openff.toolkit.topology.TopologyAtom
- class openff.toolkit.topology.TopologyAtom(atom, topology_molecule)[source]
A TopologyAtom is a lightweight data structure that represents a single openff.toolkit.topology.molecule.Atom in a Topology. A TopologyAtom consists of two references – One to its fully detailed “atom”, an openff.toolkit.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.
- __init__(atom, topology_molecule)[source]
Create a new TopologyAtom.
- Parameters
atom (An openff.toolkit.topology.molecule.Atom) – The reference atom
topology_molecule (An openff.toolkit.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.
Return a MessagePack representation.
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
Get the reference Atom for this TopologyAtom.
Get the atomic number of this atom
Get the element name of this atom.
Get the reference Molecule that this TopologyAtom belongs to.
Get the index of this atom in its parent Topology.
Get the TopologyBonds connected to this TopologyAtom.
Get the TopologyMolecule that this TopologyAtom belongs to.
Get the index of this particle in its parent Topology.
- property atom
Get the reference Atom for this TopologyAtom.
- Returns
an openff.toolkit.topology.molecule.Atom
- property topology_molecule
Get the TopologyMolecule that this TopologyAtom belongs to.
- Returns
openff.toolkit.topology.TopologyMolecule
- property molecule
Get the reference Molecule that this TopologyAtom belongs to.
- Returns
openff.toolkit.topology.molecule.Molecule
- property topology_atom_index
Get the index of this atom in its parent Topology.
- Returns
int – The index of this atom in its parent topology.
- property topology_particle_index
Get the index of this particle in its parent Topology.
- Returns
int – The index of this atom in its parent topology.
- property topology_bonds
Get the TopologyBonds connected to this TopologyAtom.
- Returns
iterator of openff.toolkit.topology.TopologyBonds
- to_dict()[source]
Convert to dictionary representation.
- classmethod from_dict(d)[source]
Static constructor from dictionary representation.
- classmethod from_bson(serialized)
Instantiate an object from a BSON serialized representation.
Specification: http://bsonspec.org/
- Parameters
serialized (bytes) – A BSON serialized representation of the object
- Returns
instance (cls) – An instantiated object
- classmethod from_json(serialized)
Instantiate an object from a JSON serialized representation.
Specification: https://www.json.org/
- Parameters
serialized (str) – A JSON serialized representation of the object
- Returns
instance (cls) – An instantiated object
- classmethod from_messagepack(serialized)
Instantiate an object from a MessagePack serialized representation.
Specification: https://msgpack.org/index.html
- Parameters
serialized (bytes) – A MessagePack-encoded bytes serialized representation
- Returns
instance (cls) – Instantiated object.
- classmethod from_pickle(serialized)
Instantiate an object from a pickle serialized representation.
Warning
This is not recommended for safe, stable storage since the pickle specification may change between Python versions.
- Parameters
serialized (str) – A pickled representation of the object
- Returns
instance (cls) – An instantiated object
- classmethod from_toml(serialized)
Instantiate an object from a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
- Parameters
serlialized (str) – A TOML serialized representation of the object
- Returns
instance (cls) – An instantiated object
- classmethod from_xml(serialized)
Instantiate an object from an XML serialized representation.
Specification: https://www.w3.org/XML/
- Parameters
serialized (bytes) – An XML serialized representation
- Returns
instance (cls) – Instantiated object.
- classmethod from_yaml(serialized)
Instantiate from a YAML serialized representation.
Specification: http://yaml.org/
- Parameters
serialized (str) – A YAML serialized representation of the object
- Returns
instance (cls) – Instantiated object
- to_bson()
Return a BSON serialized representation.
Specification: http://bsonspec.org/
- Returns
serialized (bytes) – A BSON serialized representation of the objecft
- to_json(indent=None)
Return a JSON serialized representation.
Specification: https://www.json.org/
- Parameters
indent (int, optional, default=None) – If not None, will pretty-print with specified number of spaces for indentation
- Returns
serialized (str) – A JSON serialized representation of the object
- to_messagepack()
Return a MessagePack representation.
Specification: https://msgpack.org/index.html
- Returns
serialized (bytes) – A MessagePack-encoded bytes serialized representation of the object
- to_pickle()
Return a pickle serialized representation.
Warning
This is not recommended for safe, stable storage since the pickle specification may change between Python versions.
- Returns
serialized (str) – A pickled representation of the object
- to_toml()
Return a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
- Returns
serialized (str) – A TOML serialized representation of the object
- to_xml(indent=2)
Return an XML representation.
Specification: https://www.w3.org/XML/
- Parameters
indent (int, optional, default=2) – If not None, will pretty-print with specified number of spaces for indentation
- Returns
serialized (bytes) – A MessagePack-encoded bytes serialized representation.
- to_yaml()
Return a YAML serialized representation.
Specification: http://yaml.org/
- Returns
serialized (str) – A YAML serialized representation of the object