *, _self=cmd): _self.draw(antialias=-2,quiet=quiet) def draw(width=0, height=0, antialias=-1, quiet=1, *, _self=cmd): ''' DESCRIPTION "draw" creates an OpenGL-based image of the current frame. USAGE draw [width [,height [,antialias ]]] ARGUMENTS width = integer {default: 0 (current)} height = integer {default: 0 (current)} antialias = integer {default: -1 (use antialias setting)} EXAMPLES draw draw 1600 NOTES Default width and height are taken from the current viewpoint. If one is specified but not the other, then the missing value is scaled so as to preserve the current aspect ratio. Because this feature uses the OpenGL rendering context to piece together the image, it does not work when running in the command-line only mode. On certain graphics hardware, "unset opaque_background" followed by "draw" will produce an image with a transparent background. However, better results can usually be obtained using "ray". PYMOL API cmd.draw(int width, int height, int antialias, int quiet) SEE ALSO ray, png, save ''' # stop movies and sculpting if they're on... if _self.get_movie_playing(): _self.mstop() if _self.get_setting_boolean("sculpting"): _self.set("sculpting","off",quiet=1) # def func(): with _self.lockcm: # make sure that there aren't any pending display events # TODO could this be fixed with PYMOL-3328 (SceneUpdate)? _cmd.refresh_now(_self._COb) return _cmd.draw(_self._COb,int(width),int(height), int(antialias),int(quiet)) return _self._call_with_opengl_context(func) def ray(width=0, height=0, antialias=-1, angle=0.0, shift=0.0, renderer=-1, quiet=1, async_=0, _self=cmd, **kwargs): ''' DESCRIPTION "ray" creates a ray-traced image of the current frame. This can take some time (up to several minutes, depending on image complexity). USAGE ray [width [,height [,antialias [,angle [,shift [,renderer [,quiet [,async ]]]]]]]]] ARGUMENTS width = integer {default: 0 (current)} height = integer {default: 0 (current)} antialias = integer {default: -1 (use antialias setting)} angle = float: y-axis rotation for stereo image generation {default: 0.0} shift = float: x-axis translation for stereo image generation {default: 0.0} renderer = -1, 0, 1, or 2: respectively, default, built-in, pov-ray, or dry-run {default: 0} async = 0 or 1: should rendering be done in a background thread? EXAMPLES ray ray 1024,768 ray renderer=2 NOTES Default width and height are taken from the current viewpoint. If one is specified but not the other, then the missing value is scaled so as to preserve the current aspect ratio. angle and shift can be used to generate matched stereo pairs renderer = 1 uses PovRay. This is Unix-only and you must have "povray" in your path. It utilizes two two temporary files: "tmp_pymol.pov" and "tmp_pymol.png". See "help faster" for optimization tips with the builtin renderer. See "help povray" for how to use PovRay instead of PyMOL\'s built-in ray-tracing engine. PYMOL API cmd.ray(int width, int height, int antialias, float angle, float shift, int renderer, int quiet, int async) SEE ALSO draw, png, save ''' async_ = int(kwargs.pop('async', async_)) if kwargs: raise pymol.CmdException('unknown argument: ' + ', '.join(kwargs)) arg_tup = (int(width),int(height), int(antialias),float(angle), float(shift),int(renderer),int(quiet),_self) # stop movies, rocking, and sculpting if they're on... if _self.get_movie_playing(): _self.mstop() if _self.get_setting_boolean("sculpting"): _self.set("sculpting","off",quiet=1) if _self.rock(-2)>0: _self.rock(0) # if not async_: r = _ray(*arg_tup) else: render_thread = threading.Thread(target=_ray, args=arg_tup) render_thread.setDaemon(1) render_thread.start() r = DEFAULT_SUCCESS return r def refresh(_self=cmd): ''' DESCRIPTION "refresh" causes the scene to be redrawn as soon as the operating system allows it to be done. USAGE refresh PYMOL API cmd.refresh() SEE ALSO rebuild ''' if _self.is_gui_thread(): return _self._refresh() with _self.lockcm: return _self._do("_ cmd._refresh()") def reset(object='', *, _self=cmd): ''' DESCRIPTION "reset" restores the rotation matrix to identity, sets the origin to the center of mass (approx.) and zooms the window and clipping planes to cover all objects. Alternatively, it can reset object matrices. USAGE reset [ object ] PYMOL API cmd.reset() ''' with _self.lockcm: return _cmd.reset(_self._COb, str(object)) def dirty(_self=cmd): # OBSOLETE? with _self.lockcm: r = _cmd.dirty(_self._COb) return r def meter_reset(_self=cmd): ''' DESCRIPTION "meter_reset" resets the frames per secound counter. USAGE meter_reset ''' with _self.lockcm: r = _cmd.reset_rate(_self._COb) return r def load_png(filename, movie=1, stereo=-1, quiet=0, *, _self=cmd): ''' DESCRIPTION "load_png" loads and displays a PNG file from disk. USAGE load_png filename