openforcefield.topology.
TopologyAtom
(atom, topology_molecule)[source]¶A TopologyAtom is a lightweight data structure that represents a single openforcefield.topology.molecule.Atom in a Topology. A TopologyAtom consists of two references – One to its fully detailed “atom”, an openforcefield.topology.molecule.Atom, 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 TopologyAtom. They are created on demand as the user requests them.
Warning
This API is experimental and subject to change.
atom
Get the reference Atom for this TopologyAtom.
atomic_number
Get the atomic number of this atom
molecule
Get the reference Molecule that this TopologyAtom belongs to.
topology_atom_index
Get the index of this atom in its parent Topology.
topology_bonds
Get the TopologyBonds connected to this TopologyAtom.
topology_molecule
Get the TopologyMolecule that this TopologyAtom belongs to.
topology_particle_index
Get the index of this particle in its parent Topology.
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. |
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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, atom, topology_molecule)[source]¶Create a new TopologyAtom.
The reference atom
The TopologyMolecule that this TopologyAtom belongs to
Methods
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Create a new TopologyAtom. |
|
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 reference Atom for this TopologyAtom. |
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Get the atomic number of this atom |
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Get the reference Molecule that this TopologyAtom belongs to. |
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Get the index of this atom in its parent Topology. |
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Get the TopologyBonds connected to this TopologyAtom. |
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Get the TopologyMolecule that this TopologyAtom belongs to. |
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Get the index of this particle in its parent Topology. |
atom
¶Get the reference Atom for this TopologyAtom.
atomic_number
¶Get the atomic number of this atom
topology_molecule
¶Get the TopologyMolecule that this TopologyAtom belongs to.
molecule
¶Get the reference Molecule that this TopologyAtom belongs to.
topology_atom_index
¶Get the index of this atom in its parent Topology.
The index of this atom in its parent topology.
topology_particle_index
¶Get the index of this particle in its parent Topology.
The index of this atom in its parent topology.
topology_bonds
¶Get the TopologyBonds connected to this TopologyAtom.
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