openforcefield.topology.MonovalentLonePairVirtualSite¶
-
class
openforcefield.topology.
MonovalentLonePairVirtualSite
(atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=None, epsilon=None, sigma=None, rmin_half=None, name=None, orientations=None)[source]¶ A particle representing a “Monovalent Lone Pair”-type virtual site, in which the location of the charge is specified by the positions of three atoms. This is originally intended for situations like a carbonyl, and allows placement of a virtual site S at a specified distance d, in_plane_angle, and out_of_plane_angle relative to a central atom and two connected atoms.
Warning
This API is experimental and subject to change.
- Attributes
atoms
Atoms on whose position this VirtualSite depends.
charge_increments
Charges taken from this VirtualSite’s atoms and given to the VirtualSite
distance
The distance parameter of the virtual site
epsilon
The VdW epsilon term of this VirtualSite
in_plane_angle
The in_plane_angle parameter of the virtual site
molecule
The
Molecule
this particle is part of.molecule_particle_index
Returns the index of this particle in its molecule
molecule_virtual_site_index
The index of this VirtualSite within the list of virtual sites within
Molecule
Note that this can be different fromparticle_index
.n_particles
The number of particles that the virtual site represents
name
The name of this VirtualSite
- orientations
out_of_plane_angle
The out_of_plane_angle parameter of the virtual site
particles
Particles owned by 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
from_bson
(serialized)Instantiate an object from a BSON serialized representation.
from_dict
(vsite_dict)Construct a new MonovalentLonePairVirtualSite from an serialized dictionary 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.
get_openmm_virtual_site
(atoms)Returns the OpenMMVirtualSite corresponding to this MonovalentLonePairVirtualSite.
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.
Return a MessagePack representation.
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.
index_of_orientation
-
__init__
(atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=None, epsilon=None, sigma=None, rmin_half=None, name=None, orientations=None)[source]¶ Create a bond charge-type virtual site, in which the location of the charge is specified by the position of three atoms.
- Parameters
- atomslist of three openforcefield.topology.molecule.Atom objects
The three atoms defining the virtual site’s position
- distancefloat
- out_of_plane_anglefloat
- in_plane_anglefloat
- epsilonfloat
Epsilon term for VdW properties of virtual site. Default is None.
- sigmafloat, default=None
Sigma term for VdW properties of virtual site. Default is None.
- rmin_halffloat
Rmin_half term for VdW properties of virtual site. Default is None.
- namestring or None, default=None
The name of this virtual site. Default is None.
- orientationslist of tuples of 3 Atoms or ints
The permutations of the matched atoms that should be used to define the orientation of each virtual site particle
Methods
__init__
(atoms, distance, …[, …])Create a bond charge-type virtual site, in which the location of the charge is specified by the position of three atoms.
from_bson
(serialized)Instantiate an object from a BSON serialized representation.
from_dict
(vsite_dict)Construct a new MonovalentLonePairVirtualSite from an serialized dictionary 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.
get_openmm_virtual_site
(atoms)Returns the OpenMMVirtualSite corresponding to this MonovalentLonePairVirtualSite.
index_of_orientation
(virtual_particle)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.
Return a MessagePack representation.
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 on whose position this VirtualSite depends.
Charges taken from this VirtualSite’s atoms and given to the VirtualSite
The distance parameter of the virtual site
The VdW epsilon term of this VirtualSite
The in_plane_angle parameter of the virtual site
The
Molecule
this particle is part of.Returns the index of this particle in its molecule
The index of this VirtualSite within the list of virtual sites within
Molecule
Note that this can be different fromparticle_index
.The number of particles that the virtual site represents
The name of this VirtualSite
orientations
The out_of_plane_angle parameter of the virtual site
Particles owned by 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)
-
classmethod
from_dict
(vsite_dict)[source]¶ Construct a new MonovalentLonePairVirtualSite from an serialized dictionary representation.
- Parameters
- vsite_dictdict
The VirtualSite to deserialize.
- Returns
- The newly created MonovalentLonePairVirtualSite
-
property
distance
¶ The distance parameter of the virtual site
-
property
in_plane_angle
¶ The in_plane_angle parameter of the virtual site
-
property
out_of_plane_angle
¶ The out_of_plane_angle parameter of the virtual site
-
get_openmm_virtual_site
(atoms)[source]¶ Returns the OpenMMVirtualSite corresponding to this MonovalentLonePairVirtualSite.
