openff.toolkit.topology.Atom

class openff.toolkit.topology.Atom(atomic_number, formal_charge, is_aromatic, name=None, molecule=None, stereochemistry=None)[source]

A particle representing a chemical atom.

Note that non-chemical virtual sites are represented by the VirtualSite object.

Warning

This API is experimental and subject to change.

__init__(atomic_number, formal_charge, is_aromatic, name=None, molecule=None, stereochemistry=None)[source]

Create an immutable Atom object.

Object is serializable and immutable.

Parameters

atomic_number (int) – Atomic number of the atom
formal_charge (int or openmm.unit.Quantity-wrapped int with dimension "charge") – Formal charge of the atom
is_aromatic (bool) – If True, atom is aromatic; if False, not aromatic
stereochemistry (str, optional, default=None) – Either ‘R’ or ‘S’ for specified stereochemistry, or None for ambiguous stereochemistry
name (str, optional, default=None) – An optional name to be associated with the atom

Examples

Create a non-aromatic carbon atom

>>> atom = Atom(6, 0, False)

Create a chiral carbon atom

>>> atom = Atom(6, 0, False, stereochemistry='R', name='CT')

Methods

`__init__`(atomic_number, formal_charge, ...)	Create an immutable Atom object.
`add_bond`(bond)	Adds a bond that this atom is involved in .
`add_virtual_site`(vsite)	Adds a bond that this atom is involved in .
`from_bson`(serialized)	Instantiate an object from a BSON serialized representation.
`from_dict`(atom_dict)	Create an Atom from a dict 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.
`is_bonded_to`(atom2)	Determine whether this atom is bound to another atom
`is_in_ring`([toolkit_registry])	Return whether or not this atom is in a ring(s) (of any size)
`to_bson`()	Return a BSON serialized representation.
`to_dict`()	Return a dict representation of the atom.
`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

`atomic_number`	The integer atomic number of the atom.
`bonded_atoms`	The list of `Atom` objects this atom is involved in bonds with
`bonds`	The list of `Bond` objects this atom is involved in.
`element`	The element of this atom.
`formal_charge`	The atom's formal charge
`is_aromatic`	The atom's is_aromatic flag
`mass`	The standard atomic weight (abundance-weighted isotopic mass) of the atomic site.
`molecule`	The `Molecule` this particle is part of.
`molecule_atom_index`	The index of this Atom within the the list of atoms in `Molecules`.
`molecule_particle_index`	The index of this Atom within the the list of particles in the parent `Molecule`.
`name`	The name of this atom, if any
`partial_charge`	The partial charge of the atom, if any.
`stereochemistry`	The atom's stereochemistry (if defined, otherwise None)
`virtual_sites`	The list of `VirtualSite` objects this atom is involved in.

add_bond(bond)[source]

Adds a bond that this atom is involved in .. todo :: Is this how we want to keep records?

Parameters: bond (an openff.toolkit.topology.molecule.Bond) – A bond involving this atom

add_virtual_site(vsite)[source]

Adds a bond that this atom is involved in .. todo :: Is this how we want to keep records?

Parameters: bond (an openff.toolkit.topology.molecule.Bond) – A bond involving this atom

to_dict()[source]: Return a dict representation of the atom.

classmethod from_dict(atom_dict)[source]: Create an Atom from a dict representation.

property formal_charge: The atom’s formal charge

property partial_charge

The partial charge of the atom, if any.

Returns: openmm.unit.Quantity with dimension of atomic charge, or None if no charge has been specified

property is_aromatic: The atom’s is_aromatic flag

property stereochemistry: The atom’s stereochemistry (if defined, otherwise None)

property element

The element of this atom.

Returns: openmm.openmm.app.element.Element

property atomic_number: The integer atomic number of the atom.

property mass

The standard atomic weight (abundance-weighted isotopic mass) of the atomic site.

TODO (from jeff): Are there atoms that have different chemical properties based on their isotopes?

property name: The name of this atom, if any

property bonds: The list of Bond objects this atom is involved in.

property bonded_atoms: The list of Atom objects this atom is involved in bonds with

is_bonded_to(atom2)[source]

Determine whether this atom is bound to another atom

Parameters: atom2 (openff.toolkit.topology.molecule.Atom) – a different atom in the same molecule
Returns: bool – Whether this atom is bound to atom2

is_in_ring(toolkit_registry=GLOBAL_TOOLKIT_REGISTRY) → bool[source]

Return whether or not this atom is in a ring(s) (of any size)

This Atom is expected to be attached to a molecule (Atom.molecule).

Parameters: toolkit_registry (openff.toolkit.utils.toolkits.ToolkitRegistry, default=GLOBAL_TOOLKIT_REGISTRY) – ToolkitRegistry to use to enumerate the tautomers.

property virtual_sites: The list of VirtualSite objects this atom is involved in.

property molecule_atom_index: The index of this Atom within the the list of atoms in Molecules. Note that this can be different from molecule_particle_index.

property molecule_particle_index: The index of this Atom within the the list of particles in the parent Molecule. Note that this can be different from molecule_atom_index.

classmethod from_bson(serialized)

Instantiate an object from a BSON serialized representation.

Specification: http://bsonspec.org/

Parameters: serialized (bytes) – A BSON serialized representation of the object
Returns: instance (cls) – An instantiated object

classmethod from_json(serialized)

Instantiate an object from a JSON serialized representation.

Specification: https://www.json.org/

Parameters: serialized (str) – A JSON serialized representation of the object
Returns: instance (cls) – An instantiated object

classmethod from_messagepack(serialized)

Instantiate an object from a MessagePack serialized representation.

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

Parameters: serialized (bytes) – A MessagePack-encoded bytes serialized representation
Returns: instance (cls) – 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: serialized (str) – A pickled representation of the object
Returns: instance (cls) – An instantiated object

classmethod from_toml(serialized)

Instantiate an object from a TOML serialized representation.

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

Parameters: serlialized (str) – A TOML serialized representation of the object
Returns: instance (cls) – An instantiated object

classmethod from_xml(serialized)

Instantiate an object from an XML serialized representation.

Specification: https://www.w3.org/XML/

Parameters: serialized (bytes) – An XML serialized representation
Returns: instance (cls) – Instantiated object.

classmethod from_yaml(serialized)

Instantiate from a YAML serialized representation.

Specification: http://yaml.org/

Parameters: serialized (str) – A YAML serialized representation of the object
Returns: instance (cls) – Instantiated object

property molecule: The Molecule this particle is part of.

to_bson()

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns: serialized (bytes) – A BSON serialized representation of the objecft

to_json(indent=None)

Return a JSON serialized representation.

Specification: https://www.json.org/

Parameters: indent (int, optional, default=None) – If not None, will pretty-print with specified number of spaces for indentation
Returns: serialized (str) – A JSON serialized representation of the object

to_messagepack()

Return a MessagePack representation.

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

Returns: serialized (bytes) – 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: serialized (str) – A pickled representation of the object

to_toml()

Return a TOML serialized representation.

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

Returns: serialized (str) – A TOML serialized representation of the object

to_xml(indent=2)

Return an XML representation.

Specification: https://www.w3.org/XML/

Parameters: indent (int, optional, default=2) – If not None, will pretty-print with specified number of spaces for indentation
Returns: serialized (bytes) – A MessagePack-encoded bytes serialized representation.

to_yaml()

Return a YAML serialized representation.

Specification: http://yaml.org/

Returns: serialized (str) – A YAML serialized representation of the object