openforcefield.topology.Atom

class openforcefield.topology.Atom(atomic_number, formal_charge, is_aromatic, name=None, molecule=None, stereochemistry=None)

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)

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
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.