openforcefield.topology.TopologyVirtualSite¶
-
class
openforcefield.topology.
TopologyVirtualSite
(virtual_site, topology_molecule)[source]¶ A TopologyVirtualSite is a lightweight data structure that represents a single openforcefield.topology.molecule.VirtualSite in a Topology. A TopologyVirtualSite consists of two references – One to its fully detailed “VirtualSite”, an openforcefield.topology.molecule.VirtualSite, and another to its parent “topology_molecule”, which occupies a spot in the parent Topology’s TopologyMolecule list.
As some systems can be very large, there is no always-existing representation of a TopologyVirtualSite. They are created on demand as the user requests them.
Warning
This API is experimental and subject to change.
- Attributes
atoms
Get the TopologyAtoms involved in this TopologyVirtualSite.
molecule
Get the reference Molecule that this TopologyVirtualSite belongs to.
n_particles
Get the number of particles represented by this VirtualSite
particles
Get an iterator to the reference particles that this TopologyVirtualSite contains.
topology_molecule
Get the TopologyMolecule that this TopologyVirtualSite belongs to.
topology_virtual_particle_start_index
Get the index of the first virtual site particle in its parent Topology.
topology_virtual_site_index
Get the index of this virtual site in its parent Topology.
type
Get the type of this virtual site
virtual_site
Get the reference VirtualSite for this TopologyVirtualSite.
Methods
atom
(index)Get the atom at a specific index in this TopologyVirtualSite
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.
invalidate_cached_data
-
__init__
(virtual_site, topology_molecule)[source]¶ - Parameters
- virtual_siteAn openforcefield.topology.molecule.VirtualSite
The reference virtual site
- topology_moleculeAn openforcefield.topology.TopologyMolecule
The TopologyMolecule that this TopologyVirtualSite belongs to
Methods
__init__
(virtual_site, topology_molecule)- Parameters
atom
(index)Get the atom at a specific index in this TopologyVirtualSite
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.
invalidate_cached_data
()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
Get the TopologyAtoms involved in this TopologyVirtualSite.
Get the reference Molecule that this TopologyVirtualSite belongs to.
Get the number of particles represented by this VirtualSite
Get an iterator to the reference particles that this TopologyVirtualSite contains.
Get the TopologyMolecule that this TopologyVirtualSite belongs to.
Get the index of the first virtual site particle in its parent Topology.
Get the index of this virtual site in its parent Topology.
Get the type of this virtual site
Get the reference VirtualSite for this TopologyVirtualSite.
-
atom
(index)[source]¶ Get the atom at a specific index in this TopologyVirtualSite
- Parameters
- indexint
The index of the atom in the reference VirtualSite to retrieve
- Returns
- TopologyAtom
-
property
atoms
¶ Get the TopologyAtoms involved in this TopologyVirtualSite.
- Returns
- iterator of openforcefield.topology.TopologyAtom
-
property
virtual_site
¶ Get the reference VirtualSite for this TopologyVirtualSite.
- Returns
- an openforcefield.topology.molecule.VirtualSite
-
property
topology_molecule
¶ Get the TopologyMolecule that this TopologyVirtualSite belongs to.
- Returns
- openforcefield.topology.TopologyMolecule
-
property
topology_virtual_site_index
¶ Get the index of this virtual site in its parent Topology.
- Returns
- int
The index of this virtual site in its parent topology.
-
property
n_particles
¶ Get the number of particles represented by this VirtualSite
- Returns
- intThe number of particles
-
property
topology_virtual_particle_start_index
¶ Get the index of the first virtual site particle in its parent Topology.
- Returns
- int
The index of this particle in its parent topology.
-
property
particles
¶ Get an iterator to the reference particles that this TopologyVirtualSite contains.
- Returns
- iterator of TopologyVirtualParticles
-
property
molecule
¶ Get the reference Molecule that this TopologyVirtualSite belongs to.
- Returns
- openforcefield.topology.molecule.Molecule
-
property
type
¶ Get the type of this virtual site
- Returns
- strThe class name of this virtual site
-
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
()¶ Return a BSON serialized representation.
Specification: http://bsonspec.org/
- Returns
- serializedbytes
A BSON serialized representation of the objecft
-
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