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PlantAI-dev/tools/pymol-open-source/modules/pymol/creating.py
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potaser f745ee9d7e Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00

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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 .constants import CURRENT_STATE, ALL_STATES
if True:
import pymol
from . import selector
import traceback
cmd = __import__("sys").modules["pymol.cmd"]
import re
import gzip
import os
from .cmd import _cmd, Shortcut, is_list, is_string, \
safe_list_eval, safe_alpha_list_eval, \
DEFAULT_ERROR, DEFAULT_SUCCESS, is_ok, is_error, \
is_tuple
import tempfile
import sys
from chempy import fragments
map_type_dict = {
'vdw' : 0,
'coulomb' : 1,
'gaussian' : 2, # gaussian summation
'coulomb_neutral' : 3,
'coulomb_local' : 4,
'gaussian_max' : 5, # gaussian maximum contributor
}
map_type_sc = Shortcut(map_type_dict.keys())
ramp_spectrum_dict = {
"traditional" : 1,
"sludge" : 2,
"ocean" : 3,
"hot" : 4,
"grayable" : 5,
"rainbow" : 6,
"afmhot" : 7,
"grayscale" : 8,
"object" : [[-1.0,-1.0,-1.0]]
}
ramp_spectrum_sc = Shortcut(ramp_spectrum_dict.keys())
group_action_dict = {
"add" : 1,
"remove" : 2,
"open" : 3,
"close" : 4,
"toggle" : 5,
"auto" : 6,
"ungroup" : 7,
"empty" : 8,
"purge" : 9,
"excise" : 10,
"raise" : 11
}
group_action_sc = Shortcut(group_action_dict.keys())
# must correspond to the driver's constants
reflection_format_dict = {
"cns" : 1,
"mtz" : 2,
"cif" : 3
}
def group(name, members="", action='auto', quiet=1,_self=cmd):
'''
DESCRIPTION
"group" creates or updates a group object: a container for
organizing objects into a hierarchy.
USAGE
group name [, members [, action ]]
ARGUMENTS
name = string: name of the group
members = string: space-separated list of objects to include in
the group
action = add, remove, open, close, toggle, auto, empty,
purge, excise
ACTIONS
add: add members to group
remove: remove members from group (members will be ungrouped)
empty: remove all members from group
purge: remove all members from group and delete them
excise: remove all members from group and delete group
open: expand group display in object menu panel
close: collapse group display in object menu panel
toggle: toggle group display in object menu panel
auto: add or toggle
ungroup: DEPRECATED, use ungroup command
raise: raise a group and it's members to the top level
EXAMPLE
group kinases, 1oky 1pkg 1t46 1uwh 1z5m
group kinases, open
group kinases, close
NOTES
Group objects can typically be used as arguments to commands. In
such cases, the command should be applied to all members of the
group. If the group is used as a selection, then all atoms in all
objects in the group should be included in the selection.
When a group objects is open, objects can be added or removed from
the group by right-clicking and dragging in the control panel.
SEE ALSO
ungroup, order, "group_auto_mode" setting
'''
action = group_action_dict[group_action_sc.auto_err(str(action),'group action')]
if name=='all': name='*'
if action == 6: # auto
if len(members):
action = 1 # add
elif '*' in name or name in _self.get_names():
action = 5 # toggle
else:
action = 1 # add
elif action == 7:
print('action=ungroup is deprecated, use the "ungroup" command')
with _self.lockcm:
return _cmd.group(_self._COb,str(name),str(members),int(action),int(quiet))
def ungroup(members, quiet=1, _self=cmd):
'''
DESCRIPTION
"ungroup" removes an object from a group object, returning it to
the top level.
USAGE
ungroup name
SEE ALSO
group
'''
with _self.lockcm:
return _cmd.group(_self._COb, "", str(members), 7, int(quiet))
def map_generate(name, reflection_file, amplitudes, phases, weights="None",
reso_low=50.0, reso_high=1.0,quiet=1,zoom=1,_self=cmd):
'''
DESCRIPTION
"map_generate" generates a map object from a PDB object or selection and
reflection data.
Experimental use with caution.
USAGE
map_generate name, reflection_file, amplitudes, phases, weights [,
reso_low [, reso_high ]]
ARGUMENTS
name = string: name of the map object to create or modify
reflection_file = string: name of reflection file on disk; if None, then
PyMOL attempts to download the CIF file from the PDB.
