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
)
