diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py index ce0034a5fdd3beaf2a5b0584350989689bad988c..4a416c2d192f1c019f78f5cb93ccd26ec7995787 100644 --- a/modules/mol/alg/pymod/chain_mapping.py +++ b/modules/mol/alg/pymod/chain_mapping.py @@ -524,9 +524,10 @@ class ChainMapper: alignments. Relevant for :attr:`~chem_groups` and related attributes. :type resnum_alignments: :class:`bool` - :param pep_seqid_thr: Threshold used to decide when two chains are + :param pep_seqid_thr: Sequence identity threshold (in percent of aligned + columns) used to decide when two chains are identical. 95 percent tolerates the few mutations - crystallographers like to do. + crystallographers like to do. Range: [0-100]. :type pep_seqid_thr: :class:`float` :param nuc_seqid_thr: Nucleotide equivalent for *pep_seqid_thr* :type nuc_seqid_thr: :class:`float` @@ -559,14 +560,17 @@ class ChainMapper: :class:`RuntimeError` is raised in case of bigger complexity. :type n_max_naive: :class:`int` - :param mdl_map_pep_seqid_thr: To avoid non-sensical mapping of model chains - to reference chem groups. If a value larger - than 0.0 is provided, minimal criteria for - assignment becomes a sequence identity of + :param mdl_map_pep_seqid_thr: Sequence identity threshold (in percent of + aligned columns) to avoid non-sensical + mapping of model chains to reference chem + groups. If a value larger than 0.0 is + provided, minimal criteria for assignment + becomes a sequence identity of *mdl_map_pep_seqid_thr* and at least *min_pep_length* aligned residues. If set to zero, it simply assigns a model chain to the chem group with highest sequence identity. + Range: [0-100]. :type mdl_map_pep_seqid_thr: :class:`float` :param mdl_map_nuc_seqid_thr: Nucleotide equivalent of *mdl_map_pep_seqid_thr*