def parse_tinker_arc(molecule_file, parameter_file=None):
if parameter_file:
elements, atom_types, bond_types, angle_types, dihedral_types = lammps.parse_opls_parameters(parameter_file)
atoms = []
for line in open(molecule_file):
columns = line.split()
if len(columns)>3:
atoms.append( utils.Struct(index=int(columns[0]), element=columns[1], x=float(columns[2]), y=float(columns[3]), z=float(columns[4]), bonded=[int(s) for s in columns[6:]], type=([t for t in atom_types if t.index==int(columns[5][-3:])][0] if parameter_file else None), charge=None) )
if len(columns[5])>3:
atom_types.append( copy.deepcopy(atoms[-1].type) )
atoms[-1].type.index = int(columns[5])
bond_set = {}
for a in atoms:
a.bonded = [atoms[i-1] for i in a.bonded]
for b in a.bonded:
if (b,a) not in bond_set:
bond_set[(a,b)] = True
bonds = [utils.Struct(atoms=b, d=utils.dist_squared(b[0],b[1])**0.5, e=None, type=None) for b in bond_set.keys()]
angles, dihedrals = get_angles_and_dihedrals(atoms, bonds)
return atoms, bonds, angles, dihedrals
def set_params(param_file): Molecule.elements, Molecule.atom_types, Molecule.bond_types, Molecule.angle_types, Molecule.dihedral_types = lammps.parse_opls_parameters(param_file)