openforcefield.topology.Bond¶

class openforcefield.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.

Todo

Allow bonds to have associated properties.

Attributes:

Attributes:	atom1, atom2 : openforcefield.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.

atom1, atom2 : openforcefield.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.

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.
`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.

__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.
`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.

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

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