def indicate(selection="(all)",_self=cmd):
'''
DESCRIPTION
"indicate" shows a visual representation of an atom selection.
USAGE
indicate (selection)
PYMOL API
cmd.count(string selection)
'''
r = DEFAULT_ERROR
# preprocess selection
selection = selector.process(selection)
#
try:
_self.lock(_self)
r = _cmd.select(_self._COb,"indicate","("+str(selection)+")",1,-1,'')
if is_error(r):
_self.delete("indicate")
else:
_self.enable("indicate")
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def x(st):
print st
cmd.set("raise_exceptions",0)
valu = eval(st)
print valu
if cmd.is_error(valu):
cmd.set("raise_exceptions",1)
try:
print eval(st)
except pymol.CmdException:
print "CmdException raised."
except cmd.QuietException:
print "QuietException raised."
def get_session(names='',
partial=0,
quiet=1,
compress=-1,
cache=-1,
_self=cmd):
session = {}
r = DEFAULT_SUCCESS
cache = int(cache)
compress = int(compress)
if cache:
cache_opt = int(_self.get('session_cache_optimize'))
if cache != 0:
cache_mode = int(_self.get('cache_mode'))
if ((cache_mode > 0) and (cache_opt != 0)) or (cache_opt == 1):
_self.cache('optimize')
for a in _self._pymol._session_save_tasks:
if a == None:
try:
_self.lock(_self)
r = _cmd.get_session(_self._COb, session, str(names),
int(partial), int(quiet))
finally:
_self.unlock(r, _self)
try:
session['session'] = copy.deepcopy(_self._pymol.session)
if cache and hasattr(_self._pymol, '_cache'):
session['cache'] = _self._pymol._cache
except:
traceback.print_exc()
else:
try:
if is_error(apply(a, (session, ), {'_self': _self})):
r = DEFAULT_ERROR
except:
traceback.print_exc()
print "Error: An error occurred when trying to generate session."
print "Error: The resulting session file may be incomplete."
if is_ok(r):
if (compress < 0):
compress = _self.get_setting_boolean('session_compression')
if (compress):
import zlib
session = zlib.compress(io.pkl.toString(session))
return session
elif _self._raising(r, _self):
raise QuietException
return r
def get_type(name,quiet=1,_self=cmd):
'''
DESCRIPTION
"get_type" returns a string describing the named object or
selection or the string "nonexistent" if the name in unknown.
PYMOL API
cmd.get_type(string object-name)
NOTES
Possible return values are
"object:molecule"
"object:map"
"object:mesh"
"object:slice"
"object:surface"
"object:measurement"
"object:cgo"
"object:group"
"object:volume"
"selection"
SEE ALSO
get_names
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_type(_self._COb,str(name))
finally:
_self.unlock(r,_self)
if is_error(r):
if not quiet and _feedback(fb_module.cmd,fb_mask.errors,_self):
print "Cmd-Error: unrecognized name."
elif not quiet:
print r
if _raising(r,_self): raise pymol.CmdException
return r
def get_session(names='', partial=0, quiet=1, compress=-1, cache=-1, _self=cmd):
session = {}
r = DEFAULT_SUCCESS
cache = int(cache)
compress = int(compress)
if cache:
cache_opt = int(_self.get('session_cache_optimize'))
if cache != 0:
cache_mode = int(_self.get('cache_mode'))
if ((cache_mode > 0) and (cache_opt != 0)) or (cache_opt==1):
_self.cache('optimize')
for a in _self._pymol._session_save_tasks:
if a==None:
try:
_self.lock(_self)
r = _cmd.get_session(_self._COb,session,str(names),
int(partial),int(quiet))
finally:
_self.unlock(r,_self)
try:
session['session'] = copy.deepcopy(_self._pymol.session)
if cache and hasattr(_self._pymol,'_cache'):
session['cache'] = _self._pymol._cache
except:
traceback.print_exc()
else:
try:
if is_error(apply(a,(session,),{'_self':_self})):
r = DEFAULT_ERROR
except:
traceback.print_exc()
print "Error: An error occurred when trying to generate session."
print "Error: The resulting session file may be incomplete."
if is_ok(r):
if(compress<0):
compress = _self.get_setting_boolean('session_compression')
if(compress):
import zlib
session = zlib.compress(io.pkl.toString(session))
return session
elif _self._raising(r,_self):
raise QuietException
return r
def get_type(name, quiet=1, _self=cmd):
'''
DESCRIPTION
"get_type" returns a string describing the named object or
selection or the string "nonexistent" if the name in unknown.
