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`(self)	Return a BSON serialized representation.
`to_dict`(self)	Convert to dictionary representation.
`to_json`(self[, indent])	Return a JSON serialized representation.
`to_messagepack`(self)	Return a MessagePack representation.
`to_pickle`(self)	Return a pickle serialized representation.
`to_toml`(self)	Return a TOML serialized representation.
`to_xml`(self[, indent])	Return an XML representation.
`to_yaml`(self)	Return a YAML serialized representation.

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

Methods

`__init__`(self, /, \args, \\*kwargs)	Initialize self.
`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`(self)	Return a BSON serialized representation.
`to_dict`(self)	Convert to dictionary representation.
`to_json`(self[, indent])	Return a JSON serialized representation.
`to_messagepack`(self)	Return a MessagePack representation.
`to_pickle`(self)	Return a pickle serialized representation.
`to_toml`(self)	Return a TOML serialized representation.
`to_xml`(self[, indent])	Return an XML representation.
`to_yaml`(self)	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

property molecule¶: The Molecule this atom is part of.

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

property name¶: The name of the particle

to_dict(self)[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(self)¶

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns

serializedbytes: A BSON serialized representation of the objecft

to_json(self, 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(self)¶

Return a MessagePack representation.

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

Returns

serializedbytes: A MessagePack-encoded bytes serialized representation of the object

to_pickle(self)¶

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(self)¶

Return a TOML serialized representation.

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

Returns

serializedstr: A TOML serialized representation of the object

to_xml(self, 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(self)¶

Return a YAML serialized representation.

Specification: http://yaml.org/

Returns

serializedstr: A YAML serialized representation of the object