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 chemical atom.

Bond

Chemical bond representation.

ValenceDict

Enforce uniqueness in atom indices.

ImproperDict

Symmetrize improper torsions.

HierarchyScheme

Perceives hierarchy elements from the metadata of atoms in a Molecule.

HierarchyElement

An element in a metadata hierarchy scheme, such as a residue or chain.