Default = None; attempt to download from PDB.
amplitudes = string: fully qualified apmlitudes column name. Properly
qualified names are: project/crysta/column. For example,
KINASE/cryastl1/FWT.
phases = string: fully qualified phases column name. Properly
qualified names are: project/crystal/column. For example,
KINASE/crystal1/DELPHWT.
weights = string: fully qualified phases column name. Properly
qualified names are: project/crystal/column. For example,
KINASE/crystal1/FOM.
reso_low = float : minimum resolution; if set to equal max_reso, then
reso_low and reso_high will be read from the reflection file.
reso_high = float : maximum resolution; if set to equal min_reso then
reso_low and reso_high will be read from the reflection file.
NOTES
This function can be used to synthesize x-ray maps from the reflection data.
Supported reflection file formats are "mtz". Other formats coming soon.
New in PyMOL v1.4 for Mac and Linux.
'''
quiet = int(quiet)
r = DEFAULT_ERROR
try:
_self.lock(_self)
if not os.path.isfile(reflection_file):
print(" MapGenerate-Error: Could not find file '%s'.\n Please check the filename and try again." % reflection_file)
raise pymol.CmdException
# TODO: work for CIF, MTZ, and CNS
from . import headering
mtzFile = headering.MTZHeader(reflection_file)
# FORMAT: crystal/dataset/column
_, datasetName, ampColName = ('//' + amplitudes).rsplit('/', 2)
# if datasetName is empty, take any dataset that has ampColName
for dataset in list(mtzFile.datasets.values()):
if (not datasetName or dataset["name"] == datasetName) and \
ampColName in dataset["cols"]:
break
else:
raise pymol.CmdException("no dataset found")
cellX, cellY, cellZ = dataset['x'], dataset['y'], dataset['z']
cellAlpha, cellBeta, cellGamma = dataset['alpha'], dataset['beta'], dataset['gamma']
if reso_low==reso_high:
reso_low, reso_high = mtzFile.reso_min, mtzFile.reso_max
space_group = mtzFile.space_group
phases = phases.rsplit('/', 1)[-1]
if not phases:
raise pymol.CmdException("phase name missing")
if weights and weights!="None":
weights = weights.rsplit('/', 1)[-1]
if not weights:
raise pymol.CmdException("Improperly formatted weights name")
tempFile = tempfile.NamedTemporaryFile(delete=False)
tempFileName = tempFile.name
tempFile.close()
r = _cmd.map_generate(_self._COb,str(name),str(reflection_file),str(tempFileName),
str(ampColName),str(phases),
str(weights),float(reso_low),float(reso_high),str(space_group),
float(cellX), float(cellY), float(cellZ),
float(cellAlpha), float(cellBeta), float(cellGamma),
int(quiet),int(zoom))
if r is not None:
if not quiet:
print("Loading map '%s'" % (name))
r = _self.load(r, name, format="ccp4", finish=1)
else:
print(' Error: Map generation failed')
os.remove(tempFileName)
except ImportError:
print(" MapGenerate-Error: Cannot import headering module. Cannot read MTZ file or make map.")
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return name
def map_new(name, type='gaussian', grid=None, selection="(all)",
buffer=None, box=None, state=0, quiet=1, zoom=0,
normalize=-1, clamp=[1.0,-1.0], resolution=0.0, _self=cmd):
'''
DESCRIPTION
"map_new" creates a map object using one of the built-in map
generation routines. This command not yet fully supported.
USAGE
map_new name [, type [, grid [, selection [, buffer [, box [, state ]]]]]]
ARGUMENTS
name = string: name of the map object to create or modify
type = vdw, gaussian, gaussian_max, coulomb, coulomb_neutral, coulomb_local
grid = float: grid spacing
selection = string: atoms about which to generate the map
buffer = float: cutoff
state > 0: use the indicated state
state = 0: use all states independently with independent extents
state = -1: use current global state
state = -2: use effective object state(s)
state = -3: use all states in one map
state = -4: use all states independent states by with a unified extent
NOTES
This command can be used to create low-resolution surfaces of
protein structures.