PYMOL API
cmd.get_type(string object-name)
NOTES
Possible return values are
"object:molecule"
"object:map"
"object:mesh"
"object:slice"
"object:surface"
"object:measurement"
"object:cgo"
"object:group"
"object:volume"
"selection"
SEE ALSO
get_names
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_type(_self._COb, str(name))
finally:
_self.unlock(r, _self)
if is_error(r):
if not quiet and _feedback(fb_module.cmd, fb_mask.errors, _self):
print "Cmd-Error: unrecognized name."
elif not quiet:
print r
if _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)
#
try:
_self.lock(_self)
if name==None:
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))
finally:
_self.unlock(r,_self)
if not is_error(r): # temporary inefficient implementation
if extract not in (None, 0, '0'):
if extract not in (1, '1'):
extract = selector.process(extract)
else:
extract = selection
_self.remove("(("+extract+") in (%s)) and not (%s)"%(name,name))
if _self._raising(r,_self): raise pymol.CmdException
return r
def set_key(key, fn, arg=(), kw={}, _self=cmd):
'''
DESCRIPTION
"set_key" binds a specific python function to a key press.
New in PyMOL 1.6.1: second argument can also be a string in PyMOL
command syntax.
USAGE
set_key key, command
EXAMPLE
set_key F1, as cartoon, polymer; as sticks, organic
PYMOL API (ONLY)
cmd.set_key( string key, function fn, tuple arg=(), dict kw={})
PYTHON EXAMPLE
from pymol import cmd
def color_blue(object): cmd.color("blue",object)
cmd.set_key( 'F1' , color_blue, ( "object1" ) )
// would turn object1 blue when the F1 key is pressed and
cmd.set_key( 'F2' , color_blue, ( "object2" ) )
// would turn object2 blue when the F2 key is pressed.
cmd.set_key( 'CTRL-C' , cmd.zoom )
cmd.set_key( 'ALT-A' , cmd.turn, ('x',90) )
KEYS WHICH CAN BE REDEFINED
F1 to F12
left, right, pgup, pgdn, home, insert
CTRL-A to CTRL-Z
ALT-0 to ALT-9, ALT-A to ALT-Z
SEE ALSO
button, alias
'''
r = DEFAULT_ERROR
if isinstance(fn, basestring):
if arg or kw:
raise ValueError('arg and kw must be empty if fn is string')
arg = (fn, )
fn = cmd.do
if key[0:5] == 'CTRL-':
pat = key[5:]
if len(pat) > 1: # ctrl-special key
if pat[0] != 'F':
pat = string.lower(pat)
for a in _self.ctrl_special.keys():
if _self.ctrl_special[a][0] == pat:
_self.ctrl_special[a][1] = fn
_self.ctrl_special[a][2] = arg
_self.ctrl_special[a][3] = kw
r = DEFAULT_SUCCESS
else: # std. ctrl key
for a in _self.ctrl.keys():
if a == pat:
_self.ctrl[a][0] = fn
_self.ctrl[a][1] = arg
_self.ctrl[a][2] = kw
r = DEFAULT_SUCCESS
elif key[0:4] == 'ALT-':
pat = key[4:]
if len(pat) > 1: # alt-special key
if pat[0] != 'F':
pat = string.lower(pat)
for a in _self.alt_special.keys():
if _self.alt_special[a][0] == pat:
_self.alt_special[a][1] = fn
_self.alt_special[a][2] = arg
_self.alt_special[a][3] = kw
r = DEFAULT_SUCCESS
else: # std. alt key
pat = string.lower(pat)
for a in _self.alt.keys():
if a == pat:
_self.alt[a][0] = fn
_self.alt[a][1] = arg
_self.alt[a][2] = kw
r = DEFAULT_SUCCESS
elif key[0:5] == 'SHFT-':
pat = key[5:]
if len(pat) > 1: # shft-special key
if pat[0] != 'F':
pat = string.lower(pat)
for a in _self.shft_special.keys():
if _self.shft_special[a][0] == pat:
_self.shft_special[a][1] = fn
_self.shft_special[a][2] = arg
_self.shft_special[a][3] = kw
r = DEFAULT_SUCCESS
else:
if key[0] != 'F':
pat = string.lower(key)
else:
pat = key
for a in _self.special.keys():
if _self.special[a][0] == pat:
_self.special[a][1] = fn
