From 783b39d97b5cb9307b14e7d8959a1e6d5aef5d54 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 5 Mar 2025 13:14:30 +0100
Subject: [PATCH] doc: thresholds given in percentages, between 0 and 100
---
modules/mol/alg/pymod/chain_mapping.py | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index ce0034a5f..4a416c2d1 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*
--
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