openforcefield.topology.TopologyAtom¶
-
class
openforcefield.topology.
TopologyAtom
(atom, topology_molecule)[source]¶ A TopologyAtom is a lightweight data structure that represents a single openforcefield.topology.molecule.Atom in a Topology. A TopologyAtom consists of two references – One to its fully detailed “atom”, an openforcefield.topology.molecule.Atom, 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 TopologyAtom. They are created on demand as the user requests them.
Warning
This API is experimental and subject to change.
- Attributes
atom
Get the reference Atom for this TopologyAtom.
atomic_number
Get the atomic number of this atom
molecule
Get the reference Molecule that this TopologyAtom belongs to.
topology_atom_index
Get the index of this atom in its parent Topology.
topology_bonds
Get the TopologyBonds connected to this TopologyAtom.
topology_molecule
Get the TopologyMolecule that this TopologyAtom belongs to.
topology_particle_index
Get the index of this particle in its parent Topology.
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.
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__
(atom, topology_molecule)[source]¶ Create a new TopologyAtom.
- Parameters
- atomAn openforcefield.topology.molecule.Atom
The reference atom
- topology_moleculeAn openforcefield.topology.TopologyMolecule
The TopologyMolecule that this TopologyAtom belongs to
Methods
__init__
(atom, topology_molecule)Create a new TopologyAtom.
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
atom
Get the reference Atom for this TopologyAtom.
atomic_number
Get the atomic number of this atom
molecule
Get the reference Molecule that this TopologyAtom belongs to.
topology_atom_index
Get the index of this atom in its parent Topology.
topology_bonds
Get the TopologyBonds connected to this TopologyAtom.
topology_molecule
Get the TopologyMolecule that this TopologyAtom belongs to.
topology_particle_index
Get the index of this particle in its parent Topology.