openff.recharge.charges.vsite.VirtualSiteCollection

model openff.recharge.charges.vsite.VirtualSiteCollection[source]

Bases: BaseModel

A collection of virtual site parameters that are based off of the SMIRNOFF specification.

Fields
field parameters: List[Union[openff.recharge.charges.vsite.BondChargeSiteParameter, openff.recharge.charges.vsite.MonovalentLonePairParameter, openff.recharge.charges.vsite.DivalentLonePairParameter, openff.recharge.charges.vsite.TrivalentLonePairParameter]] [Required]

The virtual site parameters to apply.

field aromaticity_model: openff.recharge.aromaticity._aromaticity.AromaticityModels = AromaticityModels.MDL

The model to use when assigning aromaticity.

field exclusion_policy: Literal['none', 'parents'] = 'parents'

…

to_smirnoff() → VirtualSiteHandler[source]

Converts this collection of virtual site parameters to a SMIRNOFF virtual site parameter handler.

Return type

The constructed parameter handler.

classmethod from_smirnoff(parameter_handler: VirtualSiteHandler, aromaticity_model=AromaticityModels.MDL) → VirtualSiteCollection[source]

Attempts to convert a SMIRNOFF virtual site parameter handler to a virtual site parameter collection.

Parameters

  • parameter_handler – The parameter handler to convert.

  • aromaticity_model – The model which describes how aromaticity should be assigned when applying the virtual site correction parameters.

Return type

The converted virtual site collection.

vectorize_coordinates(parameter_keys: List[Tuple[str, str, str, Literal['distance', 'in_plane_angle', 'out_of_plane_angle']]]) → ndarray[source]

Returns a flat vector of the local frame coordinate values associated with a specified set of ‘keys’.

Parameters

parameter_keys – A list of parameter ‘keys’ of the form (smirks, type, name, attr) that specify which local frame coordinate to include in the returned vector.

The allowed attributes are distance, in_plane_angle, out_of_plane_angle

Return type

A vector of local frame coordinate with shape=(n_keys, 1)

vectorize_charge_increments(parameter_keys: List[Tuple[str, str, str, int]]) → ndarray[source]

Returns a flat vector of the charge increment values associated with a specified set of ‘keys’.

Parameters

parameter_keys – A list of parameter ‘keys’ of the form (smirks, type, name, idx) that specify which charge increments to include in the returned vector, where idx is an integer index into a parameters’ charge_increments tuple.

Return type

A vector of charge increments with shape=(n_keys, 1)