'''
# preprocess selection
r = DEFAULT_ERROR
selection = selector.process(selection)
if box is not None: # box should be [[x1,y1,z1],[x2,y2,z2]]
if _self.is_string(box):
box = safe_list_eval(box)
box = (float(box[0][0]),
float(box[0][1]),
float(box[0][2]),
float(box[1][0]),
float(box[1][1]),
float(box[1][2]))
box_flag = 1
else:
box = (0.0,0.0,0.0,1.0,1.0,1.0)
box_flag = 0
if grid is None:
grid = _self.get_setting_float('gaussian_resolution')/3.0
if buffer is None:
buffer = -1.0
grid = float(grid) # for now, uniform xyz; later (x,y,z)
if not is_list(clamp):
clamp = safe_list_eval(str(clamp))
if len(clamp)<2:
clamp = [1.0,-1.0]
type = map_type_dict[map_type_sc.auto_err(str(type),'map type')]
try:
_self.lock(_self)
r = _cmd.map_new(_self._COb,str(name),int(type),grid,str(selection),
float(buffer),box,int(state)-1,
int(box_flag),int(quiet),int(zoom),int(normalize),
float(clamp[0]),float(clamp[1]),float(resolution))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def ramp_new(name, map_name, range=[-1.0,0.0,1.0],
color=['red',[1.0,1.0,1.0],'blue'], state=1,
selection='', beyond=2.0, within=6.0, sigma=2.0,
zero=1, quiet=1, _self=cmd):
'''
DESCRIPTION
"ramp_new" creates a color ramp based on a map potential value or
based on proximity to a molecular object.
USAGE
ramp_new name, map_name [, range [, color [, state [, selection [,
beyond [, within [, sigma [, zero ]]]]]]]]
ARGUMENTS
name = string: name of the ramp object
map_name = string: name of the map (for potential) or molecular
object (for proximity)
range = list: values corresponding to slots in the ramp
color = list: colors corresponding to slots in the ramp
state = integer: state identifier
selection = selection: for automatic ranging
beyond = number: with automatic ranging, are we excluding
values beyond a certain distance from the selection?
within = number: with automatic ranging, are we only including
valuess within a certain distance from the selection?
sigma = number: with automatic ranging, how many standard
deviations from the mean do we go?
zero = integer: with automatic ranging, do we force the central
value to be zero?
EXAMPLES
ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
NOTES
Color ramps are extremely powerful but complicated to use.
In the simplest case, they can be used to color representations
based on the potential values found in a map object at the
corresponding positions in space.
In another simple case, representations can be colored based on
proximity to a target. Note that since ramp targets must
themselves be real objects (not merely selections), the "create"
command may be needed in order to generate an appropriate target.
In more complicated cases, they can be used to color
representations on one object based atoms found in another.
Ramps can operate recursively. In other words, the output color
from one ramp can be used as the input color for another. For
example, you could color by map potential within a certain
distance of the target object, beyond which, a uniform color is applied.
PYMOL API
def ramp_new(string name, string map_name, list range, list color,
int state, string selection, float beyond, float
within, float sigma, int zero, int quiet)
SEE ALSO
ramp_update, load, color, create, slice, gradient
'''
r = DEFAULT_ERROR
safe_color = str(color).strip()
if(safe_color[0:1]=="["): # looks like a list
color = safe_alpha_list_eval(str(safe_color))
else: # looks like a literal
color = str(color)
new_color = []
# preprocess selection
if selection!='':
selection = selector.process(selection)
# coerce range
try:
if isinstance(range, str):
range = safe_list_eval(range)
range = list(map(float, range))
except:
raise pymol.CmdException('invalid range')
if is_list(color):
for a in color:
if not is_list(a):
new_color.append(list(_self.get_color_tuple(a,4))) # incl negative RGB special colors
else:
new_color.append(a)
elif is_string(color):
new_color = ramp_spectrum_dict[ramp_spectrum_sc.auto_err(str(color),'ramp color spectrum')]
else:
new_color=int(color)
try:
_self.lock(_self)
r = _cmd.ramp_new(_self._COb,str(name),str(map_name),range,new_color,
int(state)-1,str(selection),float(beyond),float(within),
float(sigma),int(zero),int(quiet))
_self._invalidate_color_sc(_self)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def ramp_update(name, range=[], color=[], quiet=1, _self=cmd):
'''
DESCRIPTION
"ramp_update" updates range and/or color of a color ramp.
