openff.toolkit.topology.Atom¶
-
class
openff.toolkit.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 withbonds
The list of
Bond
objects this atom is involved in.element
The element of this atom.
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.
Return a MessagePack representation.
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.
Return a MessagePack representation.
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
The integer atomic number of the atom.
The list of
Atom
objects this atom is involved in bonds withThe list of
Bond
objects this atom is involved in.The element of this atom.
The atom’s formal charge
The atom’s is_aromatic flag
Return whether or not this atom is in a ring(s) (of any size)
The standard atomic weight (abundance-weighted isotopic mass) of the atomic site.
The
Molecule
this particle is part of.The index of this Atom within the the list of atoms in
Molecules
.The index of this Atom within the the list of particles in the parent
Molecule
.The name of this atom, if any
The partial charge of the atom, if any.
The atom’s stereochemistry (if defined, otherwise None)
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 openff.toolkit.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 openff.toolkit.topology.molecule.Bond
A bond involving this atom
-
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 of this atom.
- Returns
- simtk.openmm.app.element.Element
-
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: openff.toolkit.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 frommolecule_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 frommolecule_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