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 ] ] ]
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
'''
r = DEFAULT_ERROR
if selection != '':
region = 1 # about a selection
else:
region = 0 # render the whole map
# preprocess selections
selection = selector.process(selection)
if selection not in ['center', 'origin']:
selection = "(" + selection + ")"
#
if carve == None:
carve = 0.0
try:
_self.lock(_self)
r = _cmd.isomesh(_self._COb, str(name), str(map), int(region),
selection, float(buffer), float(level), 1,
int(state) - 1, float(carve),
int(source_state) - 1, int(quiet), float(level))
finally:
_self.unlock(r, _self)
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 ]]]]]
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
'''
r = DEFAULT_ERROR
if selection != '':
region = 1 # about a selection
else:
region = 0 # render the whole map
# preprocess selections
selection = selector.process(selection)
if selection not in ['center', 'origin']:
selection = "(" + selection + ")"
#
if carve == None:
carve = 0.0
try:
_self.lock(_self)
r = _cmd.isomesh(_self._COb, str(name), str(map), int(region),
selection, float(buffer), float(minimum), 3,
int(state) - 1, float(carve),
int(source_state) - 1, int(quiet), float(maximum))
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
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 ] ] ]
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
'''
r = DEFAULT_ERROR
if selection!='':
region = 1 # about a selection
else:
region = 0 # render the whole map
# preprocess selections
selection = selector.process(selection)
if selection not in [ 'center', 'origin' ]:
selection = "("+selection+")"
#
if carve==None:
carve=0.0
try:
_self.lock(_self)
r = _cmd.isomesh(_self._COb,str(name),str(map),int(region),
selection,float(buffer),
float(level),1,int(state)-1,
float(carve),int(source_state)-1,int(quiet),
float(level))
finally:
_self.unlock(r,_self)
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 ]]]]]
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
'''
r = DEFAULT_ERROR
if selection!='':
region = 1 # about a selection
else:
region = 0 # render the whole map
# preprocess selections
selection = selector.process(selection)
if selection not in [ 'center', 'origin' ]:
selection = "("+selection+")"
#
if carve==None:
carve=0.0
try:
_self.lock(_self)
r = _cmd.isomesh(_self._COb,str(name),str(map),int(region),
selection,float(buffer),
float(minimum),3,int(state)-1,
float(carve),int(source_state)-1,int(quiet),
float(maximum))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
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
'''
r = DEFAULT_ERROR
if selection!='':
region = 1 # about a selection
else:
region = 0 # render the whole map
# preprocess selection
selection = selector.process(selection)
if selection not in [ 'center', 'origin' ]:
selection = "("+selection+")"
#
if carve==None:
carve=0.0
try:
_self.lock(_self)
r = _cmd.isomesh(_self._COb,str(name),str(map),int(region),
selection,float(buffer),
float(level),0,int(state)-1,float(carve),
int(source_state)-1,int(quiet),
float(level))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
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
'''
r = DEFAULT_ERROR
if selection != '':
region = 1 # about a selection
else:
region = 0 # render the whole map
# preprocess selection
selection = selector.process(selection)
if selection not in ['center', 'origin']:
selection = "(" + selection + ")"
#
if carve == None:
carve = 0.0
try:
_self.lock(_self)
r = _cmd.isomesh(_self._COb, str(name), str(map), int(region),
selection, float(buffer), float(level), 0,
int(state) - 1, float(carve),
int(source_state) - 1, int(quiet), float(level))
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r