diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py index 8ea683d80b960ff8d549b56cb7ca8838bd0d7199..3b7a20f71540f492a30e9d62891433ee32e78d93 100644 --- a/modules/mol/alg/pymod/ligand_scoring.py +++ b/modules/mol/alg/pymod/ligand_scoring.py @@ -10,8 +10,7 @@ from ost.mol.alg import chain_mapping class LigandScorer: - """ Helper class to access the various small molecule ligand (non polymer) - scores available from ost.mol.alg. + """ Scorer class to compute various small molecule ligand (non polymer) scores. .. note :: Extra requirements: @@ -19,10 +18,18 @@ class LigandScorer: - Python modules `numpy` and `networkx` must be available (e.g. use ``pip install numpy networkx``) - Mostly expects cleaned up structures (you can use the + At the moment, two scores are available: + + * lDDT-PLI + * Symmetry-corrected RMSD + + The class takes care to perform chain mapping and assignment (mapping) of + model and target ligands. This assignment may differ between scores. + + It mostly expects cleaned up structures (you can use the :class:`~ost.mol.alg.scoring.Scorer` outputs for that). In addition, you probably want to remove hydrogen atoms from the structures before - calling this function. You can do this easily with a selection: + calling this function. You can do this easily with a selection:: target_noH = target.Select("ele != H") model_noH = model.Select("ele != H") @@ -99,11 +106,11 @@ class LigandScorer: :param radius: Inclusion radius for the binding site. Any residue with atoms within this distance of the ligand will be included in the binding site. - :param radius: :class:`float` + :type radius: :class:`float` :param lddt_pli_radius: lDDT inclusion radius for lDDT-PLI. - :param lddt_pli_radius: :class:`float` + :type lddt_pli_radius: :class:`float` :param lddt_bs_radius: lDDT inclusion radius for lDDT-BS. - :param lddt_bs_radius: :class:`float` + :type lddt_bs_radius: :class:`float` """ def __init__(self, model, target, model_ligands=None, target_ligands=None, resnum_alignments=False, check_resnames=True, @@ -716,6 +723,7 @@ def ResidueToGraph(residue, by_atom_index=False): Otherwise, if False, the nodes will be labeled by atom names. :type by_atom_index: :class:`bool` + :rtype: :class:`~networkx.classes.graph.Graph` Nodes are labeled with the Atom's :attr:`~ost.mol.AtomHandle.element`. """