- Parameters
- atomsiterable of int
The indices of the atoms involved in this virtual site (not assumed to be the same as the molecule indices as this method may be accessed with regard to particles in a Topology).
- Returns
- virtual_sitea simtk.openmm LocalCoordinatesSite
-
property
atoms
¶ Atoms on whose position this VirtualSite depends.
-
property
charge_increments
¶ Charges taken from this VirtualSite’s atoms and given to the VirtualSite
-
property
epsilon
¶ The VdW epsilon term of this VirtualSite
-
classmethod
from_bson
(serialized)¶ Instantiate an object from a BSON serialized representation.
Specification: http://bsonspec.org/
- Parameters
- serializedbytes
A BSON serialized representation of the object
- Returns
- instancecls
An instantiated object
-
classmethod
from_json
(serialized)¶ Instantiate an object from a JSON serialized representation.
Specification: https://www.json.org/
- Parameters
- serializedstr
A JSON serialized representation of the object
- Returns
- instancecls
An instantiated object
-
classmethod
from_messagepack
(serialized)¶ Instantiate an object from a MessagePack serialized representation.
Specification: https://msgpack.org/index.html
- Parameters
- serializedbytes
A MessagePack-encoded bytes serialized representation
- Returns
- instancecls
Instantiated object.
-
classmethod
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
- serializedstr
A pickled representation of the object
- Returns
- instancecls
An instantiated object
-
classmethod
from_toml
(serialized)¶ Instantiate an object from a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
- Parameters
- serlializedstr
A TOML serialized representation of the object
- Returns
- instancecls
An instantiated object
-
classmethod
from_xml
(serialized)¶ Instantiate an object from an XML serialized representation.
Specification: https://www.w3.org/XML/
- Parameters
- serializedbytes
An XML serialized representation
- Returns
- instancecls
Instantiated object.
-
classmethod
from_yaml
(serialized)¶ Instantiate from a YAML serialized representation.
Specification: http://yaml.org/
- Parameters
- serializedstr
A YAML serialized representation of the object
- Returns
- instancecls
Instantiated object
-
property
molecule
¶ The
Molecule
this particle is part of.
-
property
molecule_particle_index
¶ Returns the index of this particle in its molecule
-
property
molecule_virtual_site_index
¶ The index of this VirtualSite within the list of virtual sites within
Molecule
Note that this can be different fromparticle_index
.
-
property
n_particles
¶ The number of particles that the virtual site represents
-
property
name
¶ The name of this VirtualSite
-
property
particles
¶ Particles owned by this VirtualSite
-
property
rmin_half
¶ The VdW rmin_half term of this VirtualSite
-
property
sigma
¶ The VdW sigma term of this VirtualSite
-
to_bson
()¶ Return a BSON serialized representation.
Specification: http://bsonspec.org/
- Returns
- serializedbytes
A BSON serialized representation of the objecft
-
to_json
(indent=None)¶ Return a JSON serialized representation.
Specification: https://www.json.org/
- Parameters
- indentint, optional, default=None
If not None, will pretty-print with specified number of spaces for indentation
- Returns
- serializedstr
A JSON serialized representation of the object
-
to_messagepack
()¶ Return a MessagePack representation.
Specification: https://msgpack.org/index.html
- Returns
- serializedbytes
A MessagePack-encoded bytes serialized representation of the object
-
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
- serializedstr
A pickled representation of the object
-
to_toml
()¶ Return a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
- Returns
- serializedstr
A TOML serialized representation of the object
-
to_xml
(indent=2)¶ Return an XML representation.
Specification: https://www.w3.org/XML/
- Parameters
- indentint, optional, default=2
If not None, will pretty-print with specified number of spaces for indentation
- Returns
- serializedbytes
A MessagePack-encoded bytes serialized representation.
-
to_yaml
()¶ Return a YAML serialized representation.
Specification: http://yaml.org/
- Returns
- serializedstr
A YAML serialized representation of the object
-
property
type
¶ The type of this VirtualSite (returns the class name as string)