openforcefield.topology.
TopologyVirtualSite
(virtual_site, topology_molecule)[source]¶A TopologyVirtualSite is a lightweight data structure that represents a single openforcefield.topology.molecule.VirtualSite in a Topology. A TopologyVirtualSite consists of two references – One to its fully detailed “VirtualSite”, an openforcefield.topology.molecule.VirtualSite, 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 TopologyVirtualSite. They are created on demand as the user requests them.
Warning
This API is experimental and subject to change.
atoms
Get the TopologyAtoms involved in this TopologyVirtualSite.
molecule
Get the reference Molecule that this TopologyVirtualSite belongs to.
topology_molecule
Get the TopologyMolecule that this TopologyVirtualSite belongs to.
topology_particle_index
Get the index of this particle in its parent Topology.
topology_virtual_site_index
Get the index of this virtual site in its parent Topology.
type
Get the type of this virtual site
virtual_site
Get the reference VirtualSite for this TopologyVirtualSite.
Methods
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Get the atom at a specific index in this TopologyVirtualSite |
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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, virtual_site, topology_molecule)[source]¶The reference virtual site
The TopologyMolecule that this TopologyVirtualSite belongs to
Methods
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|
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Get the atom at a specific index in this TopologyVirtualSite |
|
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 involved in this TopologyVirtualSite. |
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Get the reference Molecule that this TopologyVirtualSite belongs to. |
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Get the TopologyMolecule that this TopologyVirtualSite belongs to. |
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Get the index of this particle in its parent Topology. |
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Get the index of this virtual site in its parent Topology. |
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Get the type of this virtual site |
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Get the reference VirtualSite for this TopologyVirtualSite. |
atom
(self, index)[source]¶Get the atom at a specific index in this TopologyVirtualSite
The index of the atom in the reference VirtualSite to retrieve
atoms
¶Get the TopologyAtoms involved in this TopologyVirtualSite.
virtual_site
¶Get the reference VirtualSite for this TopologyVirtualSite.
topology_molecule
¶Get the TopologyMolecule that this TopologyVirtualSite belongs to.
topology_virtual_site_index
¶Get the index of this virtual site in its parent Topology.
The index of this virtual site in its parent topology.
topology_particle_index
¶Get the index of this particle in its parent Topology.
The index of this particle in its parent topology.
molecule
¶Get the reference Molecule that this TopologyVirtualSite belongs to.
type
¶Get the type of this virtual site
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