1.1 --- a/lib/project.py	Sun Oct 24 17:29:59 2010 +0400
     1.2 +++ b/lib/project.py	Sun Oct 24 18:12:21 2010 +0400
     1.3 @@ -167,7 +167,7 @@
     1.4          uses old Monomers and Sequences objects
     1.5          """
     1.6          tmp_file, tmp_filename = mkstemp()
     1.7 -        os.close(tmp_file) # this is file descriptor, not normal file object. security issue )
     1.8 +        os.close(tmp_file) # this is file descriptor, not normal file object.
     1.9          tmp_file = open(tmp_filename, 'w')
    1.10          self.save_fasta(tmp_file)
    1.11          tmp_file.close()
    1.12 @@ -177,7 +177,8 @@
    1.13              try:
    1.14                  new_sequence = [i for i in sequences if sequence==i][0]
    1.15              except:
    1.16 -                raise Exception("Align: Cann't find sequence %s in muscle output" % sequence.name)
    1.17 +                raise Exception("Align: Cann't find sequence %s in muscle output" % \
    1.18 +                sequence.name)
    1.19              old_monomers = iter(sequence.monomers)
    1.20              self.alignment[sequence] = []
    1.21              for monomer in alignment[new_sequence]:
    1.22 @@ -194,7 +195,7 @@
    1.23          returns list of columns of alignment
    1.24          sequence or sequences:
    1.25              if sequence is given, then column is (original_monomer, monomer)
    1.26 -            if sequences is given, then column is dict (original_monomer, {sequence: monomer}) 
    1.27 +            if sequences is given, then column is (original_monomer, {sequence: monomer}) 
    1.28              if both of them are given, it is an error
    1.29          original (Sequence type):
    1.30              if given, this filters only columns represented by original sequence
    1.31 @@ -210,11 +211,17 @@
    1.32                  if sequence:
    1.33                      yield (column[indexes[original]], column[indexes[sequence]])
    1.34                  else:
    1.35 -                    yield (column[indexes[original]], dict([(s, column[indexes[s]]) for s in sequences]))
    1.36 +                    yield (column[indexes[original]], 
    1.37 +                    dict([(s, column[indexes[s]]) for s in sequences]))
    1.38          
    1.39 -    def add_pdb(self, conformity_file=None):
    1.40 -        pass
    1.41 +    def pdb_auto_add(self, conformity_file=None):
    1.42 +        """
    1.43 +        Adds pdb information to each sequence
    1.44          
    1.45 +        TODO: conformity_file
    1.46 +        """
    1.47 +        conformity = {}
    1.48          
    1.49 +        for sequence in self.sequences:
    1.50 +            sequence.pdb_auto_add(conformity.get(sequence.name, None))
    1.51          
    1.52 -