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.
topology_molecule
Get the TopologyMolecule that this TopologyVirtualSite belongs to.
topology_particle_index
Get the index of this 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.
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__
(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.
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
atoms
Get the TopologyAtoms involved in this TopologyVirtualSite.
molecule
Get the reference Molecule that this TopologyVirtualSite belongs to.
topology_molecule
Get the TopologyMolecule that this TopologyVirtualSite belongs to.
topology_particle_index
Get the index of this 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.