BioSimSpace.Parameters.parameterise

BioSimSpace.Parameters.parameterise(molecule, forcefield, ensure_compatible=True, work_dir=None, property_map={}, **kwargs)[source]

Parameterise a molecule using a specified force field.

Parameters:

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

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

  • 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.

  • 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” }

  • kwargs (dict) – A dictionary of additional keyword arguments required for specific parameterisation functions.

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