USAGE
ramp_update name [, range [, color ]]
EXAMPLES
ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
ramp_update e_pot_color, range=[-15,0,15]
ramp_update e_pot_color, color=[green,white,orange]
SEE ALSO
ramp_new
'''
return _self.ramp_new(name, '', range, color, quiet=quiet)
def isomesh(name, map, level=1.0, selection='', buffer=0.0,
state=1, carve=None, source_state=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"isomesh" creates a mesh isosurface object from a map object.
USAGE
isomesh name, map, level [, selection [, buffer [, state [, carve ]]]]
ARGUMENTS
name = the name for the new mesh isosurface object.
map = the name of the map object to use for computing the mesh.
level = the contour level.
selection = an atom selection about which to display the mesh with
an additional "buffer" (if provided).
state = the state into which the object should be loaded (default=1)
(set state=0 to append new mesh as a new state)
carve = a radius about each atom in the selection for which to
include density. If "carve" is not provided, then the whole
brick is displayed.
NOTES
If the mesh object already exists, then the new mesh will be
appended onto the object as a new state (unless you indicate a state).
state > 0: specific state
state = 0: all states
state = -1: current state
source_state > 0: specific state
source_state = 0: include all states starting with 0
source_state = -1: current state
source_state = -2: last state in map
SEE ALSO
isodot, load
'''
# preprocess selection
selection = selector.process(selection)
if selection and selection not in ('center', 'origin'):
# force molecular selection, otherwise "all" or name patterns can
# expand to non-molecular objects (like the map itself).
selection = "(" + selection + ")"
#
if carve is None:
carve=0.0
with _self.lockcm:
return _cmd.isomesh(_self._COb,str(name),str(map),
selection,float(buffer),
float(level),0,int(state)-1,float(carve),
int(source_state)-1,int(quiet),
float(level))
def volume(name, map, ramp='', selection='', buffer=0.0,
state=1, carve=None, source_state=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"volume" creates a volume object from a map object.
USAGE
volume name, map [, ramp [, selection [, buffer [, state [, carve ]]]]]
ARGUMENTS
name = the name for the new volume object.
map = the name of the map object to use for computing the volume.
ramp = str: named color ramp {default: }
selection = an atom selection about which to display the mesh with
an additional "buffer" (if provided).
state = specifies which state to create.
carve = a radius about each atom in the selection for which to
include density. If "carve" is not provided, then the whole
brick is displayed.
NOTES
If the volume object already exists, then the new volume will
overwrite the existing object.
EXAMPLE
fetch 1oky, async=0
fetch 1oky, type=2fofc, async=0
volume 1okyVol, 1oky_2fofc
SEE ALSO
map_new, isosurface, isomesh, volume_color, volume_ramp_new
'''
r = DEFAULT_ERROR
# preprocess selection
selection = selector.process(selection)
if carve is None:
carve=0.0
try:
# legacy
level = float(ramp)
ramp = ''
except (ValueError, TypeError):
level = 0.0
with _self.lockcm:
r = _cmd.volume(_self._COb,str(name),str(map),
selection,float(buffer),
float(level),int(state)-1,float(carve),
int(source_state)-1,int(quiet))
if ramp:
_self.volume_color(name, ramp, state)
return r
def set_raw_alignment(name, raw, guide='', state=1, quiet=1, _self=cmd):
'''
DESCRIPTION
API only. Create an alignment object from lists of indices.
ARGUMENTS
name = str: alignment object name
raw = list: list (columns) of lists with (model, index) tuples
guide = str: name of guide object
state = int: object state
EXAMPLE
cmd.align('1t46', '1oky', object='aln')
raw = cmd.get_raw_alignment('aln')
cmd.delete('aln')
cmd.set_raw_alignment('alnnew', raw)
SEE ALSO
cmd.get_raw_alignment
'''
with _self.lockcm:
return _cmd.set_raw_alignment(name, raw, guide,
int(state) - 1, int(quiet), _self._COb)
def slice_new(name, map, state=1, source_state=0, _self=cmd):
'''
DESCRIPTION
"slice_map" creates a slice object from a map object.
USAGE
slice_map name, map, [opacity, [resolution, [state, [source_state]]]]
ARGUMENTS
name = the name for the new slice object.
map = the name of the map object to use for computing the slice.
opacity = opacity of the new slice (default=1)
resolution = the number of pixels per sampling (default=5)
state = the state into which the object should be loaded (default=1)
(set state=0 to append new mesh as a new state)
source_state = the state of the map from which the object should be loaded (default=0)
SEE ALSO
isomesh, isodot, load
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.slice_new(_self._COb,str(name),str(map),int(state)-1,int(source_state)-1)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def isosurface(name, map, level=1.0, selection='', buffer=0.0, state=1,
carve=None, source_state=0, side=1, mode=3, quiet=1,
_self=cmd):
'''
DESCRIPTION
"isosurface" creates a new surface object from a map object.
