def assign_atypes(self, s):
"""pysimm.forcefield.Gaff2.assign_atypes
Gaff2 specific boanglend typing rules.
Requires System object Particle objects have Particle.bonds, Particle.type
and Particle.type.name defined.
*** use after assign_ptypes ***
Args:
s: pysimm.system.System
Returns:
None
"""
all_types = set()
s.angle_style = self.angle_style
for p in s.particles:
p.bonded_to = [x.a if p is x.b else x.b for x in p.bonds]
for p1 in p.bonded_to:
for p2 in p.bonded_to:
if p1 is not p2:
unique = True
for a in s.angles:
if ((a.a is p1 and a.b is p and a.c is p2)
or (a.a is p2 and a.b is p and a.c is p1)):
unique = False
if unique:
at = self.angle_types.get(
'%s,%s,%s' %
(p1.type.name, p.type.name, p2.type.name))
if at:
s.angles.add(
Angle(type_name=at[0].name,
a=p1,
b=p,
c=p2))
all_types.add(at[0])
else:
print(
'I cant type this angle %s,%s,%s' %
(p1.type.name, p.type.name, p2.type.name))
for at in all_types:
at = at.copy()
s.angle_types.add(at)
for a in s.angles:
at = s.angle_types.get(a.type_name)
if at:
a.type = at[0]
def assign_atypes(self, s):
"""pysimm.forcefield.Dreiding.assign_atypes
Dreiding specific angle typing rules.
Requires :class:`~pysimm.system.System` object :class:`~pysimm.system.Particle` objects have bonds, type and type.name defined.
*** use after assign_ptypes ***
Args:
s: :class:`~pysimm.system.System`
Returns:
None
"""
all_types = set()
s.angle_style = self.angle_style
s.add_particle_bonding()
for p in s.particles:
for p1 in p.bonded_to:
for p2 in p.bonded_to:
if p1 is not p2:
unique = True
for a in s.angles:
if ((a.a is p1 and a.b is p and a.c is p2)
or (a.a is p2 and a.b is p and a.c is p1)):
unique = False
if unique:
at = self.angle_types.get(
'%s,%s,%s' %
(p1.type.name, p.type.name, p2.type.name))
if at:
s.angles.add(
Angle(type_name=at[0].name,
a=p1,
b=p,
c=p2))
all_types.add(at[0])
else:
print(
'I cant type this angle %s,%s,%s' %
(p1.type.name, p.type.name, p2.type.name))
for at in all_types:
at = at.copy()
s.angle_types.add(at)
for a in s.angles:
at = s.angle_types.get(a.type_name)
if at:
a.type = at[0]