def assign_dtypes(self, s):
"""pysimm.forcefield.Pcff.assign_dtypes
Pcff specific dihedral 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.dihedral_style = self.dihedral_style
for b in s.bonds:
for p1 in b.a.bonded_to:
for p2 in b.b.bonded_to:
if p1 is b.b or p2 is b.a:
continue
unique = True
for d in s.dihedrals:
if ((d.a is p1 and d.b is b.a and
d.c is b.b and d.d is p2) or
(d.a is p2 and d.b is b.b and
d.c is b.a and d.d is p1)):
unique = False
if unique:
p1_name = p1.type.eq_dihedral or p1.type.name
a_name = b.a.type.eq_dihedral or b.a.type.name
b_name = b.b.type.eq_dihedral or b.b.type.name
p2_name = p2.type.eq_dihedral or p2.type.name
dt = self.dihedral_types.get('%s,%s,%s,%s'
% (p1_name, a_name,
b_name, p2_name))
if dt:
if len(dt) == 1:
dt = dt[0]
else:
index = 0
x = 5
for i in range(len(dt)):
if dt[i].name.count('X') < x:
index = i
x = dt[i].name.count('X')
dt = dt[index]
if compare('%s,%s,%s,%s' % (p1_name, a_name,
b_name, p2_name),
dt.name, order=True):
all_types.add(dt)
s.dihedrals.add(Dihedral(type_name=dt.name,
a=p1, b=b.a,
c=b.b, d=p2))
elif compare('%s,%s,%s,%s' % (p2_name, b_name,
a_name, p1_name),
dt.name, order=True):
all_types.add(dt)
s.dihedrals.add(Dihedral(type_name=dt.name,
a=p2, b=b.b,
c=b.a, d=p1))
else:
print('cannot distinguish between forward/'
'backward for %s,%s,%s,%s'
% (p1.type.name,
b.a.type.name,
b.b.type.name,
p2.type.name))
else:
print ('I cant type this dihedral %s,%s,%s,%s'
% (p1_name, a_name, b_name, p2_name))
for dt in all_types:
dt = dt.copy()
s.dihedral_types.add(dt)
for d in s.dihedrals:
dt = s.dihedral_types.get(d.type_name)
if dt:
d.type = dt[0]
def assign_atypes(self, s):
"""pysimm.forcefield.Pcff.assign_atypes
Pcff 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:
if compare('%s,%s,%s' % (p1.type.name,
p.type.name,
p2.type.name),
at[0].name, order=True):
s.angles.add(Angle(type_name=at[0].name,
a=p1, b=p, c=p2))
all_types.add(at[0])
elif compare('%s,%s,%s' % (p2.type.name,
p.type.name,
p1.type.name),
at[0].name, order=True):
s.angles.add(Angle(type_name=at[0].name,
a=p2, b=p, c=p1))
all_types.add(at[0])
else:
print('cannot distinguish between forward/'
'backward for %s,%s,%s'
% (p1.type.name,
p.type.name,
p2.type.name))
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]