openff.toolkit.topology.Bond

class openff.toolkit.topology.Bond(atom1, atom2, bond_order, is_aromatic, fractional_bond_order=None, stereochemistry=None)[source]

Chemical bond representation.

Warning

This API is experimental and subject to change.

Attributes

atom1, atom2 (openff.toolkit.topology.Atom) – Atoms involved in the bond
bondtype (int) – Discrete bond type representation for the Open Forcefield aromaticity model TODO: Do we want to pin ourselves to a single standard aromaticity model?
type (str) – String based bond type
order (int) – Integral bond order
fractional_bond_order (float, optional) – Fractional bond order, or None.

Warning

This API is experimental and subject to change.

__init__(atom1, atom2, bond_order, is_aromatic, fractional_bond_order=None, stereochemistry=None)[source]: Create a new chemical bond.

Methods

`__init__`(atom1, atom2, bond_order, is_aromatic)	Create a new chemical bond.
`from_bson`(serialized)	Instantiate an object from a BSON serialized representation.
`from_dict`(molecule, d)	Create a Bond 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_in_ring`([toolkit_registry])	Return whether or not this bond is in a ring(s) (of any size)
`to_bson`()	Return a BSON serialized representation.
`to_dict`()	Return a dict representation of the bond.
`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

`atom1`
`atom1_index`
`atom2`
`atom2_index`
`atoms`
`bond_order`
`fractional_bond_order`
`is_aromatic`
`molecule`
`molecule_bond_index`	The index of this Bond within the the list of bonds in `Molecules`.
`stereochemistry`

to_dict()[source]: Return a dict representation of the bond.

classmethod from_dict(molecule, d)[source]: Create a Bond from a dict representation.

property molecule_bond_index: The index of this Bond within the the list of bonds in Molecules.

is_in_ring(toolkit_registry=GLOBAL_TOOLKIT_REGISTRY) → bool[source]

Return whether or not this bond is in a ring(s) (of any size)

This Bond is expected to be attached to a molecule (Bond.molecule).

Note: Bonds containing atoms that are only in separate rings, i.e. the central bond in a biphenyl,: are not considered to be bonded by this criteria.

Parameters: toolkit_registry (openff.toolkit.utils.toolkits.ToolkitRegistry, default=GLOBAL_TOOLKIT_REGISTRY) – ToolkitRegistry to use to enumerate the tautomers.
Returns: is_in_ring (bool) – Whether or not this bond is in a ring.

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

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