USAGE
isosurface name, map, [, level [, selection [, buffer [, state [, carve [, source_state [, side [, mode ]]]]]]]]
ARGUMENTS
name = the name for the new mesh isosurface object.
map = the name of the map object to use for computing the mesh.
level = the contour level. (default=1.0)
selection = an atom selection about which to display the mesh with
an additional "buffer" (if provided). (default='')
buffer = buffer around selection to display mesh (default=0.0)
state = the state into which the object should be loaded (default=1)
(set state=0 to append new surface as a new state)
carve = a radius about each atom in the selection for which to
include density. If "carve= not provided, then the whole
brick is displayed. (default=None)
source_state = the state of the map from which the object should be loaded. (default=0)
side = Front or back face. Triangle-winding/normal direction. (default=1)
mode = surface geometry (0: dots; 1: lines; 2: triangle triangle-normals;
3: triangle gradient-normals) (default=3)
NOTES
If the surface object already exists, then the new surface will be
appended onto the object as a new state (unless you indicate a state).
SEE ALSO
isodot, isomesh, load
'''
# preprocess selection
selection = selector.process(selection)
#
if carve is None:
carve=0.0
with _self.lockcm:
return _cmd.isosurface(_self._COb,str(name),str(map),
selection,float(buffer),
float(level),int(mode),int(state)-1,float(carve),
int(source_state)-1,int(side),int(quiet))
def isodot(name,map,level=1.0,selection='',buffer=0.0,state=0,
carve=None,source_state=0,quiet=1,_self=cmd):
'''
DESCRIPTION
"isodot" creates a dot isosurface object from a map object.
USAGE
isodot name, map [, level [, selection [, buffer [, state
[, carve [, source_state [, quiet ]]]]]]]
ARGUMENTS
map = the name of the map object to use.
level = the contour level.
selection = an atom selection about which to display the mesh with
an additional "buffer" (if provided).
NOTES
If the dot isosurface object already exists, then the new dots will
be appended onto the object as a new state.
SEE ALSO
load, isomesh
'''
# preprocess selections
selection = selector.process(selection)
#
if carve is None:
carve=0.0
with _self.lockcm:
return _cmd.isomesh(_self._COb,str(name),str(map),
selection,float(buffer),
float(level),1,int(state)-1,
float(carve),int(source_state)-1,int(quiet),
float(level))
def isolevel(name,level=1.0,state=0,query=0,quiet=1,_self=cmd):
'''
DESCRIPTION
"isolevel" changes the contour level of a isodot, isosurface, or isomesh object.
USAGE
isolevel name, level, state
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.isolevel(_self._COb,str(name),float(level),int(state)-1,int(query),int(quiet))
finally:
_self.unlock(r,_self)
if not int(query):
if _self._raising(r,_self): raise pymol.CmdException
return r
def gradient(name, map, minimum=1.0, maximum=-1.0,
selection='', buffer=0.0, state=0,
carve=None, source_state=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"gradient" creates a gradient object from a map object.
USAGE
gradient name, map [, minimum [, maximum [, selection [, buffer [, state
[, carve [, source_state [, quiet ]]]]]]]]
ARGUMENTS
map = the name of the map object to use.
minimum, maximum = minimum and maximum levels (default: full map range)
selection = an atom selection about which to display the mesh with
an additional "buffer" (if provided).
SEE ALSO
load, isomesh
'''
# preprocess selections
selection = selector.process(selection)
#
if carve is None:
carve=0.0
with _self.lockcm:
return _cmd.isomesh(_self._COb,str(name),str(map),
selection,float(buffer),
float(minimum),3,int(state)-1,
float(carve),int(source_state)-1,int(quiet),
float(maximum))
def copy(target,source,zoom=-1,_self=cmd):
'''
DESCRIPTION
"copy" creates a new object that is an identical copy of an
existing object.
USAGE
copy target, source [, zoom ]
NOTES
Currently, this command only works for molecular objects.
