from connector import Connector from write_coords import Writer from params import Parameterise connect = Connector() 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)
from params import Parameterise connect = Connector() propanol.bond_types = connect.find_bond_types(propanol.atom_labels, propanol.bonds) propanol.bond_labels = connect.bond_labels(propanol.atom_labels, 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)
from params import Parameterise connect = Connector() diamine.bond_types = connect.find_bond_types(diamine.atom_labels, diamine.bonds) diamine.bond_labels = connect.bond_labels(diamine.atom_labels, diamine.bonds, 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)
from connector import Connector from write_coords import Writer from params import Parameterise 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)