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
Immutable chemical representation of a molecule, such as a small molecule or biopolymer. |
|
Mutable chemical representation of a molecule, such as a small molecule or biopolymer. |
|
A Topology is a chemical representation of a system containing one or more molecules appearing in a specified order. |
Secondary objects
Base class for all particles in a molecule. |
|
A chemical atom. |
|
Chemical bond representation. |
|
Enforce uniqueness in atom indices. |
|
Symmetrize improper torsions. |
|
Perceives hierarchy elements from the metadata of atoms in a |
|
An element in a metadata hierarchy scheme, such as a residue or chain. |