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.
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
atom1
atom1_index
atom2
atom2_index
atoms
bond_order
fractional_bond_order
is_aromatic
molecule
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.
- 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