openff.toolkit.topology.VirtualParticle

class openff.toolkit.topology.VirtualParticle(vsite: VirtualSite, orientation: Tuple[int, ...], name: str)[source]

A single particle owned by a VirtualSite

Warning

This API is experimental and subject to change.

__init__(vsite: VirtualSite, orientation: Tuple[int, ...], name: str)[source]

A single particle owned by a VirtualSite

Parameters

vsite – The parent VirtualSite of this VirtualParticle
orientation – Molecule atom indices of parent atoms
name – The name of the particle

Methods

`__init__`(vsite, orientation, name)	A single particle owned by a VirtualSite
`compute_position_from_atom_positions`(...)	Compute the position of this virtual site particle given a set of coordinates.
`compute_position_from_conformer`(conformer_idx)	Compute the position of this virtual particle given an existing conformer owned by the parent molecule/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.
`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`	Atoms on whose position this VirtualParticle depends
`molecule`	The `Molecule` this particle is part of.
`molecule_particle_index`	Returns the index of this particle in its molecule
`name`	The name of the particle
`orientation`
`virtual_site`
`virtual_site_particle_index`	The index of the particle relative to its owning virtual site.

property atoms: List[openff.toolkit.topology.molecule.Atom]: Atoms on whose position this VirtualParticle depends

property virtual_site_particle_index: int: The index of the particle relative to its owning virtual site. Normally this should either be 0 or 1.

compute_position_from_conformer(conformer_idx)[source]

Compute the position of this virtual particle given an existing conformer owned by the parent molecule/virtual site.

Parameters

conformer_idx (int) – The index of the conformer in the owning molecule.

Returns

openmm.unit.Quantity of dimension [Length] in unit Angstroms wrapping a
numpy.ndarray – The positions of the virtual particles belonging to this virtual site. The array is the size (M, 3) where M is the number of virtual particles belonging to this virtual site.

compute_position_from_atom_positions(atom_positions)[source]

Compute the position of this virtual site particle given a set of coordinates.

Parameters

atom_positions (openmm.unit.Quantity of dimension [Length] wrapping a) –
numpy.ndarray – The positions of all atoms in the molecule. The array is the size (N, 3) where N is the number of atoms in the molecule.

Returns

openmm.unit.Quantity of dimension [Length] in unit Angstroms wrapping a
numpy.ndarray – The positions of the virtual particles belonging to this virtual site. The array is the size (M, 3) where M is the number of virtual particles belonging to this virtual site.

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_dict(d): Static constructor from dictionary representation.

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

property molecule: The Molecule this particle is part of.

property molecule_particle_index: Returns the index of this particle in its molecule

property name: The name of the particle

to_bson()

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns: serialized (bytes) – A BSON serialized representation of the objecft

to_dict(): Convert to dictionary representation.

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