def assign(sele, preserve=0):
from molobj import MolObj
from typer import Typer, Rules
import rules
global state
global model
result = 1
state = State()
model = cmd.get_model(sele)
# now assign atom types
ruleSet = Rules()
# ruleSet.fromList(rules.amber_types)
ruleSet.fromList(rules.simple_types)
mobj = MolObj()
mobj.fromChemPyModel(model)
typed = Typer(molObj=mobj)
print(" realtime: assigning atom types")
typed.applyRules(ruleSet)
c = 0
for a in typed.getNamedTypes():
at = model.atom[c]
if (at.text_type == '??') or (not preserve):
if a == '':
print(" warning: unable to assign atom type to atom %d" % c)
result = 0
else:
cmd.alter("((%s) and (index %s))" % (sele, at.index),
"text_type ='%s'" % a)
if feedback['tinker']:
print(" " + str(__name__) + ': %s is a %s' % (at.name, a))
at.text_type = a
c = c + 1
sm = 0
for a in model.atom:
a.resi = str(a.resi_number)
sm = sm + a.partial_charge
print(" lig: net charge on ligand is %8.4f\n" % sm)
return result
def assign(sele,preserve=0):
from molobj import MolObj
from typer import Typer,Rules
import rules
global state
global model
result = 1
state = State()
model = cmd.get_model(sele)
# now assign atom types
ruleSet = Rules()
# ruleSet.fromList(rules.amber_types)
ruleSet.fromList(rules.simple_types)
mobj = MolObj()
mobj.fromChemPyModel(model)
typed = Typer(molObj = mobj)
print(" realtime: assigning atom types")
typed.applyRules(ruleSet)
c = 0
for a in typed.getNamedTypes():
at = model.atom[c]
if (at.text_type == '??') or (not preserve):
if a=='':
print(" warning: unable to assign atom type to atom %d"%c)
result = 0
else:
cmd.alter("((%s) and (index %s))" % (sele,at.index),
"text_type ='%s'" % a)
if feedback['tinker']:
print(" "+str(__name__)+': %s is a %s' % (at.name,a))
at.text_type = a
c = c + 1
sm = 0
for a in model.atom:
a.resi = str(a.resi_number)
sm = sm + a.partial_charge
print(" lig: net charge on ligand is %8.4f\n" % sm)
return result
def assign(sele,preserve=0):
from molobj import MolObj
from typer import Typer,Rules
import rules
result = 1
state = State()
model = cmd.get_model(sele)
# now assign atom types
ruleSet = Rules()
ruleSet.fromList(rules.mmff_types)
ruleSet.mappingFromList(rules.mmff_mapping)
mobj = MolObj()
mobj.fromChemPyModel(model)
typed = Typer(molObj = mobj)
print " realtime: assigning atom types"
typed.applyRules(ruleSet)
c = 0
for a in typed.getTypes():
at = model.atom[c]
if (at.text_type == '??') or (not preserve):
if a==-99:
print " warning: unable to assign atom type to atom %d"%c
result = 0
else:
cmd.alter("((%s) and (index %s))" % (sele,at.index),
"numeric_type ='%s'" % a)
if feedback['tinker']:
print " "+str(__name__)+': %s is a %s' % (at.name,a)
at.numeric_type = a
c = c + 1
sm = 0
for a in model.atom:
a.resi = str(a.resi_number)
sm = sm + a.partial_charge
return result
