`Atom`

class openff.toolkit.topology.Atom(atomic_number: int, formal_charge: int | Quantity, is_aromatic: bool, name: str | None = None, molecule=None, stereochemistry: str | None = None, metadata: dict[str, Union[int, str]] | None = None)[source]

A chemical atom.

Warning

This API is experimental and subject to change.

__init__(atomic_number: int, formal_charge: int | Quantity, is_aromatic: bool, name: str | None = None, molecule=None, stereochemistry: str | None = None, metadata: dict[str, Union[int, str]] | None = None)[source]

Create an immutable Atom object.

Object is serializable and immutable.

Parameters:

atomic_number – Atomic number of the atom. Must be non-negative and non-zero.
formal_charge – Formal charge of the atom
is_aromatic – If True, atom is aromatic; if False, not aromatic
stereochemistry – Either ‘R’ or ‘S’ for specified stereochemistry, or None for ambiguous stereochemistry
name – An optional name to be associated with the atom
metadata – An optional dictionary where keys are strings and values are strings or ints. This is intended to record atom-level information used to inform hierarchy definition and iteration, such as grouping atom by residue and chain.

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
`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.
`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.
`metadata`	The atom's metadata dictionary
`molecule`	The `Molecule` this particle is part of.
`molecule_atom_index`	The index of this Atom within the the list of atoms in the parent `Molecule`.
`molecule_particle_index`	Returns the index of this particle in its 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)
`symbol`	Return the symbol implied by the atomic number of this atom

add_bond(bond: Bond)[source]

Adds a bond that this atom is involved in

Parameters:: bond – A bond involving this atom

to_dict() → dict[str, Union[NoneType, str, int, bool, dict[Any, Any]]][source]: Return a dict representation of the atom.

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

property metadata: The atom’s metadata dictionary

property formal_charge: The atom’s formal charge

property partial_charge

The partial charge of the atom, if any.

Returns:: unit-wrapped float 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 atomic_number: int: The integer atomic number of the atom.

property symbol: str: Return the symbol implied by the atomic number of this atom

property mass: Quantity

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

The mass is reported in units of Dalton.

property name: The name of this atom, if any

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

property bonded_atoms: Generator[Atom, None, None]: 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 – a different atom in the same molecule
Returns:: bool – Whether this atom is bound to atom2

is_in_ring(toolkit_registry: ToolkitRegistry = 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 – ToolkitRegistry to use to enumerate the tautomers.

property molecule_atom_index: int: The index of this Atom within the the list of atoms in the parent Molecule.

classmethod from_bson(serialized)

Instantiate an object from a BSON serialized representation.

Specification: http://bsonspec.org/

Parameters:: serialized – A BSON serialized representation of the object
Returns:: instance – An instantiated object

classmethod from_json(serialized: str)

Instantiate an object from a JSON serialized representation.

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

Parameters:: serialized – A JSON serialized representation of the object
Returns:: instance – An instantiated object

classmethod from_messagepack(serialized)

Instantiate an object from a MessagePack serialized representation.

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

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

classmethod from_toml(serialized)

Instantiate an object from a TOML serialized representation.

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

Parameters:: serlialized – A TOML serialized representation of the object
Returns:: instance – An instantiated object

classmethod from_xml(serialized)

Instantiate an object from an XML serialized representation.

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

Parameters:: serialized – An XML serialized representation
Returns:: instance – Instantiated object.

classmethod from_yaml(serialized)

Instantiate from a YAML serialized representation.

Specification: http://yaml.org/

Parameters:: serialized – A YAML serialized representation of the object
Returns:: instance – Instantiated object

property molecule: FrozenMolecule: The Molecule this particle is part of.

property molecule_particle_index: int: Returns the index of this particle in its molecule

to_bson()

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns:: serialized – A BSON serialized representation of the objecft

to_json(indent=None) → str

Return a JSON serialized representation.

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

Parameters:: indent – If not None, will pretty-print with specified number of spaces for indentation
Returns:: serialized – A JSON serialized representation of the object

to_messagepack()

Return a MessagePack representation.

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

Returns:: serialized – 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 – A pickled representation of the object

to_toml()

Return a TOML serialized representation.

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

Returns:: serialized – A TOML serialized representation of the object

to_xml(indent=2)

Return an XML representation.

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

Parameters:: indent – If not None, will pretty-print with specified number of spaces for indentation
Returns:: serialized – A MessagePack-encoded bytes serialized representation.

to_yaml()

Return a YAML serialized representation.

Specification: http://yaml.org/

Returns:: serialized – A YAML serialized representation of the object