openforcefield.topology.VirtualParticle

class openforcefield.topology.VirtualParticle(vsite, orientation, name=None)[source]

A single particle owned by a VirtualSite

Warning

This API is experimental and subject to change.

Attributes
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.

Methods

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.

__init__(vsite, orientation, name=None)[source]

A single particle owned by a VirtualSite

Parameters
vsiteopenforcefield.topology.VirtualSite

The parent VirtualSite of this VirtualParticle

orientationtuple of int

Molecule atom indices of parent atoms

namestr, optional

The name of the particle

Methods

__init__(vsite, orientation[, name])

A single particle owned by a VirtualSite

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

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 virtual_site_particle_index

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

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_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
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

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
serializedbytes

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
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