NOTES If the displayed image is too big for the window, it will be reduced 2-fold repeatedly until it fits. ''' filename = _self.exp_path(str(filename)) with _self.lockcm: return _cmd.load_png(_self._COb, filename, int(movie), int(stereo), int(quiet)) def rebuild(selection='all',representation='everything', *, _self=cmd): ''' DESCRIPTION "rebuild" forces PyMOL to recreate geometric objects in case any of them have gone out of sync. USAGE rebuild [selection [, representation ]] ARGUMENTS selection = string {default: all} representation = string: {default: everything} PYMOL API cmd.rebuild(string selection, string representation) SEE ALSO refresh ''' selection = selector.process(selection) representation = repres_sc.auto_err(representation,'representation') repn = repres[representation]; with _self.lockcm: return _cmd.rebuild(_self._COb, selection, repn) def recolor(selection='all', representation='everything', *, _self=cmd): ''' DESCRIPTION "recolor" forces reapplication of colors to existing objects. USAGE recolor [selection [, representation ]] ARGUMENTS selection = string {default: all} representation = string {default: everything} NOTES This command often needs to be executed after "set_color" has been used to redefine one or more existing colors. PYMOL API cmd.recolor(string selection = 'all', string representation = 'everything') SEE ALSO color, set_color ''' selection = selector.process(selection) representation = repres_sc.auto_err(representation,'representation') repn = repres[representation]; with _self.lockcm: return _cmd.recolor(_self._COb, selection, repn) def color(color, selection="(all)", quiet=1, flags=0, *, _self=cmd): ''' DESCRIPTION "color" changes the color of objects or atoms. USAGE color color [, selection ] ARGUMENTS color = string: color name or number selection = string: selection-expression or name-pattern corresponding to the atoms or objects to be colored {default: (all)}. NOTES When using color ramps, the ramp can be used as a color. PYMOL API cmd.color(string color, string selection, int quiet) SEE ALSO color_deep, set_color, recolor EXAMPLE color cyan color yellow, chain A ''' # preprocess selection selection = selector.process(selection) color = _self._interpret_color(_self,str(color)) with _self.lockcm: return _cmd.color(_self._COb, str(color), str(selection), int(flags), int(quiet)) def color_deep(color, name='all', quiet=1, *, _self=cmd): ''' DESCRIPTION Unset all object and atom level (not global) color settings and apply given color. ARGUMENTS color = str: color name or number name = str: object name or pattern {default: all} SEE ALSO color, unset_deep ''' from pymol.menu import rep_setting_lists _self.unset_deep([s for L in rep_setting_lists for (r, s) in L if s], name, updates=0, quiet=quiet) _self.color(color, name, quiet=quiet) import colorsys _spectrumany_interpolations = { 'hls': (colorsys.rgb_to_hls, colorsys.hls_to_rgb), 'hsv': (colorsys.rgb_to_hsv, colorsys.hsv_to_rgb), 'rgb': ((lambda *rgb: rgb), (lambda *rgb: rgb)), } def spectrumany(expression, colors, selection='(all)', minimum=None, maximum=None, quiet=1, interpolation='rgb', *, _self=cmd): ''' DESCRIPTION Pure python implementation of the spectrum command. Supports arbitrary color lists instead of palettes and any numerical atom property which works in iterate as expression. Non-numeric values (like resn) will be enumerated. This is not a separate PyMOL command but is used as a fallback in "spectrum". ''' from . import CmdException try: from_rgb, to_rgb = _spectrumany_interpolations[interpolation] except KeyError: raise CmdException('interpolation must be one of {}'.format( list(_spectrumany_interpolations))) if ' ' not in colors: colors = palette_colors_dict.get(colors) or colors.replace('_', ' ') quiet, colors = int(quiet), colors.split() n_colors = len(colors) if n_colors < 2: raise CmdException('please provide at least 2 colors') col_tuples = [_self.get_color_tuple(i) for i in colors] if None in col_tuples: raise CmdException('unknown color') col_tuples = [from_rgb(*c) for c in col_tuples] expression = {'pc': 'partial_charge', 'fc': 'formal_charge', 'resi': 'resv'}.get(expression, expression) if expression == 'count': e_list = list(range(_self.count_atoms(selection))) else: e_list = [] _self.iterate(selection, 'e_list.append(%s)' % (expression), space=locals()) try: v_list = [float(v) for v in e_list if v is not None] except (TypeError, ValueError): if not quiet: print(' Spectrum: Expression is non-numeric, enumerating values') v_list = e_list = list(map(sorted(set(e_list)).index, e_list)) if not v_list: return (0., 0.) if minimum is None: minimum = min(v_list) if maximum is None: maximum = max(v_list) r = minimum, maximum = float(minimum), float(maximum) if not quiet: print(' Spectrum: