openforcefield.topology.VirtualSite

class 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.

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)

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

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.

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)