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.
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)
Methods
|
Instantiate an object from a BSON serialized representation. |
|
Create a virtual site from a dict 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. |
|
Return a dict representation of the virtual site. |
|
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. |
__init__
(self, atoms, charge_increments=None, epsilon=None, sigma=None, rmin_half=None, name=None)[source]¶Base class for VirtualSites
atoms[index] is the corresponding Atom for weights[index]
The amount of charge to remove from the VirtualSite’s atoms and put in the VirtualSite. Indexing in this list should match the ordering in the atoms list. Default is None.
Sigma term for VdW properties of virtual site. Default is None.
Epsilon term for VdW properties of virtual site. Default is None.
Rmin_half term for VdW properties of virtual site. Default is None.
The name of this virtual site. Default is None.
Virtual site type.
The name of this virtual site. Default is None
Methods
|
Base class for VirtualSites |
|
Instantiate an object from a BSON serialized representation. |
|
Create a virtual site from a dict 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. |
|
Return a dict representation of the virtual site. |
|
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
Atoms on whose position this VirtualSite depends. |
|
Charges taken from this VirtualSite’s atoms and given to the VirtualSite |
|
The VdW epsilon term of this VirtualSite |
|
The |
|
The index of this VirtualSite within the the list of particles in the parent |
|
The index of this VirtualSite within the list of virtual sites within |
|
The name of this VirtualSite |
|
The VdW rmin_half term of this VirtualSite |
|
The VdW sigma term of this VirtualSite |
|
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/
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
molecule
¶The Molecule
this atom is part of.
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