openforcefield.topology.TrivalentLonePairVirtualSite

class openforcefield.topology.TrivalentLonePairVirtualSite(atoms, distance, charge_increments=None, epsilon=None, sigma=None, rmin_half=None, name=None, orientations=None)

A particle representing a “Trivalent Lone Pair”-type virtual site, in which the location of the charge is specified by the positions of four atoms. This is suitable for planar or tetrahedral nitrogen lone pairs; a charge site S lies above the central atom (e.g. nitrogen a distance d along the vector perpendicular to the plane of the three connected atoms (2,3,4). With positive values of d the site lies above the nitrogen and with negative values it lies below the nitrogen.

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

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 from particle_index.

n_particles

The number of particles that the virtual site represents

name

The name of this VirtualSite

orientations

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 TrivalentPairVirtualSite 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 TrivalentLonePairVirtualSite.
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.

index_of_orientation

__init__(atoms, distance, charge_increments=None, epsilon=None, sigma=None, rmin_half=None, name=None, orientations=None)

Create a trivalent lone pair-type virtual site, in which the location of the charge is specified by the position of four atoms.

Parameters

atomslist of 4 openforcefield.topology.molecule.Atom objects

The three atoms defining the virtual site’s position

distancefloat

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 trivalent lone pair-type virtual site, in which the location of the charge is specified by the position of four atoms.
from_bson(serialized)	Instantiate an object from a BSON serialized representation.
from_dict(vsite_dict)	Construct a new TrivalentPairVirtualSite 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 TrivalentLonePairVirtualSite.
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.
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
distance	The distance parameter of the virtual site
epsilon	The VdW epsilon term of this VirtualSite
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 from particle_index.
n_particles	The number of particles that the virtual site represents
name	The name of this VirtualSite
orientations
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)

to_dict()

Return a dict representation of the virtual site.

classmethod from_dict(vsite_dict)

Construct a new TrivalentPairVirtualSite from an serialized dictionary representation.

Parameters

vsite_dictdict

The VirtualSite to deserialize.

Returns

The newly created TrivalentLonePairVirtualSite

property distance

The distance parameter of the virtual site

get_openmm_virtual_site(atoms)

Returns the OpenMMVirtualSite corresponding to this TrivalentLonePairVirtualSite.

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 amy 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 from particle_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)