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. |
TopologyMolecule
|
TopologyMolecules are built to be an efficient way to store large numbers of copies of the same molecule for parameterization and system preparation. |
Secondary objects
Particle
|
Base class for all particles in a molecule. |
Atom
|
A particle representing a chemical atom. |
Bond
|
Chemical bond representation. |
VirtualSite
|
A container representing one or more virtual particles whose positions are defined in terms of Atom positions. |
VirtualParticle
|
A single particle owned by a VirtualSite |
TopologyVirtualParticle
|
- Attributes
|
BondChargeVirtualSite
|
A particle representing a “Bond Charge”-type virtual site, in which the location of the charge is specified by the positions of two atoms. |
MonovalentLonePairVirtualSite
|
A particle representing a “Monovalent Lone Pair”-type virtual site, in which the location of the charge is specified by the positions of three atoms. |
DivalentLonePairVirtualSite
|
A particle representing a “Divalent Lone Pair”-type virtual site, in which the location of the charge is specified by the positions of three atoms. |
TrivalentLonePairVirtualSite
|
A particle representing a “Trivalent Lone Pair”-type virtual site, in which the location of the charge is specified by the positions of four atoms. |
TopologyAtom
|
A TopologyAtom is a lightweight data structure that represents a single openforcefield.topology.molecule.Atom in a Topology. |
TopologyBond
|
A TopologyBond is a lightweight data structure that represents a single openforcefield.topology.molecule.Bond in a Topology. |
TopologyVirtualSite
|
A TopologyVirtualSite is a lightweight data structure that represents a single openforcefield.topology.molecule.VirtualSite in a Topology. |
ValenceDict
|
Enforce uniqueness in atom indices. |
ImproperDict
|
Symmetrize improper torsions. |