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 fromparticle_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 fromparticle_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)