From d8c4242ee571f51ef4e9804cb72ad086dd033bdd Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 9 Sep 2011 10:20:53 +0200
Subject: [PATCH] Added handling of 'X', '?' to AlignToSeqres
---
modules/seq/alg/pymod/__init__.py | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index bd108a603..63157ea31 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -85,6 +85,10 @@ def AlignToSEQRES(chain, seqres, try_resnum_first=False, validate=True):
:returns: The alignment of the residues in the chain and the SEQRES entries.
:rtype: :class:`~ost.seq.AlignmentHandle`
"""
+
+ def IsEqual(olc1, olc2):
+ return olc1 in ('X', '?') or olc2 in ('X', '?') or olc1 == olc2
+
from ost import seq
from ost import mol
from ost import LogWarning
@@ -96,7 +100,7 @@ def AlignToSEQRES(chain, seqres, try_resnum_first=False, validate=True):
aln_seq = seq.CreateSequence('atoms', '-'*len(seqres))
for r1 in residues:
if r1.number.num <= len(seqres) and r1.number.num > 0:
- if seqres[r1.number.num - 1] == r1.one_letter_code:
+ if IsEqual(seqres[r1.number.num - 1], r1.one_letter_code):
aln_seq[r1.number.num - 1] = r1.one_letter_code
else:
LogWarning('Sequence mismatch: chain has "' + r1.one_letter_code +
--
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