From 8a47dff6c59a77ca5e072bfdafcab9aff808efff Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 6 Aug 2020 13:46:14 +0200
Subject: [PATCH] Residue numbers must be unique when using them to align
residues to a SEQRES
---
modules/seq/alg/pymod/__init__.py | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index f97771723..3be1b5845 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -100,10 +100,17 @@ def AlignToSEQRES(chain, seqres, try_resnum_first=False, validate=True):
return seq.CreateAlignment()
if try_resnum_first:
aln_seq = seq.CreateSequence('atoms', '-'*len(seqres))
+ aligned_resnums = set()
for r1 in residues:
+ if r1.number.num in aligned_resnums:
+ LogWarning('Residue numbers must be unique. Already observed %i, ' \
+ 'cannot align %s anymore.'%(r1.number.num, r1.qualified_name))
+ try_resnum_first = False
+ break
if r1.number.num <= len(seqres) and r1.number.num > 0:
if IsEqual(seqres[r1.number.num - 1], r1.one_letter_code):
aln_seq[r1.number.num - 1] = r1.one_letter_code
+ aligned_resnums.add(r1.number.num)
else:
LogWarning('Sequence mismatch: chain has "' + r1.one_letter_code +
'", while SEQRES is "' + seqres[r1.number.num - 1] +
--
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