def generate_connections(self): try: self.atom_labels, self.bonds except AttributeError: raise Exception("Simulation has not been assigned atom types and bonds yet") connect = Connector() self.bond_types = connect.find_bond_types(self.atom_labels, self.bonds) self.bond_labels = connect.bond_labels( self.atom_labels, self.bonds, self.bond_types ) self.bond_graph = self.generate_bond_graph(self.bonds) self.angles = connect.angles(self.bonds, self.bond_graph) self.angle_types = connect.find_angle_types(self.atom_labels, self.angles) self.angle_labels = connect.angle_labels( self.atom_labels, self.angles, self.angle_types ) self.dihedrals = connect.dihedrals(self.bonds, self.bond_graph) self.dihedral_types = connect.find_dihedral_types( self.atom_labels, self.dihedrals ) self.dihedral_labels = connect.dihedral_labels( self.atom_labels, self.dihedrals, self.dihedral_types ) self.impropers = connect.impropers(self.bonds, self.bond_graph) self.improper_types = connect.find_improper_types( self.atom_labels, self.impropers ) self.improper_labels = connect.improper_labels( self.atom_labels, self.impropers, self.improper_types )
epoxy.bond_types = connect.find_bond_types(epoxy.atom_labels, epoxy.bonds) epoxy.bond_labels = connect.bond_labels(epoxy.atom_labels, epoxy.bonds, epoxy.bond_types) epoxy.angles = connect.angles(epoxy.bonds) epoxy.angle_types = connect.find_angle_types(epoxy.atom_labels, epoxy.angles) epoxy.angle_labels = connect.angle_labels(epoxy.atom_labels, epoxy.angles, epoxy.angle_types) epoxy.torsions = connect.torsions(epoxy.bonds) epoxy.torsion_types = connect.find_torsion_types(epoxy.atom_labels, epoxy.torsions) epoxy.torsion_labels = connect.torsion_labels(epoxy.atom_labels, epoxy.torsions, epoxy.torsion_types) epoxy.impropers = connect.impropers(epoxy.bonds) epoxy.improper_types = connect.find_improper_types(epoxy.atom_labels, epoxy.impropers) epoxy.improper_labels = connect.improper_labels(epoxy.atom_labels, epoxy.impropers, epoxy.improper_types) epoxy.masses = [0] * len(epoxy.coords) #output.write_xyz('epoxy.xyz') p = Parameterise(epoxy.vdw_defs) epoxy.bond_coeffs = p.match_bonds(epoxy.bond_types) epoxy.angle_coeffs = p.match_angles(epoxy.angle_types) epoxy.torsion_coeffs = p.match_torsions(epoxy.torsion_types) epoxy.improper_coeffs = p.match_impropers(epoxy.improper_types) epoxy.pair_coeffs = p.match_pairs() epoxy.masses = p.match_masses()
propanol.bonds, propanol.bond_types) propanol.angles = connect.angles(propanol.bonds) propanol.angle_types = connect.find_angle_types(propanol.atom_labels, propanol.angles) propanol.angle_labels = connect.angle_labels(propanol.atom_labels, propanol.angles, propanol.angle_types) propanol.torsions = connect.torsions(propanol.bonds) propanol.torsion_types = connect.find_torsion_types(propanol.atom_labels, propanol.torsions) propanol.torsion_labels = connect.torsion_labels(propanol.atom_labels, propanol.torsions, propanol.torsion_types) propanol.impropers = connect.impropers(propanol.bonds) propanol.improper_types = connect.find_improper_types(propanol.atom_labels, propanol.impropers) propanol.improper_labels = connect.improper_labels(propanol.atom_labels, propanol.impropers, propanol.improper_types) propanol.masses = [0] * len(propanol.coords) #output.write_xyz('propanol.xyz') p = Parameterise(propanol.vdw_defs) propanol.bond_coeffs = p.match_bonds(propanol.bond_types) propanol.angle_coeffs = p.match_angles(propanol.angle_types) propanol.torsion_coeffs = p.match_torsions(propanol.torsion_types) propanol.improper_coeffs = p.match_impropers(propanol.improper_types) propanol.pair_coeffs = p.match_pairs() propanol.masses = p.match_masses()
diamine.bond_types) diamine.angles = connect.angles(diamine.bonds) diamine.angle_types = connect.find_angle_types(diamine.atom_labels, diamine.angles) diamine.angle_labels = connect.angle_labels(diamine.atom_labels, diamine.angles, diamine.angle_types) diamine.torsions = connect.torsions(diamine.bonds) diamine.torsion_types = connect.find_torsion_types(diamine.atom_labels, diamine.torsions) diamine.torsion_labels = connect.torsion_labels(diamine.atom_labels, diamine.torsions, diamine.torsion_types) diamine.impropers = connect.impropers(diamine.bonds) diamine.improper_types = connect.find_improper_types(diamine.atom_labels, diamine.impropers) diamine.improper_labels = connect.improper_labels(diamine.atom_labels, diamine.impropers, diamine.improper_types) diamine.masses = [0] * len(diamine.coords) #output.write_xyz('diamine.xyz') p = Parameterise(diamine.vdw_defs) diamine.bond_coeffs = p.match_bonds(diamine.bond_types) diamine.angle_coeffs = p.match_angles(diamine.angle_types) diamine.torsion_coeffs = p.match_torsions(diamine.torsion_types) diamine.improper_coeffs = p.match_impropers(diamine.improper_types) diamine.pair_coeffs = p.match_pairs() diamine.masses = p.match_masses()
connect = Connector() bp.bond_types = connect.find_bond_types(bp.atom_labels,bp.bonds) bp.bond_labels = connect.bond_labels(bp.atom_labels,bp.bonds,bp.bond_types) bp.angles = connect.angles(bp.bonds) bp.angle_types = connect.find_angle_types(bp.atom_labels, bp.angles) bp.angle_labels = connect.angle_labels(bp.atom_labels,bp.angles, bp.angle_types) bp.torsions = connect.torsions(bp.bonds) bp.torsion_types = connect.find_torsion_types(bp.atom_labels, bp.torsions) bp.torsion_labels = connect.torsion_labels(bp.atom_labels,bp.torsions, bp.torsion_types) bp.impropers = connect.impropers(bp.bonds) bp.improper_types = connect.find_improper_types(bp.atom_labels, bp.impropers) bp.improper_labels = connect.improper_labels(bp.atom_labels,bp.impropers, bp.improper_types) bp.masses = [0] * len(bp.coords) #output.write_xyz('bp.xyz') p = Parameterise(bp.vdw_defs) bp.bond_coeffs = p.match_bonds(bp.bond_types) bp.angle_coeffs = p.match_angles(bp.angle_types) bp.torsion_coeffs = p.match_torsions(bp.torsion_types) bp.improper_coeffs = p.match_impropers(bp.improper_types) bp.pair_coeffs = p.match_pairs() bp.masses = p.match_masses() bp.charge_coeffs = p.match_charges()