openff.toolkit.topology.VirtualParticle
- class openff.toolkit.topology.VirtualParticle(vsite, orientation, name=None)[source]
A single particle owned by a VirtualSite
Warning
This API is experimental and subject to change.
- __init__(vsite, orientation, name=None)[source]
A single particle owned by a VirtualSite
- Parameters
vsite (openff.toolkit.topology.VirtualSite) – The parent VirtualSite of this VirtualParticle
orientation (tuple of int) – Molecule atom indices of parent atoms
name (str, optional) – The name of the particle
Methods
__init__
(vsite, orientation[, name])A single particle owned by a VirtualSite
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.
Return a MessagePack representation.
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
The
Molecule
this particle is part of.Returns the index of this particle in its molecule
The name of the particle
orientation
virtual_site
The index of the particle relative to its owning virtual site.
- property virtual_site_particle_index
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 anumpy.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 anumpy.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_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