openforcefield.topology.Topology
================================

.. currentmodule:: openforcefield.topology

.. autoclass:: Topology

   
   .. automethod:: __init__

   
   .. rubric:: Methods

   .. autosummary::
   
      ~Topology.__init__
      ~Topology.add_constraint
      ~Topology.add_molecule
      ~Topology.add_particle
      ~Topology.assert_bonded
      ~Topology.atom
      ~Topology.bond
      ~Topology.chemical_environment_matches
      ~Topology.from_bson
      ~Topology.from_dict
      ~Topology.from_json
      ~Topology.from_mdtraj
      ~Topology.from_messagepack
      ~Topology.from_molecules
      ~Topology.from_openmm
      ~Topology.from_parmed
      ~Topology.from_pickle
      ~Topology.from_toml
      ~Topology.from_xml
      ~Topology.from_yaml
      ~Topology.get_bond_between
      ~Topology.get_fractional_bond_order
      ~Topology.is_bonded
      ~Topology.is_constrained
      ~Topology.to_bson
      ~Topology.to_dict
      ~Topology.to_json
      ~Topology.to_messagepack
      ~Topology.to_parmed
      ~Topology.to_pickle
      ~Topology.to_toml
      ~Topology.to_xml
      ~Topology.to_yaml
      ~Topology.virtual_site
   
   

   
   
   .. rubric:: Attributes

   .. autosummary::
   
      ~Topology.angles
      ~Topology.aromaticity_model
      ~Topology.box_vectors
      ~Topology.charge_model
      ~Topology.constrained_atom_pairs
      ~Topology.fractional_bond_order_model
      ~Topology.impropers
      ~Topology.n_angles
      ~Topology.n_impropers
      ~Topology.n_propers
      ~Topology.n_reference_molecules
      ~Topology.n_topology_atoms
      ~Topology.n_topology_bonds
      ~Topology.n_topology_molecules
      ~Topology.n_topology_particles
      ~Topology.n_topology_virtual_sites
      ~Topology.propers
      ~Topology.reference_molecules
      ~Topology.topology_atoms
      ~Topology.topology_bonds
      ~Topology.topology_molecules
      ~Topology.topology_particles
      ~Topology.topology_virtual_sites