BioSimSpace.Convert.toRDKit

BioSimSpace.Convert.toRDKit(obj, force_stereo_inference=False, determine_bond_orders=True, property_map={})[source]

Convert an object to RDKit format.

Parameters:

  • obj – The input object to convert.

  • bool (determine_bond_orders) – Whether to force inference of stereochemistry, overriding any stereochemistry present in the input object. This is useful when the object has been loaded from a file with invalid stereochemistry.

  • bool – Whether to use RDKit’s determineBondOrders function when bond orders need to be inferred. This is more robust than the internal heuristic, but can be slow for large molecules, e.g. proteins.

  • 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:

The object in OpenMM format.

Return type:

converted_obj