fixed mmalign output parsing

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')