openforcefield.topology.TopologyVirtualSite

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

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.

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.

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.

invalidate_cached_data

__init__(virtual_site, topology_molecule)[source]
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.

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

atoms

Get the TopologyAtoms involved in this TopologyVirtualSite.

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.

atom(index)[source]

Get the atom at a specific index in this TopologyVirtualSite

Parameters
indexint

The index of the atom in the reference VirtualSite to retrieve

Returns
TopologyAtom
property atoms

Get the TopologyAtoms involved in this TopologyVirtualSite.

Returns
iterator of openforcefield.topology.TopologyAtom
property virtual_site

Get the reference VirtualSite for this TopologyVirtualSite.

Returns
an openforcefield.topology.molecule.VirtualSite
property topology_molecule

Get the TopologyMolecule that this TopologyVirtualSite belongs to.

Returns
openforcefield.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
intThe 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
openforcefield.topology.molecule.Molecule
property type

Get the type of this virtual site

Returns
strThe 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
serializedbytes

A BSON serialized representation of the object

Returns
instancecls

An instantiated object

classmethod from_json(serialized)

Instantiate an object from a JSON serialized representation.

Specification: https://www.json.org/

Parameters
serializedstr

A JSON serialized representation of the object

Returns
instancecls

An instantiated object

classmethod from_messagepack(serialized)

Instantiate an object from a MessagePack serialized representation.

Specification: https://msgpack.org/index.html

Parameters
serializedbytes

A MessagePack-encoded bytes serialized representation

Returns
instancecls

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
serializedstr

A pickled representation of the object

Returns
instancecls

An instantiated object

classmethod from_toml(serialized)

Instantiate an object from a TOML serialized representation.

Specification: https://github.com/toml-lang/toml

Parameters
serlializedstr

A TOML serialized representation of the object

Returns
instancecls

An instantiated object

classmethod from_xml(serialized)

Instantiate an object from an XML serialized representation.

Specification: https://www.w3.org/XML/

Parameters
serializedbytes

An XML serialized representation

Returns
instancecls

Instantiated object.

classmethod from_yaml(serialized)

Instantiate from a YAML serialized representation.

Specification: http://yaml.org/

Parameters
serializedstr

A YAML serialized representation of the object

Returns
instancecls

Instantiated object

to_bson()

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns
serializedbytes

A BSON serialized representation of the objecft

to_json(indent=None)

Return a JSON serialized representation.

Specification: https://www.json.org/

Parameters
indentint, optional, default=None

If not None, will pretty-print with specified number of spaces for indentation

Returns
serializedstr

A JSON serialized representation of the object

to_messagepack()

Return a MessagePack representation.

Specification: https://msgpack.org/index.html

Returns
serializedbytes

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
serializedstr

A pickled representation of the object

to_toml()

Return a TOML serialized representation.

Specification: https://github.com/toml-lang/toml

Returns
serializedstr

A TOML serialized representation of the object

to_xml(indent=2)

Return an XML representation.

Specification: https://www.w3.org/XML/

Parameters
indentint, optional, default=2

If not None, will pretty-print with specified number of spaces for indentation

Returns
serializedbytes

A MessagePack-encoded bytes serialized representation.

to_yaml()

Return a YAML serialized representation.

Specification: http://yaml.org/

Returns
serializedstr

A YAML serialized representation of the object