# 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`(self, bond) | Adds a bond that this atom is involved in ..
  `add_virtual_site`(self, 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`(self, atom2) | Determine whether this atom is bound to another atom
  `to_bson`(self) | Return a BSON serialized representation.
  `to_dict`(self) | Return a dict representation of the atom.
  `to_json`(self[, indent]) | Return a JSON serialized representation.
  `to_messagepack`(self) | Return a MessagePack representation.
  `to_pickle`(self) | Return a pickle serialized representation.
  `to_toml`(self) | Return a TOML serialized representation.
  `to_xml`(self[, indent]) | Return an XML representation.
  `to_yaml`(self) | Return a YAML serialized representation.

  `__init__`(self, atomic_number, formal_charge, is_aromatic, name=None, molecule=None, stereochemistry=None)

    Create an immutable Atom object.

    Object is serializable and immutable.

    Parameters
      atomic_number int

        Atomic number of the atom

      formal_charge int or simtk.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__`(self, atomic_number, formal_charge, …) | Create an immutable Atom object.
  `add_bond`(self, bond) | Adds a bond that this atom is involved in ..
  `add_virtual_site`(self, 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`(self, atom2) | Determine whether this atom is bound to another atom
  `to_bson`(self) | Return a BSON serialized representation.
  `to_dict`(self) | Return a dict representation of the atom.
  `to_json`(self[, indent]) | Return a JSON serialized representation.
  `to_messagepack`(self) | Return a MessagePack representation.
  `to_pickle`(self) | Return a pickle serialized representation.
  `to_toml`(self) | Return a TOML serialized representation.
  `to_xml`(self[, indent]) | Return an XML representation.
  `to_yaml`(self) | 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.