1.1 --- a/allpy/structure.py	Sat Mar 26 02:16:01 2011 +0300
     1.2 +++ b/allpy/structure.py	Sat Mar 26 02:18:36 2011 +0300
     1.3 @@ -98,7 +98,6 @@
     1.4          a.append_sequence(self)
     1.5          a.append_sequence(pdb_sequence)
     1.6          a.process(processors.Muscle())
     1.7 -        mutations = 0
     1.8          Block = self.types.Block
     1.9          matches = Block.from_alignment(a, columns=[])
    1.10          for column in a.columns:
    1.11 @@ -118,10 +117,17 @@
    1.12          for block in match_blocks:
    1.13              for column in block.columns:
    1.14                  matched_pdb.append(column[pdb_sequence])
    1.15 -        central_start = pdb_sequence.index(matched_pdb[0])
    1.16 -        central_stop = pdb_sequence.index(matched_pdb[-1]) + 1
    1.17 -        central_pdb = pdb_sequence[central_start:central_stop]
    1.18 -        central_pdb = [m for m in central_pdb if hasattr(m, 'pdb_residue')]
    1.19 +        central_start = matched_pdb[0]
    1.20 +        central_stop = matched_pdb[-1]
    1.21 +        central_pdb = []
    1.22 +        started = False
    1.23 +        for m in pdb_sequence:
    1.24 +            if m is central_start:
    1.25 +                started = True
    1.26 +            if started and hasattr(m, 'pdb_residue'):
    1.27 +                central_pdb.append(m)
    1.28 +            if m is central_stop:
    1.29 +                break
    1.30          assert len(set(central_pdb) - set(matched_pdb)) <= max_waste_in_pdb
    1.31          assert len(matched_pdb) >= min_match
    1.32