def bonds(self):
types, bonds = [], []
for i, a in enumerate(self.atoms):
for j in a.conn:
if i > j: continue
ij = [i, j]
t, ij = sort_bond_or_angle([self.atoms[p].ff for p in ij], ij)
if not t in types: types.append(t)
bonds.append(AtomSet(ij, types.index(t)))
return bonds, types
def bonds(self):
types,bonds = [],[]
for i, a in enumerate(self.atoms):
for j in a.conn:
if i > j: continue
ij = [i,j]
t, ij = sort_bond_or_angle([self.atoms[p].ff for p in ij], ij)
if not t in types: types.append(t)
bonds.append(AtomSet(ij, types.index(t)))
return bonds, types
def angles(self):
types,angles = [],[]
# Center is atom j.
for j, a in enumerate(self.atoms):
for i in a.conn:
for k in a.conn:
if k <= i: continue
ijk = [i,j,k]
t,ijk = sort_bond_or_angle([self.atoms[p].ff for p in ijk], ijk)
if not t in types:
types.append(t)
angles.append(AtomSet(ijk, types.index(t)))
return angles, types
def angles(self):
types, angles = [], []
# Center is atom j.
for j, a in enumerate(self.atoms):
for i in a.conn:
for k in a.conn:
if k <= i: continue
ijk = [i, j, k]
t, ijk = sort_bond_or_angle(
[self.atoms[p].ff for p in ijk], ijk)
if not t in types:
types.append(t)
angles.append(AtomSet(ijk, types.index(t)))
return angles, types
