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.

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.

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