openforcefield.topology.
VirtualSite
(atoms, charge_increments=None, epsilon=None, sigma=None, rmin_half=None, name=None)[source]¶A particle representing a virtual site whose position is defined in terms of Atom
positions.
Note that chemical atoms are represented by the Atom
.
Warning
This API is experimental and subject to change.
Todo
Attributes: |
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Methods
from_bson (serialized) |
Instantiate an object from a BSON serialized representation. |
from_dict (vsite_dict) |
Create a virtual site 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 virtual site. |
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__
(atoms, charge_increments=None, epsilon=None, sigma=None, rmin_half=None, name=None)[source]¶Base class for VirtualSites
Todo
Parameters: |
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Methods
__init__ (atoms[, charge_increments, …]) |
Base class for VirtualSites |
from_bson (serialized) |
Instantiate an object from a BSON serialized representation. |
from_dict (vsite_dict) |
Create a virtual site 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 virtual site. |
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
atoms |
Atoms on whose position this VirtualSite depends. |
charge_increments |
Charges taken from this VirtualSite’s atoms and given to the VirtualSite |
epsilon |
The VdW epsilon term of this VirtualSite |
molecule |
The Molecule this atom is part of. |
molecule_particle_index |
The index of this VirtualSite within the the list of particles in the parent Molecule . |
molecule_virtual_site_index |
The index of this VirtualSite within the list of virtual sites within Molecule Note that this can be different from particle_index . |
name |
The name of this VirtualSite |
rmin_half |
The VdW rmin_half term of this VirtualSite |
sigma |
The VdW sigma term of this VirtualSite |
type |
The type of this VirtualSite (returns the class name as string) |
molecule_virtual_site_index
¶The index of this VirtualSite within the list of virtual sites within Molecule
Note that this can be different from particle_index
.
molecule_particle_index
¶The index of this VirtualSite within the the list of particles in the parent Molecule
.
Note that this can be different from molecule_virtual_site_index
.
atoms
¶Atoms on whose position this VirtualSite depends.
charge_increments
¶Charges taken from this VirtualSite’s atoms and given to the VirtualSite
epsilon
¶The VdW epsilon term of this VirtualSite
sigma
¶The VdW sigma term of this VirtualSite
rmin_half
¶The VdW rmin_half term of this VirtualSite
name
¶The name of this VirtualSite
type
¶The type of this VirtualSite (returns the class name as string)
from_bson
(serialized)¶Instantiate an object from a BSON serialized representation.
Specification: http://bsonspec.org/
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Returns: |
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from_json
(serialized)¶Instantiate an object from a JSON serialized representation.
Specification: https://www.json.org/
Parameters: |
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Returns: |
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from_messagepack
(serialized)¶Instantiate an object from a MessagePack serialized representation.
Specification: https://msgpack.org/index.html
Parameters: |
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Returns: |
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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.
Parameters: |
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Returns: |
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from_toml
(serialized)¶Instantiate an object from a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
Parameters: |
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Returns: |
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from_xml
(serialized)¶Instantiate an object from an XML serialized representation.
Specification: https://www.w3.org/XML/
Parameters: |
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Returns: |
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from_yaml
(serialized)¶Instantiate from a YAML serialized representation.
Specification: http://yaml.org/
Parameters: |
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Returns: |
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molecule
¶The Molecule
this atom is part of.
Todo
Molecule
for each molecule type in the system,or if we have multiple copies of the same molecule, should we have multiple ``Molecule``s?
to_bson
()¶Return a BSON serialized representation.
Specification: http://bsonspec.org/
Returns: |
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to_json
(indent=None)¶Return a JSON serialized representation.
Specification: https://www.json.org/
Parameters: |
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Returns: |
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to_messagepack
()¶Return a MessagePack representation.
Specification: https://msgpack.org/index.html
Returns: |
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to_pickle
()¶Return a pickle serialized representation.
Warning
This is not recommended for safe, stable storage since the pickle specification may change between Python versions.
Returns: |
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to_toml
()¶Return a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
Returns: |
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to_xml
(indent=2)¶Return an XML representation.
Specification: https://www.w3.org/XML/
Parameters: |
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Returns: |
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to_yaml
()¶Return a YAML serialized representation.
Specification: http://yaml.org/
Returns: |
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