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 – Atoms involved in the bond

  • bond_order – The (integer) bond order of this bond.

  • is_aromatic – Whether or not this bond is aromatic.

  • fractional_bond_order – The fractional bond order, or partial bond order of this bond.

  • stereochemstry – A string representing this stereochemistry of this bond.

  • .. 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() → dict[str, Union[int, bool, str, float]][source]

Return a dict representation of the bond.

classmethod from_dict(molecule: FM, d: dict) → B[source]

Create a Bond from a dict representation.

property molecule_bond_index: int

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

is_in_ring(toolkit_registry: ToolkitRegistry = 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 – ToolkitRegistry to use to enumerate the tautomers.

Returns:

is_in_ring – 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 – A BSON serialized representation of the object

Returns:

instance – An instantiated object

classmethod from_json(serialized: str)

Instantiate an object from a JSON serialized representation.

Specification: https://www.json.org/

Parameters:

serialized – A JSON serialized representation of the object

Returns:

instance – An instantiated object

classmethod from_messagepack(serialized)

Instantiate an object from a MessagePack serialized representation.

Specification: https://msgpack.org/index.html

Parameters:

serialized – A MessagePack-encoded bytes serialized representation

Returns:

instance – 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 – A pickled representation of the object

Returns:

instance – An instantiated object

classmethod from_toml(serialized)

Instantiate an object from a TOML serialized representation.

Specification: https://github.com/toml-lang/toml

Parameters:

serlialized – A TOML serialized representation of the object

Returns:

instance – An instantiated object

classmethod from_xml(serialized)

Instantiate an object from an XML serialized representation.

Specification: https://www.w3.org/XML/

Parameters:

serialized – An XML serialized representation

Returns:

instance – Instantiated object.

classmethod from_yaml(serialized)

Instantiate from a YAML serialized representation.

Specification: http://yaml.org/

Parameters:

serialized – A YAML serialized representation of the object

Returns:

instance – Instantiated object

to_bson()

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns:

serialized – A BSON serialized representation of the objecft

to_json(indent=None) → str

Return a JSON serialized representation.

Specification: https://www.json.org/

Parameters:

indent – If not None, will pretty-print with specified number of spaces for indentation

Returns:

serialized – A JSON serialized representation of the object

to_messagepack()

Return a MessagePack representation.

Specification: https://msgpack.org/index.html

Returns:

serialized – 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 – A pickled representation of the object

to_toml()

Return a TOML serialized representation.

Specification: https://github.com/toml-lang/toml

Returns:

serialized – A TOML serialized representation of the object

to_xml(indent=2)

Return an XML representation.

Specification: https://www.w3.org/XML/

Parameters:

indent – If not None, will pretty-print with specified number of spaces for indentation

Returns:

serialized – A MessagePack-encoded bytes serialized representation.

to_yaml()

Return a YAML serialized representation.

Specification: http://yaml.org/

Returns:

serialized – A YAML serialized representation of the object