SEE ALSO
create
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.copy(_self._COb,str(source),str(target),int(zoom))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def symexp(prefix, object, selection, cutoff, segi=0, quiet=1,_self=cmd):
'''
DESCRIPTION
"symexp" creates all symmetry-related objects for the specified
object that occur within a cutoff about an atom selection.
USAGE
symexp prefix, object, selection, cutoff
NOTES
The newly objects are labeled using the prefix provided along with
their crystallographic symmetry operation and translation.
SEE ALSO
load
'''
r = DEFAULT_ERROR
# preprocess selection
selection=selector.process(selection)
#
try:
_self.lock(_self)
r = _cmd.symexp(_self._COb,str(prefix),str(object),
"("+str(selection)+")",float(cutoff),
int(segi),int(quiet))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def fragment(name, object=None, origin=1, zoom=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"fragment" retrieves a 3D structure from the fragment library,
which is currently pretty meager (just amino acids).
USAGE
fragment name
'''
r = DEFAULT_ERROR
try:
if object is None:
object=name
model = fragments.get(str(name))
la = len(model.atom)
if la and int(origin):
position = _self.get_position()
for c in range(0,3):
mean_c = sum([a.coord[c] for a in model.atom]) / la
mean_c = position[c] - mean_c
for a in model.atom:
a.coord[c] += mean_c
r = _self.load_model(model,str(object),quiet=quiet,zoom=zoom, _self=_self)
except IOError:
raise pymol.CmdException("unable to load fragment '%s'." % name)
if _self._raising(r,_self): raise pymol.CmdException
return r
def create(name, selection, source_state=0,
target_state=0, discrete=0, zoom=-1, quiet=1,
singletons=0, extract=None, copy_properties=False, _self=cmd):
'''
DESCRIPTION
"create" creates a new molecule object from a selection. It can
also be used to create states in an existing object.
USAGE
create name, selection [,source_state [,target_state ] ]
ARGUMENTS
name = string: name of object to create or modify
selection = string: atoms to include in the new object
source_state = integer: {default: 0 -- copy all states}
target_state = integer: -1 appends after last state {default: 0}
PYMOL API
cmd.create(string name, string selection, int state,
int target_state, int discrete)
NOTES
If the source and target states are zero (default), then all
states will be copied. Otherwise, only the indicated states will
be copied.
SEE ALSO
load, copy, extract
'''
r = DEFAULT_ERROR
target_state = int(target_state)
if target_state == -1:
target_state = _self.count_states('?' + name) + 1
if copy_properties:
print(' Warning: properties are not supported in Open-Source PyMOL')
# preprocess selection
selection = selector.process(selection)
# TODO is this too much convenience? 'extract' should be a simple boolean
if extract in (None, 0, '0', ''):
extract = ''
elif extract in (1, '1'):
extract = selection
else:
print(' Warning: non-boolean extract values are deprecated!')
extract = selector.process(extract)
if extract:
extract_sele = _self.get_unused_name('_extract')
_self.select(extract_sele, extract, 0)
try:
_self.lock(_self)
if not name:
name = _self.get_unused_name("obj")
r = _cmd.create(_self._COb,str(name),"("+str(selection)+")",
int(source_state)-1,int(target_state)-1,
int(discrete),int(zoom),int(quiet),int(singletons), int(copy_properties))
finally:
_self.unlock(r,_self)
if extract:
if not is_error(r):
_self.remove(extract_sele)
_self.delete(extract_sele)
if _self._raising(r,_self): raise pymol.CmdException
return r
def extract(name, selection, *arg, _self=cmd, **kw):
'''
DESCRIPTION
"extract" is simply a shorthand way calling the "create" command
with the extract argument activated, so that atoms in the new
object are removed from the source object.
USAGE
extract name, selection [, source_state [, target_state ]]
SEE ALSO
create
'''
kw['extract'] = 1
return _self.create(name, selection, *arg, **kw)
pseudoatom_mode_dict = {
"unit" : 0, # radius 0.5
"extent" : 1,
"rms" : 2,
# "ellipse" : 2, for anisotropic b-factors?
}
pseudoatom_mode_sc = Shortcut(pseudoatom_mode_dict.keys())
unquote_re = re.compile(r"r?('.*'|\".*\")$")
def unquote(s):
if isinstance(s, bytes):
s = s.decode('utf-8', 'replace')
s = str(s)
if unquote_re.match(s):
s = s.strip('\"')
return s
def pseudoatom(object='', selection='', name='PS1', resn='PSD', resi='1', chain='P',
segi='PSDO', elem='PS', vdw=-1.0, hetatm=1, b=0.0, q=0.0, color='',
label='', pos=None, state=ALL_STATES, mode='rms', quiet=1,_self=cmd):
'''
DESCRIPTION
"pseudoatom" adds a pseudoatom to a molecular object, and will
creating the molecular object if it does not yet exist.
