.. _topology :: Molecular topology representations ================================== This module provides pure-Python classes for representing molecules and molecular systems. These classes offer several advantages over corresponding ``Topology`` objects in `OpenMM `_ and `MDTraj `_, including offering serialization to a variety of standard formats (including `XML `_, `JSON `_, `YAML `_, `BSON `_, `TOML `_, and `MessagePack `_). Primary objects --------------- .. currentmodule:: openforcefield.topology .. autosummary:: :nosignatures: :toctree: api/generated/ FrozenMolecule Molecule Topology Secondary objects ----------------- .. currentmodule:: openforcefield.topology .. autosummary:: :nosignatures: :toctree: api/generated/ Particle Atom Bond VirtualSite