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.
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
|
Instantiate an object from a BSON serialized representation. |
|
Static constructor from dictionary representation. |
|
Instantiate an object from a JSON serialized representation. |
|
Instantiate an object from a MessagePack serialized representation. |
|
Instantiate an object from a pickle serialized representation. |
|
Instantiate an object from a TOML serialized representation. |
|
Instantiate an object from an XML serialized representation. |
|
Instantiate from a YAML serialized representation. |
|
Return a BSON serialized representation. |
|
Convert to dictionary representation. |
|
Return a JSON serialized representation. |
|
Return a MessagePack representation. |
|
Return a pickle serialized representation. |
|
Return a TOML serialized representation. |
|
Return an XML representation. |
|
Return a YAML serialized representation. |
__init__
(self, /, *args, **kwargs)¶Initialize self. See help(type(self)) for accurate signature.
Methods
|
Instantiate an object from a BSON serialized representation. |
|
Static constructor from dictionary representation. |
|
Instantiate an object from a JSON serialized representation. |
|
Instantiate an object from a MessagePack serialized representation. |
|
Instantiate an object from a pickle serialized representation. |
|
Instantiate an object from a TOML serialized representation. |
|
Instantiate an object from an XML serialized representation. |
|
Instantiate from a YAML serialized representation. |
|
Return a BSON serialized representation. |
|
Convert to dictionary representation. |
|
Return a JSON serialized representation. |
|
Return a MessagePack representation. |
|
Return a pickle serialized representation. |
|
Return a TOML serialized representation. |
|
Return an XML representation. |
|
Return a YAML serialized representation. |
Attributes
The |
|
Returns the index of this particle in its molecule |
|
The name of the particle |
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
from_bson
(serialized)¶Instantiate an object from a BSON serialized representation.
Specification: http://bsonspec.org/
A BSON serialized representation of the object
An instantiated object
from_json
(serialized)¶Instantiate an object from a JSON serialized representation.
Specification: https://www.json.org/
A JSON serialized representation of the object
An instantiated object
from_messagepack
(serialized)¶Instantiate an object from a MessagePack serialized representation.
Specification: https://msgpack.org/index.html
A MessagePack-encoded bytes serialized representation
Instantiated object.
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.
A pickled representation of the object
An instantiated object
from_toml
(serialized)¶Instantiate an object from a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
A TOML serialized representation of the object
An instantiated object
from_xml
(serialized)¶Instantiate an object from an XML serialized representation.
Specification: https://www.w3.org/XML/
An XML serialized representation
Instantiated object.
from_yaml
(serialized)¶Instantiate from a YAML serialized representation.
Specification: http://yaml.org/
A YAML serialized representation of the object
Instantiated object
to_bson
(self)¶Return a BSON serialized representation.
Specification: http://bsonspec.org/
A BSON serialized representation of the objecft
to_json
(self, indent=None)¶Return a JSON serialized representation.
Specification: https://www.json.org/
If not None, will pretty-print with specified number of spaces for indentation
A JSON serialized representation of the object
to_messagepack
(self)¶Return a MessagePack representation.
Specification: https://msgpack.org/index.html
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.
A pickled representation of the object
to_toml
(self)¶Return a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
A TOML serialized representation of the object
to_xml
(self, indent=2)¶Return an XML representation.
Specification: https://www.w3.org/XML/
If not None, will pretty-print with specified number of spaces for indentation
A MessagePack-encoded bytes serialized representation.
to_yaml
(self)¶Return a YAML serialized representation.
Specification: http://yaml.org/
A YAML serialized representation of the object