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¶

`FrozenMolecule`	Immutable chemical representation of a molecule, such as a small molecule or biopolymer.
`Molecule`	Mutable chemical representation of a molecule, such as a small molecule or biopolymer.
`Topology`	A Topology is a chemical representation of a system containing one or more molecules appearing in a specified order.

Secondary objects¶

`Particle`	Base class for all particles in a molecule.
`Atom`	A particle representing a chemical atom.
`Bond`	Chemical bond representation.
`VirtualSite`	A particle representing a virtual site whose position is defined in terms of `Atom` positions.