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pymol-open-source/modules/pymol/viewing.py
ye11owSub fef4a02642 refactoring shortcut.py script (#391)
2025-01-24 23:34:53 -05:00

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#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 pymol.shortcut import Shortcut
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, \
_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)
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