openff.toolkit.topology.TopologyBond
- class openff.toolkit.topology.TopologyBond(bond, topology_molecule)[source]
A TopologyBond is a lightweight data structure that represents a single openff.toolkit.topology.molecule.Bond in a Topology. A TopologyBond consists of two references – One to its fully detailed “bond”, an openff.toolkit.topology.molecule.Bond, 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 TopologyBond. They are created on demand as the user requests them.
Warning
This API is experimental and subject to change.
- __init__(bond, topology_molecule)[source]
- Parameters
- bondAn openff.toolkit.topology.molecule.Bond
The reference bond.
- topology_moleculeAn openff.toolkit.topology.TopologyMolecule
The TopologyMolecule that this TopologyBond belongs to.
Methods
__init__
(bond, topology_molecule)- Parameters
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 TopologyAtoms connected to this TopologyBond.
Get the reference Bond for this TopologyBond.
Get the order of this TopologyBond.
Get the reference Molecule that this TopologyBond belongs to.
Get the index of this bond in its parent Topology.
Get the TopologyMolecule that this TopologyBond belongs to.
- property bond
Get the reference Bond for this TopologyBond.
- Returns
- an openff.toolkit.topology.molecule.Bond
- property topology_molecule
Get the TopologyMolecule that this TopologyBond belongs to.
- Returns
- openff.toolkit.topology.TopologyMolecule
- property topology_bond_index
Get the index of this bond in its parent Topology.
- Returns
- int
The index of this bond in its parent topology.
- property molecule
Get the reference Molecule that this TopologyBond belongs to.
- Returns
- openff.toolkit.topology.molecule.Molecule
- property atoms
Get the TopologyAtoms connected to this TopologyBond.
- Returns
- iterator of openff.toolkit.topology.TopologyAtom
- 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
- serializedbytes
A BSON serialized representation of the object
- Returns
- instancecls
An instantiated object
- classmethod from_json(serialized)
Instantiate an object from a JSON serialized representation.
Specification: https://www.json.org/
- Parameters
- serializedstr
A JSON serialized representation of the object
- Returns
- instancecls
An instantiated object
- classmethod from_messagepack(serialized)
Instantiate an object from a MessagePack serialized representation.
Specification: https://msgpack.org/index.html
- Parameters
- serializedbytes
A MessagePack-encoded bytes serialized representation
- Returns
- instancecls
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
- serializedstr
A pickled representation of the object
- Returns
- instancecls
An instantiated object
- classmethod from_toml(serialized)
Instantiate an object from a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
- Parameters
- serlializedstr
A TOML serialized representation of the object
- Returns
- instancecls
An instantiated object
- classmethod from_xml(serialized)
Instantiate an object from an XML serialized representation.
Specification: https://www.w3.org/XML/
- Parameters
- serializedbytes
An XML serialized representation
- Returns
- instancecls
Instantiated object.
- classmethod from_yaml(serialized)
Instantiate from a YAML serialized representation.
Specification: http://yaml.org/
- Parameters
- serializedstr
A YAML serialized representation of the object
- Returns
- instancecls
Instantiated object
- to_bson()
Return a BSON serialized representation.
Specification: http://bsonspec.org/
- Returns
- serializedbytes
A BSON serialized representation of the objecft
- to_json(indent=None)
Return a JSON serialized representation.
Specification: https://www.json.org/
- Parameters
- indentint, optional, default=None
If not None, will pretty-print with specified number of spaces for indentation
- Returns
- serializedstr
A JSON serialized representation of the object
- to_messagepack()
Return a MessagePack representation.
Specification: https://msgpack.org/index.html
- Returns
- serializedbytes
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
- serializedstr
A pickled representation of the object
- to_toml()
Return a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
- Returns
- serializedstr
A TOML serialized representation of the object
- to_xml(indent=2)
Return an XML representation.
Specification: https://www.w3.org/XML/
- Parameters
- indentint, optional, default=2
If not None, will pretty-print with specified number of spaces for indentation
- Returns
- serializedbytes
A MessagePack-encoded bytes serialized representation.
- to_yaml()
Return a YAML serialized representation.
Specification: http://yaml.org/
- Returns
- serializedstr
A YAML serialized representation of the object