From 3be3cf3d098343bd3b7028dbfc8ddcc996cf725d Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 5 Mar 2025 17:33:46 +0100
Subject: [PATCH] log: warn user when things get filtered out
---
modules/mol/alg/pymod/chain_mapping.py | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 4a416c2d1..ab36ee495 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -790,6 +790,8 @@ class ChainMapper:
seq_id_thr = self.mdl_map_pep_seqid_thr,
min_aln_length = self.min_pep_length)
if idx is None:
+ ost.LogWarning("Could not map model chain %s to any chem group"
+ " in the target" % s.name)
mdl_chains_without_chem_mapping.append(s.GetName())
else:
mapping[idx].append(s.GetName())
@@ -802,6 +804,8 @@ class ChainMapper:
seq_id_thr = self.mdl_map_nuc_seqid_thr,
min_aln_length = self.min_nuc_length)
if idx is None:
+ ost.LogWarning("Could not map model chain %s to any chem group"
+ " in the target" % s.name)
mdl_chains_without_chem_mapping.append(s.GetName())
else:
mapping[idx].append(s.GetName())
@@ -1601,9 +1605,11 @@ class ChainMapper:
# filter out short chains
if n_pep > 0 and n_pep < self.min_pep_length:
+ ost.LogWarning("Skipping short peptide chain: %s" % ch.name)
continue
if n_nuc > 0 and n_nuc < self.min_nuc_length:
+ ost.LogWarning("Skipping short nucleotide chain: %s" % ch.name)
continue
# the superfast residue number based alignment adds some
--
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