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.
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
|
Adds a bond that this atom is involved in .. |
|
Adds a bond that this atom is involved in .. |
|
Instantiate an object from a BSON serialized representation. |
|
Create an Atom from a dict representation. |
|
Instantiate an object from a JSON serialized representation. |
|
Instantiate an object from a MessagePack serialized representation. |
|
Instantiate an object from a pickle serialized representation. |
|
Instantiate an object from a TOML serialized representation. |
|
Instantiate an object from an XML serialized representation. |
|
Instantiate from a YAML serialized representation. |
|
Determine whether this atom is bound to another atom |
|
Return a BSON serialized representation. |
|
Return a dict representation of the atom. |
|
Return a JSON serialized representation. |
|
Return a MessagePack representation. |
|
Return a pickle serialized representation. |
|
Return a TOML serialized representation. |
|
Return an XML representation. |
|
Return a YAML serialized representation. |
__init__
(self, atomic_number, formal_charge, is_aromatic, name=None, molecule=None, stereochemistry=None)[source]¶Create an immutable Atom object.
Object is serializable and immutable.
Atomic number of the atom
Formal charge of the atom
If True, atom is aromatic; if False, not aromatic
Either ‘R’ or ‘S’ for specified stereochemistry, or None for ambiguous stereochemistry
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
|
Create an immutable Atom object. |
|
Adds a bond that this atom is involved in .. |
|
Adds a bond that this atom is involved in .. |
|
Instantiate an object from a BSON serialized representation. |
|
Create an Atom from a dict representation. |
|
Instantiate an object from a JSON serialized representation. |
|
Instantiate an object from a MessagePack serialized representation. |
|
Instantiate an object from a pickle serialized representation. |
|
Instantiate an object from a TOML serialized representation. |
|
Instantiate an object from an XML serialized representation. |
|
Instantiate from a YAML serialized representation. |
|
Determine whether this atom is bound to another atom |
|
Return a BSON serialized representation. |
|
Return a dict representation of the atom. |
|
Return a JSON serialized representation. |
|
Return a MessagePack representation. |
|
Return a pickle serialized representation. |
|
Return a TOML serialized representation. |
|
Return an XML representation. |
|
Return a YAML serialized representation. |
Attributes
The integer atomic number of the atom. |
|
The list of |
|
The list of |
|
The element name |
|
The atom’s formal charge |
|
The atom’s is_aromatic flag |
|
The standard atomic weight (abundance-weighted isotopic mass) of the atomic site. |
|
The |
|
The index of this Atom within the the list of atoms in |
|
The index of this Atom within the the list of particles in the parent |
|
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 |
add_bond
(self, bond)[source]¶Adds a bond that this atom is involved in .. todo :: Is this how we want to keep records?
A bond involving this atom
add_virtual_site
(self, vsite)[source]¶Adds a bond that this atom is involved in .. todo :: Is this how we want to keep records?
A bond involving this atom
formal_charge
¶The atom’s formal charge
partial_charge
¶The partial charge of the atom, if any.
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
(self, atom2)[source]¶Determine whether this atom is bound to another atom
a different atom in the same molecule
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
.
from_bson
(serialized)¶Instantiate an object from a BSON serialized representation.
Specification: http://bsonspec.org/
A BSON serialized representation of the object
An instantiated object
from_json
(serialized)¶Instantiate an object from a JSON serialized representation.
Specification: https://www.json.org/
A JSON serialized representation of the object
An instantiated object
from_messagepack
(serialized)¶Instantiate an object from a MessagePack serialized representation.
Specification: https://msgpack.org/index.html
A MessagePack-encoded bytes serialized representation
Instantiated object.
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.
A pickled representation of the object
An instantiated object
from_toml
(serialized)¶Instantiate an object from a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
A TOML serialized representation of the object
An instantiated object
from_xml
(serialized)¶Instantiate an object from an XML serialized representation.
Specification: https://www.w3.org/XML/
An XML serialized representation
Instantiated object.
from_yaml
(serialized)¶Instantiate from a YAML serialized representation.
Specification: http://yaml.org/
A YAML serialized representation of the object
Instantiated object
molecule
¶The Molecule
this atom is part of.
to_bson
(self)¶Return a BSON serialized representation.
Specification: http://bsonspec.org/
A BSON serialized representation of the objecft
to_json
(self, indent=None)¶Return a JSON serialized representation.
Specification: https://www.json.org/
If not None, will pretty-print with specified number of spaces for indentation
A JSON serialized representation of the object
to_messagepack
(self)¶Return a MessagePack representation.
Specification: https://msgpack.org/index.html
A MessagePack-encoded bytes serialized representation of the object
to_pickle
(self)¶Return a pickle serialized representation.
Warning
This is not recommended for safe, stable storage since the pickle specification may change between Python versions.
A pickled representation of the object
to_toml
(self)¶Return a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
A TOML serialized representation of the object
to_xml
(self, indent=2)¶Return an XML representation.
Specification: https://www.w3.org/XML/
If not None, will pretty-print with specified number of spaces for indentation
A MessagePack-encoded bytes serialized representation.
to_yaml
(self)¶Return a YAML serialized representation.
Specification: http://yaml.org/
A YAML serialized representation of the object