topology.md

(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

:::{eval-rst} .. currentmodule:: openff.toolkit.topology .. autosummary:: :nosignatures: :toctree: api/generated/

FrozenMolecule
Molecule
Topology
TopologyMolecule

:::

Secondary objects

:::{eval-rst} .. currentmodule:: openff.toolkit.topology .. autosummary:: :nosignatures: :toctree: api/generated/

Particle
Atom
Bond
VirtualSite
VirtualParticle
TopologyVirtualParticle
BondChargeVirtualSite
MonovalentLonePairVirtualSite
DivalentLonePairVirtualSite
TrivalentLonePairVirtualSite
TopologyAtom
TopologyBond
TopologyVirtualSite
ValenceDict
ImproperDict

:::