openff.toolkit.topology.TopologyVirtualSite

class openff.toolkit.topology.TopologyVirtualSite(virtual_site, topology_molecule)[source]

A TopologyVirtualSite is a lightweight data structure that represents a single openff.toolkit.topology.molecule.VirtualSite in a Topology.

A TopologyVirtualSite consists of two references – One to its fully detailed “VirtualSite”, an openff.toolkit.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.

__init__(virtual_site, topology_molecule)[source]

Parameters

virtual_site (An openff.toolkit.topology.molecule.VirtualSite) – The reference virtual site
topology_molecule (An openff.toolkit.topology.TopologyMolecule) – The TopologyMolecule that this TopologyVirtualSite belongs to

Methods

`__init__`(virtual_site, topology_molecule)	param virtual_site The reference virtual site
`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.
`invalidate_cached_data`()
`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

`molecule`	Get the reference Molecule that this TopologyVirtualSite belongs to.
`n_particles`	Get the number of particles represented by this VirtualSite
`particles`	Get an iterator to the reference particles that this TopologyVirtualSite contains.
`topology_molecule`	Get the TopologyMolecule that this TopologyVirtualSite belongs to.
`topology_virtual_particle_start_index`	Get the index of the first virtual site 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.

property virtual_site

Get the reference VirtualSite for this TopologyVirtualSite.

Returns: an openff.toolkit.topology.molecule.VirtualSite

property topology_molecule

Get the TopologyMolecule that this TopologyVirtualSite belongs to.

Returns: openff.toolkit.topology.TopologyMolecule

property topology_virtual_site_index

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

Returns: int – The index of this virtual site in its parent topology.

property n_particles

Get the number of particles represented by this VirtualSite

Returns: int (The number of particles)

property topology_virtual_particle_start_index

Get the index of the first virtual site particle in its parent Topology.

Returns: int – The index of this particle in its parent topology.

property particles

Get an iterator to the reference particles that this TopologyVirtualSite contains.

Returns: iterator of TopologyVirtualParticles

property molecule

Get the reference Molecule that this TopologyVirtualSite belongs to.

Returns: openff.toolkit.topology.molecule.Molecule

property type

Get the type of this virtual site

Returns: str (The class name of this virtual site)

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