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

mass

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

molecule

The Molecule this atom 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_number : int

Atomic number of the atom

formal_charge : int

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
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
mass The standard atomic weight (abundance-weighted isotopic mass) of the atomic site.
molecule The Molecule this atom 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.

formal_charge

The atom’s formal charge

partial_charge

The partial charge of the atom, if any.

Returns:
float or None
is_aromatic

The atom’s is_aromatic flag

stereochemistry

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

element

The element name

atomic_number

The integer atomic number of the atom.

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?

name

The name of this atom, if any

bonds

The list of Bond objects this atom is involved in.

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

virtual_sites

The list of VirtualSite objects this atom is involved in.

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.

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

molecule

The Molecule this atom 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