def assign_charges(self, s, charges='default'):
"""pysimm.forcefield.Pcff.assign_charges
Default Pcff charge assignment. Gasteiger is also an option.
Args:
s: :class:`~pysimm.system.System`
charges: default
Returns:
None
"""
if charges == 'gasteiger':
print('adding gasteiger charges')
gasteiger.set_charges(s)
elif charges == 'default':
print('adding default PCFF charges')
for p in s.particles:
p.charge = 0
for b in s.bonds:
n1 = b.a.type.eq_bond or b.a.type.name
n2 = b.b.type.eq_bond or b.b.type.name
btype = self.bond_types.get('%s,%s' % (n1, n2))
if btype:
btype = btype[0]
if btype.name == '%s,%s' % (n1, n2):
b.a.charge += float(btype.q1)
b.b.charge += float(btype.q2)
elif btype.name == '%s,%s' % (n2, n1):
b.a.charge += float(btype.q2)
b.b.charge += float(btype.q1)
def assign_charges(self, s, charges='default'):
"""pysimm.forcefield.Tip3p.assign_charges
Tip3p specific charge assignment.
There are none.
Args:
s: pysimm.system.System
charges: default
Returns:
None
"""
if charges == 'gasteiger':
print('adding gasteiger charges')
gasteiger.set_charges(s)
elif charges == 'default':
print('adding default TIP3P charges')
for p in s.particles:
p.charge = 0
for b in s.bonds:
n1 = b.a.type.eq_bond or b.a.type.name
n2 = b.b.type.eq_bond or b.b.type.name
btype = self.bond_types.get('%s,%s' % (n1, n2))
if btype:
btype = btype[0]
if btype.name == '%s,%s' % (n1, n2):
b.a.charge += float(btype.q1)
b.b.charge += float(btype.q2)
elif btype.name == '%s,%s' % (n2, n1):
b.a.charge += float(btype.q2)
b.b.charge += float(btype.q1)
def assign_charges(self, s, charges='gasteiger'):
"""pysimm.forcefield.Gaff.assign_charges
Charge assignment. Gasteiger is default for now.
Args:
s: :class:`~pysimm.system.System`
charges: gasteiger
Returns:
None
"""
if charges == 'gasteiger':
print('adding gasteiger charges')
gasteiger.set_charges(s)
