openforcefield.topology.TopologyBond

class openforcefield.topology.TopologyBond(bond, topology_molecule)

A TopologyBond is a lightweight data structure that represents a single openforcefield.topology.molecule.Bond in a Topology. A TopologyBond consists of two references – One to its fully detailed “bond”, an openforcefield.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.

Attributes

atoms

Get the TopologyAtoms connected to this TopologyBond.

bond

Get the reference Bond for this TopologyBond.

bond_order

Get the order of this TopologyBond.

molecule

Get the reference Molecule that this TopologyBond belongs to.

topology_bond_index

Get the index of this bond in its parent Topology.

topology_molecule

Get the TopologyMolecule that this TopologyBond belongs to.

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__(bond, topology_molecule)

Parameters

bondAn openforcefield.topology.molecule.Bond

The reference bond.

topology_moleculeAn openforcefield.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.
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

atoms	Get the TopologyAtoms connected to this TopologyBond.
bond	Get the reference Bond for this TopologyBond.
bond_order	Get the order of this TopologyBond.
molecule	Get the reference Molecule that this TopologyBond belongs to.
topology_bond_index	Get the index of this bond in its parent Topology.
topology_molecule	Get the TopologyMolecule that this TopologyBond belongs to.