openforcefield.topology.Bond

class openforcefield.topology.Bond(atom1, atom2, bond_order, is_aromatic, fractional_bond_order=None, stereochemistry=None)

Chemical bond representation.

Warning

This API is experimental and subject to change.

Attributes

atom1, atom2openforcefield.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.
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)

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