USAGE
pseudoatom object [, selection [, name [, resn [, resi [, chain
[, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label
[, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]
NOTES
"pseudoatom" can be used for a wide variety of random tasks where
on must place an atom or a label in 3D space.
'''
r = DEFAULT_ERROR
# preprocess selection
if len(color):
color = _self.get_color_index(str(color))
else:
color = -1 # default
selection = selector.process(selection)
mode = pseudoatom_mode_dict[pseudoatom_mode_sc.auto_err(str(mode),'pseudoatom mode')]
(name,resn,resi,chain,segi,elem,label) = list(map(unquote,(name,resn,resi,chain,segi,elem,label)))
#
try:
_self.lock(_self)
if pos is not None:
if not (is_list(pos) or is_tuple(pos)):
pos = safe_list_eval(pos)
pos = (float(pos[0]), # tuple-ize
float(pos[1]),
float(pos[2]))
if len(selection.split())>1:
selection = "("+str(selection)+")"
r = _cmd.pseudoatom(_self._COb,str(object), str(selection),
str(name), str(resn), str(resi), str(chain),
str(segi), str(elem), float(vdw), int(hetatm),
float(b), float(q), str(label), pos, int(color),
int(state)-1, int(mode), int(quiet))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def join_states(name, selection='all', mode=2, zoom=0, quiet=1, _self=cmd):
'''
DESCRIPTION
The reverse of split_states. Create a multi-state object from a
selection which spans multiple objects.
ARGUMENTS
name = string: name of object to create or modify
selection = string: atoms to include in the new object
mode = int: how to match states {default: 2}
0: Create discrete object, input objects can be (totally) different
1: Assume identical topology (same number of atoms and matching atom
identifiers) in all input objects
2: Assume matching atom identifiers in all input objects, but also
check for missing atoms and only include atoms that are present
in all input objects
3: match atoms by sequence alignment, slowest but most robust option
EXAMPLE
fragment ala
fragment his
join_states multi, (ala|his), mode=0
'''
mode, quiet = int(mode), int(quiet)
if mode == 3:
aln_name = _self.get_unused_name('_join_states_aln')
sele_name = _self.get_unused_name('_join_states_sele1')
msel_name = _self.get_unused_name('_join_states_sele2')
_self.select(sele_name, selection, 0)
models = _self.get_object_list('?' + sele_name)
for i, model in enumerate(models):
_self.select(msel_name, '?%s & ?%s' % (sele_name, model), 0)
if mode == 2 and i > 0:
_self.remove('?%s & ! ((alt A+) & (?%s in ?%s))' % (name, name, msel_name))
_self.create(name, '?%s in ?%s' % (msel_name, name), 0, -1, 0, 0, quiet)
elif mode == 3 and i > 0:
_self.align(msel_name, name, cycles=0, transform=0, object=aln_name)
_self.select(msel_name, '?%s & ?%s' % (sele_name, aln_name), 0)
_self.remove('?%s and not ?%s' % (name, aln_name))
_self.delete(aln_name)
n = _self.count_states('?' + name)
for j in range(_self.count_states('?' + model)):
_self.create(name, name, 1, -1, 0, 0, quiet)
_self.update(name, '?' + msel_name, n + j + 1, 1, 0, quiet)
else:
_self.create(name, msel_name, 0, -1, mode == 0, 0, quiet)
_self.delete(sele_name)
_self.delete(msel_name)
_self.rebuild('?' + name)
if int(zoom):
_self.zoom(name, state=0)
def curve_new(name="", curve_type="bezier", *, _self=cmd):
"""
DESCRIPTION
"curve_new" creates a new curve object.
ARGUMENTS
name = string: name of object to create
curve_type = string: type of curve (currently only "bezier" supported)
"""
if not name:
name = _self.get_unused_name("Curve")
with _self.lockcm:
_cmd.curve_new(_self._COb, name, curve_type)
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