_self.special[a][2] = arg
_self.special[a][3] = kw
r = DEFAULT_SUCCESS
if is_error(r):
print "Error: special '%s' key not found." % key
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, _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: {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
# preprocess selection
selection = selector.process(selection)
#
try:
_self.lock(_self)
if name==None:
avoid = {}
for obj in cmd.get_names("all"):
avoid[obj] = 1
sel_cnt = _cmd.get(_self._COb,"sel_counter")
while 1:
sel_cnt = sel_cnt + 1.0
name = "obj%02.0f" % sel_cnt
if not avoid.has_key(name):
_cmd.legacy_set(_self._COb,"sel_counter","%1.0f" % sel_cnt)
break
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))
finally:
_self.unlock(r,_self)
if not is_error(r): # temporary inefficient implementation
if extract not in (None, 0, '0'):
if extract not in (1, '1'):
extract = selector.process(extract)
else:
extract = selection
_self.remove("(("+extract+") in (%s)) and not (%s)"%(name,name))
if _self._raising(r,_self): raise pymol.CmdException
return r
def set_key(key,fn,arg=(),kw={},_self=cmd):
'''
DESCRIPTION
"set_key" binds a specific python function to a key press.
PYMOL API (ONLY)
cmd.set_key( string key, function fn, tuple arg=(), dict kw={})
PYTHON EXAMPLE
from pymol import cmd
def color_blue(object): cmd.color("blue",object)
cmd.set_key( 'F1' , color_blue, ( "object1" ) )
// would turn object1 blue when the F1 key is pressed and
cmd.set_key( 'F2' , color_blue, ( "object2" ) )
// would turn object2 blue when the F2 key is pressed.
cmd.set_key( 'CTRL-C' , cmd.zoom )
cmd.set_key( 'ALT-A' , cmd.turn, ('x',90) )
KEYS WHICH CAN BE REDEFINED
F1 to F12
left, right, pgup, pgdn, home, insert
CTRL-A to CTRL-Z
ALT-0 to ALT-9, ALT-A to ALT-Z
SEE ALSO
button
'''
r = DEFAULT_ERROR
if key[0:5]=='CTRL-':
pat=key[5:]
if len(pat)>1: # ctrl-special key
if pat[0]!='F':
pat=string.lower(pat)
for a in _self.ctrl_special.keys():
if _self.ctrl_special[a][0]==pat:
_self.ctrl_special[a][1]=fn
_self.ctrl_special[a][2]=arg
_self.ctrl_special[a][3]=kw
r = DEFAULT_SUCCESS
else: # std. ctrl key
for a in _self.ctrl.keys():
if a==pat:
_self.ctrl[a][0]=fn
_self.ctrl[a][1]=arg
_self.ctrl[a][2]=kw
r = DEFAULT_SUCCESS
elif key[0:4]=='ALT-':
pat=key[4:]
if len(pat)>1: # alt-special key
if pat[0]!='F':
pat=string.lower(pat)
for a in _self.alt_special.keys():
if _self.alt_special[a][0]==pat:
_self.alt_special[a][1]=fn
_self.alt_special[a][2]=arg
_self.alt_special[a][3]=kw
r = DEFAULT_SUCCESS
else: # std. alt key
pat=string.lower(pat)
for a in _self.alt.keys():
if a==pat:
_self.alt[a][0]=fn
_self.alt[a][1]=arg
_self.alt[a][2]=kw
r = DEFAULT_SUCCESS
elif key[0:5]=='SHFT-':
pat=key[5:]
if len(pat)>1: # shft-special key
if pat[0]!='F':
pat=string.lower(pat)
for a in _self.shft_special.keys():
if _self.shft_special[a][0]==pat:
_self.shft_special[a][1]=fn
_self.shft_special[a][2]=arg
_self.shft_special[a][3]=kw
r = DEFAULT_SUCCESS
else:
if key[0]!='F':
pat=string.lower(key)
else:
pat=key
for a in _self.special.keys():
if _self.special[a][0]==pat:
_self.special[a][1]=fn
_self.special[a][2]=arg
_self.special[a][3]=kw
r = DEFAULT_SUCCESS
if is_error(r):
print "Error: special '%s' key not found."%key
if _self._raising(r,_self): raise pymol.CmdException
return r
def set_key(key,fn,arg=(),kw={},_self=cmd):
'''
DESCRIPTION
"set_key" binds a specific python function to a key press.
