openforcefield.topology.
TopologyBond
(bond, topology_molecule)[source]¶A TopologyBond is a lightweight data structure that represents a single openforcefield.topology.molecule.Bond in a Topology. A TopologyBond consists of two references – One to its fully detailed “bond”, an openforcefield.topology.molecule.Bond, and another to its parent “topology_molecule”, which occupies a spot in the parent Topology’s TopologyMolecule list.
As some systems can be very large, there is no always-existing representation of a TopologyBond. They are created on demand as the user requests them.
Warning
This API is experimental and subject to change.
atoms
Get the TopologyAtoms connected to this TopologyBond.
bond
Get the reference Bond for this TopologyBond.
bond_order
Get the order of this TopologyBond.
molecule
Get the reference Molecule that this TopologyBond belongs to.
topology_bond_index
Get the index of this bond in its parent Topology.
topology_molecule
Get the TopologyMolecule that this TopologyBond belongs to.
Methods
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Instantiate an object from a BSON serialized representation. |
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Static constructor from dictionary 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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Convert to dictionary representation. |
|
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, bond, topology_molecule)[source]¶The reference bond.
The TopologyMolecule that this TopologyBond belongs to.
Methods
|
|
|
Instantiate an object from a BSON serialized representation. |
|
Static constructor from dictionary representation. |
|
Instantiate an object from a JSON serialized representation. |
|
Instantiate an object from a MessagePack serialized representation. |
|
Instantiate an object from a pickle serialized representation. |
|
Instantiate an object from a TOML serialized representation. |
|
Instantiate an object from an XML serialized representation. |
|
Instantiate from a YAML serialized representation. |
|
Return a BSON serialized representation. |
|
Convert to dictionary representation. |
|
Return a JSON serialized representation. |
|
Return a MessagePack representation. |
|
Return a pickle serialized representation. |
|
Return a TOML serialized representation. |
|
Return an XML representation. |
|
Return a YAML serialized representation. |
Attributes
Get the TopologyAtoms connected to this TopologyBond. |
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Get the reference Bond for this TopologyBond. |
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Get the order of this TopologyBond. |
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Get the reference Molecule that this TopologyBond belongs to. |
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Get the index of this bond in its parent Topology. |
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Get the TopologyMolecule that this TopologyBond belongs to. |
bond
¶Get the reference Bond for this TopologyBond.
topology_molecule
¶Get the TopologyMolecule that this TopologyBond belongs to.
topology_bond_index
¶Get the index of this bond in its parent Topology.
The index of this bond in its parent topology.
molecule
¶Get the reference Molecule that this TopologyBond belongs to.
bond_order
¶Get the order of this TopologyBond.
atoms
¶Get the TopologyAtoms connected to this TopologyBond.
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