openforcefield.topology.Particle¶

class openforcefield.topology.Particle[source]¶

Base class for all particles in a molecule.

A particle object could be an Atom or a VirtualSite.

Warning

This API is experimental and subject to change.

Attributes:	`molecule` The `Molecule` this atom is part of. `molecule_particle_index` Returns the index of this particle in its molecule `name` The name of the particle

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__($self, /, *args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

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.

Attributes

`molecule`	The `Molecule` this atom is part of.
`molecule_particle_index`	Returns the index of this particle in its molecule
`name`	The name of the particle

molecule¶

The Molecule this atom is part of.

Todo

Should we have a single unique Molecule for each molecule type in the system,

or if we have multiple copies of the same molecule, should we have multiple ``Molecule``s?

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

name¶: The name of the particle

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