openforcefield.topology.Atom¶

class openforcefield.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.

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 name
formal_charge: The atom’s formal charge
is_aromatic: The atom’s is_aromatic flag
is_in_ring: Return whether or not this atom is in a ring(s) (of any size)
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.

Methods

`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
`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.

__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_numberint: Atomic number of the atom
formal_chargeint or simtk.unit.Quantity-wrapped int with dimension “charge”: Formal charge of the atom
is_aromaticbool: If True, atom is aromatic; if False, not aromatic
stereochemistrystr, optional, default=None: Either ‘R’ or ‘S’ for specified stereochemistry, or None for ambiguous stereochemistry
namestr, 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
`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 name
`formal_charge`	The atom’s formal charge
`is_aromatic`	The atom’s is_aromatic flag
`is_in_ring`	Return whether or not this atom is in a ring(s) (of any size)
`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 openforcefield.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 openforcefield.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

simtk.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 name

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: openforcefield.topology.molecule.Atom: a different atom in the same molecule

Returns

bool: Whether this atom is bound to atom2

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

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

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

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

to_bson()¶

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns

serializedbytes: A BSON serialized representation of the objecft

to_json(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()¶

Return a MessagePack representation.

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

Returns

serializedbytes: 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

serializedstr: A pickled representation of the object

to_toml()¶

Return a TOML serialized representation.

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

Returns

serializedstr: A TOML serialized representation of the object

to_xml(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()¶

Return a YAML serialized representation.

Specification: http://yaml.org/

Returns

serializedstr: A YAML serialized representation of the object