if __name__=='pymol.experimenting':
import selector
from cmd import _cmd,lock,unlock,Shortcut,QuietException, \
DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error
import cmd
import threading
import pymol
import string
def get_bond_print(obj,max_bond,max_type,_self=cmd):
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_bond_print(_self._COb,str(obj),int(max_bond),int(max_type))
finally:
_self.unlock(_self=_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def expfit(a,b,_self=cmd):
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.fit(_self._COb,a,b,2)
finally:
_self.unlock(_self=_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def spheroid(object="",average=0,_self=cmd):
'''
DESCRIPTION
"spheroid" averages trajectory frames together to create
an ellipsoid-like approximation of the actual anisotropic
motion exhibited by the atom over a series of trajectory frames.
USAGE
spheroid object,average
average = number of states to average for each resulting spheroid state
'''
r = DEFAULT_ERROR
try:
print "Warning: 'spheroid' is experimental, incomplete, and unstable."
_self.lock(_self)
r = _cmd.spheroid(_self._COb,str(object),int(average))
finally:
_self.unlock(_self=_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def mem(_self=cmd):
'''
DESCRIPTION
"mem" Dumps current memory state to standard output. This is a
debugging feature, not an official part of the API.
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.mem(_self._COb)
finally:
_self.unlock(_self=_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def check(selection=None, preserve=0):
'''
DESCRIPTION
"check" is unsupported command that may eventually have something
to do with assigning forcefield parameters to a selection of
atoms.
'''
from chempy.tinker import realtime
if selection==None:
arg = cmd.get_names("objects")
arg = arg[0:1]
if arg:
if len(arg):
selection = arg
if selection!=None:
selection = selector.process(selection)
realtime.assign("("+selection+")",int(preserve))
realtime.setup("("+selection+")")
def fast_minimize(*arg):
'''
DESCRIPTION
"fast_minimize" is an unsupported nonfunctional command that may
eventually have something to do with doing a quick clean up of the
molecular structure.
'''
from chempy.tinker import realtime
grad = 0.01
iter = 500
interval = 50
la = len(arg)
if not la:
arg = cmd.get_names("objects")
arg = arg[0:1]
la = len(arg)
if la:
sele = "("+arg[0]+")"
if la>1:
iter = int(arg[1])
if la>2:
grad = float(arg[2])
if la>3:
interval = int(arg[3])
t = threading.Thread(target=realtime.mini,args=(iter,grad,interval,arg[0]))
t.setDaemon(1)
t.start()
def minimize(*arg):
'''
DESCRIPTION
"fast_minimize" is an unsupported nonfunctional command that may
eventually have something to do with minimization.
'''
from chempy.tinker import realtime
grad = 0.01
iter = 500
interval = 50
la = len(arg)
if not la:
arg = cmd.get_names("objects")
arg = arg[0:1]
la = len(arg)
if la:
sele = "("+arg[0]+")"
if la>1:
iter = int(arg[1])
if la>2:
grad = float(arg[2])
if la>3:
interval = int(arg[3])
if realtime.setup(sele):
t = threading.Thread(target=realtime.mini,args=(iter,grad,interval,arg[0]))
t.setDaemon(1)
t.start()
else:
print " minimize: missing parameters, can't continue"
def dump(fnam,obj,_self=cmd):
'''
DESCRIPTION
"dump" is an unsupported command which may have something to do
with outputing isosurface meshes and surface objects to a file.
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.dump(_self._COb,str(fnam),obj)
finally:
_self.unlock(_self=_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def dummy(*arg):
return None
def test(group=0,index=0,_self=cmd):
'''
DESCRIPTION
"dump" is an unsupported internal command.
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r=_cmd.test(_self._COb,int(group),int(index))
finally:
_self.unlock(_self=_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def import_coords(obj,state,mechio,_self=cmd):
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.import_coords(_self._COb,str(obj),int(state)-1,mechio)
finally:
_self.unlock(_self=_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def load_coords(*arg):
_self = cmd
r = DEFAULT_ERROR
try:
_self.lock(_self)
ok = 1
ftype = loadable.model
state = 0
model = arg[0];
if len(arg)<2:
ok=0
if len(arg)>=2:
oname = string.strip(arg[1])
if len(arg)>=3:
state = int(arg[2])-1
if ok:
r = _cmd.load_coords(_self._COb,str(oname),model,
int(state)-1,int(ftype))
else:
print "Error: invalid arguments."
finally:
_self.unlock(_self=_self)
if _self._raising(r,_self): raise pymol.CmdException
return r