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, atom2openff.toolkit.topology.Atom
Atoms involved in the bond
- bondtypeint
Discrete bond type representation for the Open Forcefield aromaticity model TODO: Do we want to pin ourselves to a single standard aromaticity model?
- typestr
String based bond type
- orderint
Integral bond order
- fractional_bond_orderfloat, optional
Fractional bond order, or None.
- .. warning :: This API is experimental and subject to change.
Methods
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.
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.
-
__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.
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
Return whether or not this bond is in a ring(s) (of any size)
molecule
The index of this Bond within the the list of bonds in
Molecules
.stereochemistry
-
property
molecule_bond_index
¶ The index of this Bond within the the list of bonds in
Molecules
.
-
property
is_in_ring
¶ Return whether or not this bond is in a ring(s) (of any size)
-
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
-
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