New in PyMOL 1.6.1: second argument can also be a string in PyMOL
command syntax.
USAGE
set_key key, command
EXAMPLE
set_key F1, as cartoon, polymer; as sticks, organic
PYMOL API (ONLY)
cmd.set_key( string key, function fn, tuple arg=(), dict kw={})
PYTHON EXAMPLE
from pymol import cmd
def color_blue(object): cmd.color("blue",object)
cmd.set_key( 'F1' , color_blue, ( "object1" ) )
// would turn object1 blue when the F1 key is pressed and
cmd.set_key( 'F2' , color_blue, ( "object2" ) )
// would turn object2 blue when the F2 key is pressed.
cmd.set_key( 'CTRL-C' , cmd.zoom )
cmd.set_key( 'ALT-A' , cmd.turn, ('x',90) )
KEYS WHICH CAN BE REDEFINED
F1 to F12
left, right, pgup, pgdn, home, insert
CTRL-A to CTRL-Z
ALT-0 to ALT-9, ALT-A to ALT-Z
SEE ALSO
button, alias
'''
r = DEFAULT_ERROR
if isinstance(fn, basestring):
if arg or kw:
raise ValueError('arg and kw must be empty if fn is string')
arg = (fn,)
fn = cmd.do
if key[0:5]=='CTRL-':
pat=key[5:]
if len(pat)>1: # ctrl-special key
if pat[0]!='F':
pat=string.lower(pat)
for a in _self.ctrl_special.keys():
if _self.ctrl_special[a][0]==pat:
_self.ctrl_special[a][1]=fn
_self.ctrl_special[a][2]=arg
_self.ctrl_special[a][3]=kw
r = DEFAULT_SUCCESS
else: # std. ctrl key
for a in _self.ctrl.keys():
if a==pat:
_self.ctrl[a][0]=fn
_self.ctrl[a][1]=arg
_self.ctrl[a][2]=kw
r = DEFAULT_SUCCESS
elif key[0:4]=='ALT-':
pat=key[4:]
if len(pat)>1: # alt-special key
if pat[0]!='F':
pat=string.lower(pat)
for a in _self.alt_special.keys():
if _self.alt_special[a][0]==pat:
_self.alt_special[a][1]=fn
_self.alt_special[a][2]=arg
_self.alt_special[a][3]=kw
r = DEFAULT_SUCCESS
else: # std. alt key
pat=string.lower(pat)
for a in _self.alt.keys():
if a==pat:
_self.alt[a][0]=fn
_self.alt[a][1]=arg
_self.alt[a][2]=kw
r = DEFAULT_SUCCESS
elif key[0:5]=='SHFT-':
pat=key[5:]
if len(pat)>1: # shft-special key
if pat[0]!='F':
pat=string.lower(pat)
for a in _self.shft_special.keys():
if _self.shft_special[a][0]==pat:
_self.shft_special[a][1]=fn
_self.shft_special[a][2]=arg
_self.shft_special[a][3]=kw
r = DEFAULT_SUCCESS
else:
if key[0]!='F':
pat=string.lower(key)
else:
pat=key
for a in _self.special.keys():
if _self.special[a][0]==pat:
_self.special[a][1]=fn
_self.special[a][2]=arg
_self.special[a][3]=kw
r = DEFAULT_SUCCESS
if is_error(r):
print "Error: special '%s' key not found."%key
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,
_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
# preprocess selection
selection = selector.process(selection)
#
try:
_self.lock(_self)
if name == None:
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))
finally:
_self.unlock(r, _self)
if not is_error(r): # temporary inefficient implementation
if extract not in (None, 0, '0'):
if extract not in (1, '1'):
extract = selector.process(extract)
else:
extract = selection
_self.remove("((" + extract + ") in (%s)) and not (%s)" %
(name, name))
if _self._raising(r, _self): raise pymol.CmdException
return r
def set_key(key, fn, arg=(), kw={}, _self=cmd):
'''
DESCRIPTION
"set_key" binds a specific python function to a key press.
