diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py index 0f73d2005f6a0fdca0bbcaa39285871536d7a890..07ebe9a15b79661dab1e55772fe8be92f3575bc7 100644 --- a/modules/mol/alg/pymod/ligand_scoring.py +++ b/modules/mol/alg/pymod/ligand_scoring.py @@ -56,14 +56,12 @@ class LigandScorer: Note that this global chain mapping currently ignores non polymer entities such as small ligands, and may result in overly pessimistic scores. - By default, target-model ligand assignments are computed independently - for the RMSD and lDDT-PLI scores. For RMSD, each model ligand is uniquely - assigned to a target ligand, starting from the "best" possible mapping - (lowest RMSD) and using each target and model ligand in a single - assignment. Ties are resolved by best (highest) lDDT-PLI. Similarly, - for lDDT-PLI, the assignment is based on the highest lDDT-PLI, and ties - broken by lowest RMSD. Setting `rmsd_assignment=True` forces a single - ligand assignment, based on RMSD only. Ties are broken arbitrarily. + By default, target-model ligand assignments are computed identically + for the RMSD and lDDT-PLI scores. Each model ligand is uniquely assigned + to a target ligand, starting from the lowest RMSD and using each target and + model ligand in a single assignment. If `rmsd_assignment` is set to False, + RMSD and lDDT-PLI are assigned separately to optimize each score, and the + other score is used as a tiebreaker. By default, only exact matches between target and model ligands are considered. This is a problem when the target only contains a subset @@ -236,9 +234,10 @@ class LigandScorer: chain names as value. Only has an effect if *global_chain_mapping* is True. :type custom_mapping: :class:`dict` - :param rmsd_assignment: assign ligands based on RMSD only. The default - (False) is to use a combination of lDDT-PLI and - RMSD for the assignment. + :param rmsd_assignment: set to False to assign lDDT-PLI and RMSD separately + using a combination of these two scores to + optimize the assignment. By default (True), only + RMSD is considered for the ligand assignment. :type rmsd_assignment: :class:`bool` :param n_max_naive: Parameter for global chain mapping. If *model* and *target* have less or equal that number of chains,