From 9f2ae1c3fb86eb1e30627eed57f26ca13f16700c Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 13 Oct 2014 10:13:40 +0200
Subject: [PATCH] Fixed issue with local alignments in Superpose, now only the
longest alignment (most res in match/ mismatch state) is used
---
modules/mol/alg/pymod/superpose.py | 29 +++++++++++++++++++++--------
1 file changed, 21 insertions(+), 8 deletions(-)
diff --git a/modules/mol/alg/pymod/superpose.py b/modules/mol/alg/pymod/superpose.py
index 4f1ac1e0a..3f756c2a0 100644
--- a/modules/mol/alg/pymod/superpose.py
+++ b/modules/mol/alg/pymod/superpose.py
@@ -202,16 +202,29 @@ def _MatchResidueByAln(ent_a, ent_b, atoms, alnmethod):
seq_b = ost.seq.CreateSequence(chain_b.name, s_b)
aln_a_b = alnmethod(seq_a, seq_b, ost.seq.alg.BLOSUM62)
## evaluate alignment
- for aln in aln_a_b:
- ## bind chain to alignment
- aln.AttachView(0, chain_a.Select('protein=True'))
- aln.AttachView(1, chain_b.Select('protein=True'))
- ## select residues (only replacement edges)
+ max_aln_res = 0
+ for a in range(0, len(aln_a_b)):
+ aln = aln_a_b[a]
+ aln_res_len = 0
+ match_list = list()
for i in range(0, aln.GetLength()):
if aln.sequences[0][i]!='-' and aln.sequences[1][i]!='-':
- r_a = aln.GetResidue(0,i)
- r_b = aln.GetResidue(1,i)
- result_a,result_b=_fetch_atoms(r_a, r_b, result_a, result_b, atmset)
+ aln_res_len += 1
+ match_list.append(i)
+ if aln_res_len > max_aln_res:
+ max_aln_res = aln_res_len
+ max_aln_idx = a
+ max_matches = match_list
+
+ aln = aln_a_b[max_aln_idx]
+ ## bind chain to alignment
+ aln.AttachView(0, chain_a.Select('protein=True'))
+ aln.AttachView(1, chain_b.Select('protein=True'))
+ ## select residues (only replacement edges)
+ for i in max_matches:
+ r_a = aln.GetResidue(0,i)
+ r_b = aln.GetResidue(1,i)
+ result_a,result_b=_fetch_atoms(r_a, r_b, result_a, result_b, atmset)
result_a.AddAllInclusiveBonds()
result_b.AddAllInclusiveBonds()
return result_a, result_b
--
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