openforcefield.topology.TopologyAtom

class openforcefield.topology.TopologyAtom(atom, topology_molecule)

A TopologyAtom is a lightweight data structure that represents a single openforcefield.topology.molecule.Atom in a Topology. A TopologyAtom consists of two references – One to its fully detailed “atom”, an openforcefield.topology.molecule.Atom, and another to its parent “topology_molecule”, which occupies a spot in the parent Topology’s TopologyMolecule list.

As some systems can be very large, there is no always-existing representation of a TopologyAtom. They are created on demand as the user requests them.

Warning

This API is experimental and subject to change.

Attributes

atom

Get the reference Atom for this TopologyAtom.

atomic_number

Get the atomic number of this atom

molecule

Get the reference Molecule that this TopologyAtom belongs to.

topology_atom_index

Get the index of this atom in its parent Topology.

topology_bonds

Get the TopologyBonds connected to this TopologyAtom.

topology_molecule

Get the TopologyMolecule that this TopologyAtom belongs to.

topology_particle_index

Get the index of this particle in its parent Topology.

Methods

from_bson(serialized)	Instantiate an object from a BSON serialized representation.
from_dict(d)	Static constructor from dictionary representation.
from_json(serialized)	Instantiate an object from a JSON serialized representation.
from_messagepack(serialized)	Instantiate an object from a MessagePack serialized representation.
from_pickle(serialized)	Instantiate an object from a pickle serialized representation.
from_toml(serialized)	Instantiate an object from a TOML serialized representation.
from_xml(serialized)	Instantiate an object from an XML serialized representation.
from_yaml(serialized)	Instantiate from a YAML serialized representation.
to_bson()	Return a BSON serialized representation.
to_dict()	Convert to dictionary representation.
to_json([indent])	Return a JSON serialized representation.
to_messagepack()	Return a MessagePack representation.
to_pickle()	Return a pickle serialized representation.
to_toml()	Return a TOML serialized representation.
to_xml([indent])	Return an XML representation.
to_yaml()	Return a YAML serialized representation.

__init__(atom, topology_molecule)

Create a new TopologyAtom.

Parameters

atomAn openforcefield.topology.molecule.Atom

The reference atom

topology_moleculeAn openforcefield.topology.TopologyMolecule

The TopologyMolecule that this TopologyAtom belongs to

Methods

__init__(atom, topology_molecule)	Create a new TopologyAtom.
from_bson(serialized)	Instantiate an object from a BSON serialized representation.
from_dict(d)	Static constructor from dictionary representation.
from_json(serialized)	Instantiate an object from a JSON serialized representation.
from_messagepack(serialized)	Instantiate an object from a MessagePack serialized representation.
from_pickle(serialized)	Instantiate an object from a pickle serialized representation.
from_toml(serialized)	Instantiate an object from a TOML serialized representation.
from_xml(serialized)	Instantiate an object from an XML serialized representation.
from_yaml(serialized)	Instantiate from a YAML serialized representation.
to_bson()	Return a BSON serialized representation.
to_dict()	Convert to dictionary representation.
to_json([indent])	Return a JSON serialized representation.
to_messagepack()	Return a MessagePack representation.
to_pickle()	Return a pickle serialized representation.
to_toml()	Return a TOML serialized representation.
to_xml([indent])	Return an XML representation.
to_yaml()	Return a YAML serialized representation.

Attributes

atom	Get the reference Atom for this TopologyAtom.
atomic_number	Get the atomic number of this atom
molecule	Get the reference Molecule that this TopologyAtom belongs to.
topology_atom_index	Get the index of this atom in its parent Topology.
topology_bonds	Get the TopologyBonds connected to this TopologyAtom.
topology_molecule	Get the TopologyMolecule that this TopologyAtom belongs to.
topology_particle_index	Get the index of this particle in its parent Topology.