range (%.5f to %.5f)' % r) val_range = maximum - minimum if not val_range: _self.color(colors[0], selection) return r e_it = iter(e_list) def next_color(): v = next(e_it) if v is None: return False v = min(1.0, max(0.0, (float(v) - minimum) / val_range)) * (n_colors - 1) i = min(int(v), n_colors - 2) p = v - i col = [(col_tuples[i+1][j] * p + col_tuples[i][j] * (1.0 - p)) for j in range(3)] rgb = [int(0xFF * v) for v in to_rgb(*col)] return 0x40000000 + rgb[0] * 0x10000 + rgb[1] * 0x100 + rgb[2] _self.alter(selection, 'color = next_color() or color', space=locals()) _self.recolor(selection) return r def spectrum(expression="count", palette="rainbow", selection="(all)", minimum=None, maximum=None, byres=0, quiet=1, interpolation='rgb', *, _self=cmd): ''' DESCRIPTION "spectrum" colors atoms with a spectrum of colors based on an atomic property. USAGE spectrum [expression [, palette [, selection [, minimum [, maximum [, byres ]]]]]] ARGUMENTS expression = count, b, q, or pc: respectively, atom count, temperature factor, occupancy, or partial charge {default: count} palette = string: palette name or space separated list of colors {default: rainbow} selection = string: atoms to color {default: (all)} minimum = float: {default: None (automatic)} maximum = float: {default: None (automatic)} byres = integer: controls whether coloring is applied per-residue {default: 0} EXAMPLES spectrum b, blue_red, minimum=10, maximum=50 spectrum count, rainbow_rev, chain A, byres=1 NOTES Available palettes include: blue_green blue_magenta blue_red blue_white_green blue_white_magenta blue_white_red blue_white_yellow blue_yellow cbmr cyan_magenta cyan_red cyan_white_magenta cyan_white_red cyan_white_yellow cyan_yellow gcbmry green_blue green_magenta green_red green_white_blue green_white_magenta green_white_red green_white_yellow green_yellow green_yellow_red magenta_blue magenta_cyan magenta_green magenta_white_blue magenta_white_cyan magenta_white_green magenta_white_yellow magenta_yellow rainbow rainbow2 rainbow2_rev rainbow_cycle rainbow_cycle_rev rainbow_rev red_blue red_cyan red_green red_white_blue red_white_cyan red_white_green red_white_yellow red_yellow red_yellow_green rmbc yellow_blue yellow_cyan yellow_cyan_white yellow_green yellow_magenta yellow_red yellow_white_blue yellow_white_green yellow_white_magenta yellow_white_red yrmbcg PYMOL API def spectrum(string expression, string palette, string selection, float minimum, float maximum, int byres, int quiet) ''' palette_hit = palette_sc.shortcut.get(palette) if palette_hit: palette = palette_hit if not expression.replace('_', '').isalpha() or not palette_hit: return spectrumany(expression, palette, selection, minimum, maximum, quiet, interpolation, _self=_self) (prefix,digits,first,last) = palette_dict[str(palette)] if (maximum is None) or (minimum is None): minimum = 0 # signal to auto-adjust levels maximum = -1 # preprocess selection selection = selector.process(selection) # with _self.lockcm: r = _cmd.spectrum(_self._COb,str(selection),str(expression), float(minimum),float(maximum), int(first),int(last),str(prefix), int(digits),int(byres),int(quiet)) return r def set_color(name, rgb, mode=0, quiet=1, *, _self=cmd): ''' DESCRIPTION "set_color" defines a new color using the red, green, and blue (RGB) color components. USAGE set_color name, rgb ARGUMENTS name = string: name for the new or existing color rgb = list of numbers: [red, green, blue] each and all in the range (0.0, 1.0) or (0, 255) EXAMPLES set_color red, [ 1.0, 0.0, 0.0 ] set_color yellow, [ 255, 255, 0 ] NOTES PyMOL automatically infers the range based on the input arguments. It may be necessary to issue "recolor" command in order to force recoloring of existing objects. SEE ALSO recolor PYMOL API cmd.set_color(string name, list-of-numbers rgb, int mode ) ''' if isinstance(rgb, (str, bytes)): rgb = safe_list_eval(rgb) if not isinstance(rgb, (list, tuple)) or len(rgb) != 3: raise pymol.CmdException( "color specification must be a list such as [ 1.0, 0.0, 0.0 ]") rgb = [float(c) for c in rgb] if rgb[0] > 1.0 or rgb[1] > 1.0 or rgb[2] > 1.0: rgb = [c / 0xFF for c in rgb] with _self.lockcm: r = _cmd.colordef(_self._COb, str(name), rgb[0], rgb[1], rgb[2], int(mode), int(quiet)) _self._invalidate_color_sc() return r # Aliases for Mother England. colour = color set_colour = set_color bg_colour = bg_color recolour = recolor def ipython_image(*args, _self=cmd, **kwargs): """Render the scene and return the image as an IPython.display.Image. All arguments are forwarded to cmd.png(). @rtype IPython.display.Image """ import os, tempfile from IPython.display import Image filename = tempfile.mktemp(".png") _self.png(filename, *args, **kwargs) try: return Image(filename) finally: os.unlink(filename)