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(self)

Return a BSON serialized representation.

to_dict(self)

Convert to dictionary representation.

to_json(self[, indent])

Return a JSON serialized representation.

to_messagepack(self)

Return a MessagePack representation.

to_pickle(self)

Return a pickle serialized representation.

to_toml(self)

Return a TOML serialized representation.

to_xml(self[, indent])

Return an XML representation.

to_yaml(self)

Return a YAML serialized representation.

__init__(self, 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__(self, 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(self)

Return a BSON serialized representation.

to_dict(self)

Convert to dictionary representation.

to_json(self[, indent])

Return a JSON serialized representation.

to_messagepack(self)

Return a MessagePack representation.

to_pickle(self)

Return a pickle serialized representation.

to_toml(self)

Return a TOML serialized representation.

to_xml(self[, indent])

Return an XML representation.

to_yaml(self)

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.

property atom

Get the reference Atom for this TopologyAtom.

Returns
an openforcefield.topology.molecule.Atom
property atomic_number

Get the atomic number of this atom

Returns
int
property topology_molecule

Get the TopologyMolecule that this TopologyAtom belongs to.

Returns
openforcefield.topology.TopologyMolecule
property molecule

Get the reference Molecule that this TopologyAtom belongs to.

Returns
openforcefield.topology.molecule.Molecule
property topology_atom_index

Get the index of this atom in its parent Topology.

Returns
int

The index of this atom in its parent topology.

property topology_particle_index

Get the index of this particle in its parent Topology.

Returns
int

The index of this atom in its parent topology.

property topology_bonds

Get the TopologyBonds connected to this TopologyAtom.

Returns
iterator of openforcefield.topology.TopologyBonds
to_dict(self)[source]

Convert to dictionary representation.

classmethod from_dict(d)[source]

Static constructor from dictionary representation.

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(self)

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns
serializedbytes

A BSON serialized representation of the objecft

to_json(self, 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(self)

Return a MessagePack representation.

Specification: https://msgpack.org/index.html

Returns
serializedbytes

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.

Returns
serializedstr

A pickled representation of the object

to_toml(self)

Return a TOML serialized representation.

Specification: https://github.com/toml-lang/toml

Returns
serializedstr

A TOML serialized representation of the object

to_xml(self, 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(self)

Return a YAML serialized representation.

Specification: http://yaml.org/

Returns
serializedstr

A YAML serialized representation of the object