From c726014048029c54695e7405ef31bf38bef335b4 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Thu, 11 Aug 2011 14:23:56 +0200
Subject: [PATCH] improve error messages for ValidateSEQRESAlignment
---
modules/seq/alg/pymod/__init__.py | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index 4207f80eb..9907b011f 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -15,6 +15,7 @@ def ValidateSEQRESAlignment(aln, chain=None):
:returns: True if all residues (beside gaped ones) are connected, False
otherwise.
"""
+ from ost import LogWarning
from ost import seq
from ost import mol
if aln.GetCount() != 2:
@@ -41,11 +42,15 @@ def ValidateSEQRESAlignment(aln, chain=None):
i += 1
r1 = residues[i-1]
r2 = residues[i]
+ if r1.one_letter_code=='?' or r2.one_letter_code=='?':
+ continue
if l != '-':
if not mol.InSequence(r1.handle, r2.handle):
+ LogWarning('%s and %s are not connected by peptide bond' % (str(r1), str(r2)))
return False
else:
if mol.InSequence(r1.handle, r2.handle):
+ LogWarning('%s and %s are connected by peptide bond' % (str(r1), str(r2)))
return False
l = s
return True
@@ -98,6 +103,7 @@ def AlignToSEQRES(chain, seqres, try_resnum_first=False, validate=True):
'", while SEQRES is "' + seqres[r1.number.num - 1] +
'" at the corresponding position.')
try_resnum_first = False
+ break
if not try_resnum_first:
fragments=[residues[0].one_letter_code]
for r1, r2 in zip(residues[:-1], residues[1:]):
--
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