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.
Atoms involved in the bond
Discrete bond type representation for the Open Forcefield aromaticity model TODO: Do we want to pin ourselves to a single standard aromaticity model?
String based bond type
Integral bond order
Fractional bond order, or None.
Methods
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Instantiate an object from a BSON serialized representation. |
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Create a Bond from a dict representation. |
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Instantiate an object from a JSON serialized representation. |
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Instantiate an object from a MessagePack serialized representation. |
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Instantiate an object from a pickle serialized representation. |
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Instantiate an object from a TOML serialized representation. |
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Instantiate an object from an XML serialized representation. |
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Instantiate from a YAML serialized representation. |
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Return a BSON serialized representation. |
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Return a dict representation of the bond. |
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Return a JSON serialized representation. |
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Return a MessagePack representation. |
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Return a pickle serialized representation. |
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Return a TOML serialized representation. |
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Return an XML representation. |
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Return a YAML serialized representation. |
__init__
(self, atom1, atom2, bond_order, is_aromatic, fractional_bond_order=None, stereochemistry=None)[source]¶Create a new chemical bond.
Methods
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Create a new chemical bond. |
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Instantiate an object from a BSON serialized representation. |
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Create a Bond from a dict representation. |
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Instantiate an object from a JSON serialized representation. |
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Instantiate an object from a MessagePack serialized representation. |
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Instantiate an object from a pickle serialized representation. |
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Instantiate an object from a TOML serialized representation. |
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Instantiate an object from an XML serialized representation. |
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Instantiate from a YAML serialized representation. |
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Return a BSON serialized representation. |
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Return a dict representation of the bond. |
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Return a JSON serialized representation. |
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Return a MessagePack representation. |
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Return a pickle serialized representation. |
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Return a TOML serialized representation. |
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Return an XML representation. |
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Return a YAML serialized representation. |
Attributes
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The index of this Bond within the the list of bonds in |
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molecule_bond_index
¶The index of this Bond within the the list of bonds in Molecules
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from_bson
(serialized)¶Instantiate an object from a BSON serialized representation.
Specification: http://bsonspec.org/
A BSON serialized representation of the object
An instantiated object
from_json
(serialized)¶Instantiate an object from a JSON serialized representation.
Specification: https://www.json.org/
A JSON serialized representation of the object
An instantiated object
from_messagepack
(serialized)¶Instantiate an object from a MessagePack serialized representation.
Specification: https://msgpack.org/index.html
A MessagePack-encoded bytes serialized representation
Instantiated object.
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.
A pickled representation of the object
An instantiated object
from_toml
(serialized)¶Instantiate an object from a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
A TOML serialized representation of the object
An instantiated object
from_xml
(serialized)¶Instantiate an object from an XML serialized representation.
Specification: https://www.w3.org/XML/
An XML serialized representation
Instantiated object.
from_yaml
(serialized)¶Instantiate from a YAML serialized representation.
Specification: http://yaml.org/
A YAML serialized representation of the object
Instantiated object
to_bson
(self)¶Return a BSON serialized representation.
Specification: http://bsonspec.org/
A BSON serialized representation of the objecft
to_json
(self, indent=None)¶Return a JSON serialized representation.
Specification: https://www.json.org/
If not None, will pretty-print with specified number of spaces for indentation
A JSON serialized representation of the object
to_messagepack
(self)¶Return a MessagePack representation.
Specification: https://msgpack.org/index.html
A MessagePack-encoded bytes serialized representation of the object
to_pickle
(self)¶Return a pickle serialized representation.
Warning
This is not recommended for safe, stable storage since the pickle specification may change between Python versions.
A pickled representation of the object
to_toml
(self)¶Return a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
A TOML serialized representation of the object
to_xml
(self, indent=2)¶Return an XML representation.
Specification: https://www.w3.org/XML/
If not None, will pretty-print with specified number of spaces for indentation
A MessagePack-encoded bytes serialized representation.
to_yaml
(self)¶Return a YAML serialized representation.
Specification: http://yaml.org/
A YAML serialized representation of the object