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.
Return a MessagePack representation.
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.
Return a MessagePack representation.
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
The
Molecule
this particle is part of.Returns the index of this particle in its molecule
The name of the particle
orientation
virtual_site
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