openforcefield.topology.VirtualSite

class openforcefield.topology.VirtualSite(atoms, charge_increments=None, epsilon=None, sigma=None, rmin_half=None, name=None, orientations=None)[source]

A container representing one or more virtual particles whose positions are defined in terms of Atom positions. This container enables the coupling of particles that are symmetric about some axis/plane of the underlying atoms. For example, a single virtual site can represent two lone pairs of a water molecule, where the angle and distance parameters are expected to stay coupled, and are reflections across the plane of symmetry.

Note that chemical atoms are represented by the Atom.

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

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)

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.

index_of_orientation

__init__(atoms, charge_increments=None, epsilon=None, sigma=None, rmin_half=None, name=None, orientations=None)[source]

Base class for VirtualSites

Parameters
atomslist of Atom of shape [N]

atoms[index] is the corresponding Atom for weights[index]

charge_incrementslist of floats of shape [N], optional, default=None

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.

sigmafloat, default=None

Sigma term for VdW properties of virtual site. Default is None.

epsilonfloat

Epsilon 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.

virtual_site_typestr

Virtual site type.

namestr or None, default=None

The name of this virtual site. Default is None

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.

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

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()[source]

Return a dict representation of the virtual site.

classmethod from_dict(vsite_dict)[source]

Create a virtual site from a dict representation.

property particles

Particles owned by this VirtualSite

property n_particles

The number of particles that the virtual site represents

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 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

property sigma

The VdW sigma term of this VirtualSite

property rmin_half

The VdW rmin_half term of this VirtualSite

property name

The name of this VirtualSite

property type

The type of this VirtualSite (returns the class name as string)

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

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