LigParGenForceFieldSource

class openff.evaluator.forcefield.LigParGenForceFieldSource(preferred_charge_model=ChargeModel.CM1A_1_14_LBCC, cutoff=9.0 * unit.angstrom, request_url='', download_url='')[source]

A wrapper and the OPLSAAM force field which can be applied via the LigParGen server.

References

[1] Potential energy functions for atomic-level simulations of water and organic and: biomolecular systems. Jorgensen, W. L.; Tirado-Rives, J. Proc. Nat. Acad. Sci. USA 2005, 102, 6665-6670
[2] 1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase: Simulations. Dodda, L. S.; Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B, 2017, 121 (15), pp 3864-3870
[3] LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands.: Dodda, L. S.;Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L. Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W331-W336

__init__(preferred_charge_model=ChargeModel.CM1A_1_14_LBCC, cutoff=9.0 * unit.angstrom, request_url='', download_url='')[source]

Constructs a new LigParGenForceFieldSource object

Parameters

preferred_charge_model (ChargeModel) – The preferred charge model to apply. In some cases the preferred charge model may not be applicable (e.g. 1.14*CM1A-LBCC may only be applied to neutral molecules) and so another model may be applied in its place.
cutoff (openff.evaluator.unit.Quantity) – The non-bonded interaction cutoff.
request_url (str) – The URL of the LIGPARGEN server file to send the parametrization to request to.
download_url (str) – The URL of the LIGPARGEN server file to download the results of a request from.

Methods

`__init__`([preferred_charge_model, cutoff, ...])	Constructs a new LigParGenForceFieldSource object
`from_json`(file_path)	Create this object from a JSON file.
`json`([file_path, format])	Creates a JSON representation of this class.
`parse_json`(string_contents)	Parses a typed json string into the corresponding class structure.

Attributes

`cutoff`	The non-bonded interaction cutoff.
`download_url`	The URL of the LIGPARGEN server file to download the results of a request from.
`preferred_charge_model`	The preferred charge model to apply.
`request_url`	The URL of the LIGPARGEN server file to send the parametrization to request to.

class ChargeModel(value)[source]: An enumeration.

property preferred_charge_model

The preferred charge model to apply. In some cases the preferred charge model may not be applicable (e.g. 1.14*CM1A-LBCC may only be applied to neutral molecules) and so another model may be applied in its place.

Type: ChargeModel

property cutoff

The non-bonded interaction cutoff.

Type: openff.evaluator.unit.Quantity

property request_url

The URL of the LIGPARGEN server file to send the parametrization to request to.

Type: str

property download_url

The URL of the LIGPARGEN server file to download the results of a request from.

Type: str

classmethod from_json(file_path)

Create this object from a JSON file.

Parameters: file_path (str) – The path to load the JSON from.
Returns: The parsed class.
Return type: cls

json(file_path=None, format=False)

Creates a JSON representation of this class.

Parameters

file_path (str, optional) – The (optional) file path to save the JSON file to.
format (bool) – Whether to format the JSON or not.

Returns

The JSON representation of this class.

Return type

str

classmethod parse_json(string_contents)

Parses a typed json string into the corresponding class structure.

Parameters: string_contents (str or bytes) – The typed json string.
Returns: The parsed class.
Return type: Any