From 31c3a281835a59b44e5675f1b19f7cac66dfb822 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 13 Sep 2022 08:34:13 +0200
Subject: [PATCH] chain mapping: guarantee that proper EntityViews are attached
---
modules/mol/alg/pymod/chain_mapping.py | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 286b440aa..a7b2f824f 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1089,6 +1089,9 @@ class ChainMapper:
# strip the reference sequence in alignments to only contain
# sequence from substructure
substructure_ref_mdl_alns = dict()
+ mdl_views = dict()
+ for ch in mdl.chains:
+ mdl_views[ch.GetName()] = mdl.Select(f"cname={ch.GetName()}")
for chem_group, mapping in zip(substructure_chem_groups,
substructure_chem_mapping):
for ref_ch in chem_group:
@@ -1104,9 +1107,13 @@ class ChainMapper:
tmp[idx_in_seq] = ref_seq[idx_in_seq]
ref_seq = seq.CreateSequence(ref_ch, ''.join(tmp))
ref_seq.AttachView(substructure.Select(f"cname={ref_ch}"))
+ mdl_seq = full_aln.GetSequence(1)
+ mdl_seq = seq.CreateSequence(mdl_seq.GetName(),
+ mdl_seq.GetString())
+ mdl_seq.AttachView(mdl_views[mdl_ch])
aln = seq.CreateAlignment()
aln.AddSequence(ref_seq)
- aln.AddSequence(full_aln.GetSequence(1))
+ aln.AddSequence(mdl_seq)
substructure_ref_mdl_alns[(ref_ch, mdl_ch)] = aln
lddt_scorer = lddt.lDDTScorer(substructure,
--
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