openforcefield.topology.TopologyVirtualSite

class openforcefield.topology.TopologyVirtualSite(virtual_site, topology_molecule)

A TopologyVirtualSite is a lightweight data structure that represents a single openforcefield.topology.molecule.VirtualSite in a Topology. A TopologyVirtualSite consists of two references – One to its fully detailed “VirtualSite”, an openforcefield.topology.molecule.VirtualSite, 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 TopologyVirtualSite. They are created on demand as the user requests them.

Warning

This API is experimental and subject to change.

Attributes

atoms

Get the TopologyAtoms involved in this TopologyVirtualSite.

molecule

Get the reference Molecule that this TopologyVirtualSite belongs to.

topology_molecule

Get the TopologyMolecule that this TopologyVirtualSite belongs to.

topology_particle_index

Get the index of this particle in its parent Topology.

topology_virtual_site_index

Get the index of this virtual site in its parent Topology.

type

Get the type of this virtual site

virtual_site

Get the reference VirtualSite for this TopologyVirtualSite.

Methods

atom(index)	Get the atom at a specific index in this TopologyVirtualSite
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__(virtual_site, topology_molecule)

Parameters

virtual_siteAn openforcefield.topology.molecule.VirtualSite

The reference virtual site

topology_moleculeAn openforcefield.topology.TopologyMolecule

The TopologyMolecule that this TopologyVirtualSite belongs to

Methods

__init__(virtual_site, topology_molecule)	Parameters
atom(index)	Get the atom at a specific index in this TopologyVirtualSite
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 involved in this TopologyVirtualSite.
molecule	Get the reference Molecule that this TopologyVirtualSite belongs to.
topology_molecule	Get the TopologyMolecule that this TopologyVirtualSite belongs to.
topology_particle_index	Get the index of this particle in its parent Topology.
topology_virtual_site_index	Get the index of this virtual site in its parent Topology.
type	Get the type of this virtual site
virtual_site	Get the reference VirtualSite for this TopologyVirtualSite.