def addCharges(self, atoms):
"""
compute gasteiger charges, add them to atoms, return list of new
charges
NB: assumes MolKit atoms have bonds
NB: calls type atoms if all the atoms haven't been babel typed.
if babel_types have been set by hand, they will be ok IF every
atom has a babel type
"""
#print 'in computeGasteiger'
#check that atoms have babel_types
w_babel_types = atoms.get(lambda x: hasattr(x, 'babel_type'))
if w_babel_types is None or len(w_babel_types)!=len(atoms):
babel = AtomHybridization()
#have to have bonds for this
babel.assignHybridization(atoms)
Gast = Gasteiger()
Gast.compute(atoms)
gastCharges = []
for c in atoms.gast_charge:
gastCharges.append(round(c, 4))
#NB THIS adds entry 'gasteiger' to atom._charges dict
atoms.addCharges('gasteiger', gastCharges)
atoms.chargeSet = 'gasteiger'
#clean-up
delattr(atoms, 'gast_charge')
return gastCharges
def addCharges(self, atoms):
"""
compute gasteiger charges, add them to atoms, return list of new
charges
NB: assumes MolKit atoms have bonds
NB: calls type atoms if all the atoms haven't been babel typed.
if babel_types have been set by hand, they will be ok IF every
atom has a babel type
"""
#print 'in computeGasteiger'
#check that atoms have babel_types
w_babel_types = atoms.get(lambda x: hasattr(x, 'babel_type'))
if w_babel_types is None or len(w_babel_types) != len(atoms):
babel = AtomHybridization()
#have to have bonds for this
babel.assignHybridization(atoms)
Gast = Gasteiger()
Gast.compute(atoms)
gastCharges = []
for c in atoms.gast_charge:
gastCharges.append(round(c, 4))
#NB THIS adds entry 'gasteiger' to atom._charges dict
atoms.addCharges('gasteiger', gastCharges)
atoms.chargeSet = 'gasteiger'
#clean-up
delattr(atoms, 'gast_charge')
return gastCharges
def computeGasteiger(self):
#to compute Gasteiger need to:
# create an AtomHybridization()
# call its assignHybridization method on self.allAtoms
# create a Gasteiger()
# call its compute method on self.allAtoms
# THEN move gast_charge into _charges with gasteiger key
# set allAtoms.chargeSet to 'gasteiger'
# THEN delattr gast_charge from allAtoms
allAts = self.allAtoms
ah = AtomHybridization()
ah.assignHybridization(allAts)
Gast = Gasteiger()
Gast.compute(allAts)
gastCharges = []
for c in allAts.gast_charge:
gastCharges.append(round(c, 3))
allAts.addCharges('gasteiger', gastCharges)
del allAts.gast_charge
allAts.chargeSet = 'gasteiger'
def computeGasteiger(self):
#to compute Gasteiger need to:
# create an AtomHybridization()
# call its assignHybridization method on self.allAtoms
# create a Gasteiger()
# call its compute method on self.allAtoms
# THEN move gast_charge into _charges with gasteiger key
# set allAtoms.chargeSet to 'gasteiger'
# THEN delattr gast_charge from allAtoms
allAts = self.allAtoms
ah = AtomHybridization()
ah.assignHybridization(allAts)
Gast = Gasteiger()
Gast.compute(allAts)
gastCharges = []
for c in allAts.gast_charge:
gastCharges.append(round(c, 3))
allAts.addCharges('gasteiger', gastCharges)
del allAts.gast_charge
allAts.chargeSet = 'gasteiger'