From 64db2dd40d376e489d11b8f4af0b3e5becbd9a0c Mon Sep 17 00:00:00 2001
From: Martino Bertoni <martino.bertoni@unibas.ch>
Date: Mon, 23 Sep 2013 17:52:03 +0200
Subject: [PATCH] fixed mmalign output parsing
---
modules/bindings/pymod/tmtools.py | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 294da0e50..876318841 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -128,12 +128,11 @@ def _RunTmAlign(tmalign, tmp_dir):
return _ParseTmAlign(lines,lines_matrix)
class MMAlignResult:
- def __init__(self, rmsd, tm_score, aligned_length, transform, ref_sequence, alignment):
+ def __init__(self, rmsd, aligned_length, tm_score, transform, alignment):
self.rmsd=rmsd
self.tm_score=tm_score
self.aligned_length=aligned_length
self.transform=transform
- self.ref_sequence =ref_sequence
self.alignment=alignment
def _ParseMmAlign(lines):
@@ -153,7 +152,7 @@ def _ParseMmAlign(lines):
alignment = seq.CreateAlignment()
alignment.AddSequence(seq2)
alignment.AddSequence(seq1)
- return MMAlignResult(rmsd, aln_length, tm_score, tf, seq2, alignment)
+ return MMAlignResult(rmsd, aln_length, tm_score, tf, alignment)
def _RunMmAlign(mmalign, tmp_dir):
model1_filename=os.path.join(tmp_dir, 'model01.pdb')
--
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