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()
