BioSimSpace.Parameters.openff_unconstrained_1_3_1

BioSimSpace.Parameters.openff_unconstrained_1_3_1(molecule, ensure_compatible=True, use_nagl=True, work_dir=None, property_map={})

Parameterise a molecule using the named force field from the Open Force Field initiative.

Parameters:

  • molecule (Molecule, str) – The molecule to parameterise, either as a Molecule object or SMILES string.

  • ensure_compatible (bool) – Whether to ensure that the topology of the parameterised molecule is compatible with that of the original molecule. An exception will be raised if this isn’t the case, e.g. if atoms have been added. Set this to False is parameterising lone oxygen atoms corresponding to structural (crystal) water molecules. When True, the parameterised molecule will preserve the topology of the original molecule, e.g. the original atom and residue names will be kept.

  • use_nagl (bool) – Whether to use NAGL to compute AM1-BCC charges. If False, the default is to use AmberTools via antechamber and sqm. (This option is only used if NAGL is available.)

  • work_dir (str) – The working directory for the process.

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

Returns:

process – A process to parameterise the molecule in the background. Call the .getMolecule() method on the returned process to block until the parameterisation is complete and get the parameterised molecule.

Return type:

Process