openff.toolkit.topology.TopologyVirtualParticle

class openff.toolkit.topology.TopologyVirtualParticle(virtual_site, virtual_particle, topology_molecule, topology_virtual_site)[source]

__init__(virtual_site, virtual_particle, topology_molecule, topology_virtual_site)[source]

Methods

`__init__`(virtual_site, virtual_particle, ...)
`atom`(index)	Get the atom at a specific index in this TopologyVirtualParticle
`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 TopologyVirtualParticle.
`molecule`	Get the reference Molecule that this TopologyVirtualParticle belongs to.
`topology_molecule`	Get the TopologyMolecule that this TopologyVirtualSite belongs to.
`topology_parent_atom_index`	Returns the index of the 'parent' atom as determined by the virtual site type in the topology.
`topology_particle_index`	Get the index of this particle in its parent Topology.
`type`	Get the type of this virtual site
`virtual_particle`	Get the reference VirtualParticle for this TopologyVirtualParticle.
`virtual_site`	Get the reference VirtualSite for this TopologyVirtualSite.

property molecule

Get the reference Molecule that this TopologyVirtualParticle belongs to.

Returns: openff.toolkit.topology.molecule.Molecule

property virtual_site

Get the reference VirtualSite for this TopologyVirtualSite.

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

property virtual_particle

Get the reference VirtualParticle for this TopologyVirtualParticle.

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

property type

Get the type of this virtual site

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

atom(index)[source]

Get the atom at a specific index in this TopologyVirtualParticle

Parameters: index (int) – The index of the atom in the reference VirtualParticle to retrieve
Returns: TopologyAtom

property atoms: Get the TopologyAtoms involved in this TopologyVirtualParticle. :returns: iterator of openff.toolkit.topology.TopologyAtom

property topology_molecule

Get the TopologyMolecule that this TopologyVirtualSite belongs to.

Returns: openff.toolkit.topology.TopologyMolecule

property topology_particle_index

Get the index of this particle in its parent Topology.

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

property topology_parent_atom_index: int: Returns the index of the ‘parent’ atom as determined by the virtual site type in the topology.

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