PYMOL API (ONLY)
cmd.set_key( string key, function fn, tuple arg=(), dict kw={})
PYTHON EXAMPLE
from pymol import cmd
def color_blue(object): cmd.color("blue",object)
cmd.set_key( 'F1' , color_blue, ( "object1" ) )
// would turn object1 blue when the F1 key is pressed and
cmd.set_key( 'F2' , color_blue, ( "object2" ) )
// would turn object2 blue when the F2 key is pressed.
cmd.set_key( 'CTRL-C' , cmd.zoom )
cmd.set_key( 'ALT-A' , cmd.turn, ('x',90) )
KEYS WHICH CAN BE REDEFINED
F1 to F12
left, right, pgup, pgdn, home, insert
CTRL-A to CTRL-Z
ALT-0 to ALT-9, ALT-A to ALT-Z
SEE ALSO
button
'''
r = DEFAULT_ERROR
if key[0:5] == 'CTRL-':
pat = key[5:]
if len(pat) > 1: # ctrl-special key
if pat[0] != 'F':
pat = string.lower(pat)
for a in _self.ctrl_special.keys():
if _self.ctrl_special[a][0] == pat:
_self.ctrl_special[a][1] = fn
_self.ctrl_special[a][2] = arg
_self.ctrl_special[a][3] = kw
r = DEFAULT_SUCCESS
else: # std. ctrl key
for a in _self.ctrl.keys():
if a == pat:
_self.ctrl[a][0] = fn
_self.ctrl[a][1] = arg
_self.ctrl[a][2] = kw
r = DEFAULT_SUCCESS
elif key[0:4] == 'ALT-':
pat = key[4:]
if len(pat) > 1: # alt-special key
if pat[0] != 'F':
pat = string.lower(pat)
for a in _self.alt_special.keys():
if _self.alt_special[a][0] == pat:
_self.alt_special[a][1] = fn
_self.alt_special[a][2] = arg
_self.alt_special[a][3] = kw
r = DEFAULT_SUCCESS
else: # std. alt key
pat = string.lower(pat)
for a in _self.alt.keys():
if a == pat:
_self.alt[a][0] = fn
_self.alt[a][1] = arg
_self.alt[a][2] = kw
r = DEFAULT_SUCCESS
elif key[0:5] == 'SHFT-':
pat = key[5:]
if len(pat) > 1: # shft-special key
if pat[0] != 'F':
pat = string.lower(pat)
for a in _self.shft_special.keys():
if _self.shft_special[a][0] == pat:
_self.shft_special[a][1] = fn
_self.shft_special[a][2] = arg
_self.shft_special[a][3] = kw
r = DEFAULT_SUCCESS
else:
if key[0] != 'F':
pat = string.lower(key)
else:
pat = key
for a in _self.special.keys():
if _self.special[a][0] == pat:
_self.special[a][1] = fn
_self.special[a][2] = arg
_self.special[a][3] = kw
r = DEFAULT_SUCCESS
if is_error(r):
print "Error: special '%s' key not found." % key
if _self._raising(r, _self): raise pymol.CmdException
return r
