From bea30154ec77fddbf253e891b90e41a9e8ff508d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 4 Apr 2025 15:01:48 +0200
Subject: [PATCH] Scorer: lddt bugfix
If it happens that stereochemistry checks remove a full chain,
this chain still exists in the chain mapping that is passed to
the lDDT scorer. The input check in the lDDT scorer then raises
because it gets a mapping for a model chain that does not exist.
---
modules/mol/alg/pymod/scoring.py | 19 +++++++++++++++----
1 file changed, 15 insertions(+), 4 deletions(-)
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 9f88d18fc..500a046cd 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -2225,10 +2225,6 @@ class Scorer:
flat_mapping = self.mapping.GetFlatMapping(mdl_as_key=True)
# make alignments accessible by mdl seq name
- stereochecked_alns = dict()
- for aln in self.stereochecked_aln:
- mdl_seq = aln.GetSequence(1)
- stereochecked_alns[mdl_seq.name] = aln
alns = dict()
for aln in self.aln:
mdl_seq = aln.GetSequence(1)
@@ -2284,10 +2280,25 @@ class Scorer:
else:
+ # keep track what chains we have in the stereochecked model
+ # there might be really wild cases where a full model
+ # chain is removed in the stereochemistry checks.
+ # We need to adapt lddt chain mapping in these cases
+ mdl_chains = set([ch.name for ch in self.stereochecked_model.chains])
+
+ # make alignments accessible by mdl seq name
+ stereochecked_alns = dict()
+ for aln in self.stereochecked_aln:
+ mdl_seq = aln.GetSequence(1)
+ if mdl_seq.GetName() in mdl_chains:
+ stereochecked_alns[mdl_seq.name] = aln
+
lddt_chain_mapping = dict()
for mdl_ch, trg_ch in flat_mapping.items():
if mdl_ch in stereochecked_alns:
lddt_chain_mapping[mdl_ch] = trg_ch
+
+
lddt_score = self.lddt_scorer.lDDT(self.stereochecked_model,
chain_mapping = lddt_chain_mapping,
residue_mapping = stereochecked_alns,
--
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