BioSimSpace.Parameters.parameterise

BioSimSpace.Parameters.parameterise(molecule, forcefield, water_model=None, work_dir=None, property_map={})

Parameterise a molecule using a specified force field.

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

  • water_model (str) – The water model used to parameterise any structural ions. This will be ignored when it is not supported by the chosen force field, or when ions aren’t present. Run ‘BioSimSpace.Solvent.waterModels()’ to see the supported water models.

  • forcefield (str) – The force field. Run BioSimSpace.Parameters.forceFields() to get a list of the supported force fields.

  • 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

molecule – The parameterised molecule.

Return type

Molecule