1.1 --- a/pair_cores/rasmol_output.py	Thu Jul 14 18:15:45 2011 +0400
     1.2 +++ b/pair_cores/rasmol_output.py	Fri Jul 15 18:29:55 2011 +0400
     1.3 @@ -26,6 +26,8 @@
     1.4      str = ' or '.join(monomer2str(sequence, column[sequence]) for column in cc)
     1.5      return '((%s) and name ca)' % str
     1.6  
     1.7 +flank_size = 5 #flanks' size
     1.8 +
     1.9  aln_file = sys.argv[1]
    1.10  blocks_file = sys.argv[2]
    1.11  out_pdb = sys.argv[3]
    1.12 @@ -44,14 +46,18 @@
    1.13  alignment.superimpose(columns, extra_columns=True)
    1.14  map = alignment.save_pdb(open(out_pdb, 'w'))
    1.15  
    1.16 +sequence_names = []
    1.17  for sequence, chain_model in map.items():
    1.18 -    print 'define str_%s *:%s' % (sequence.name, chain_model[0])
    1.19 +    sequence_names.append('str_%s' % sequence.name.replace('/','_').replace(':','_'))
    1.20 +    print 'define str_%s *:%s' % (sequence.name.replace('/','_').replace(':','_'), chain_model[0])
    1.21  
    1.22  print 'select all'
    1.23  print 'color chain'
    1.24  print 'restrict none'
    1.25  print 'background [230, 240, 250]'
    1.26 -print 'select none'
    1.27 +print 'select %s' % ', '.join(sequence_names)
    1.28 +print 'backbone '
    1.29 +print 'None '
    1.30  
    1.31  n = 0
    1.32  
    1.33 @@ -62,20 +68,27 @@
    1.34      for b in block.continuous_blocks():
    1.35          n += 1
    1.36          selections = []
    1.37 +        with_flanks = []
    1.38          for sequence in b.sequences:
    1.39              try:
    1.40                  chain = map[sequence][0]
    1.41                  resi_from = b.columns[0][sequence].pdb_residue.get_id()[1]
    1.42                  resi_to = b.columns[-1][sequence].pdb_residue.get_id()[1]
    1.43 +                with_flanks.append('%i-%i:%s' % (resi_from-flank_size, resi_to+flank_size, chain))
    1.44                  selections.append('%i-%i:%s' % (resi_from, resi_to, chain))
    1.45              except:
    1.46                  pass
    1.47          print ''
    1.48 -        print 'backbone'
    1.49 +        print 'backbone 30'
    1.50 +        print 'define with_flanks_%i %s' % (n, ','.join(with_flanks))
    1.51          print 'define block_%i %s' % (n, ','.join(selections))
    1.52 +        print 'select with_flanks_%i' % n
    1.53 +        print 'backbone 60'
    1.54          print 'select block_%i' % n
    1.55          print 'echo block_%i %s %i-%i' % (n, ', '.join([b.sequences[0].name, b.sequences[1].name]),
    1.56              column2pos[b.columns[0]], column2pos[b.columns[-1]])
    1.57 -        print 'backbone 100'
    1.58 +        print 'echo with_flanks_%i %s %i-%i' % (n, ', '.join([b.sequences[0].name.replace('/','_').replace(':','_'), b.sequences[1].name.replace('/','_').replace(':','_')]),
    1.59 +            column2pos[b.columns[0]], column2pos[b.columns[-1]])
    1.60 +        print 'backbone 150'
    1.61          print 'pause'
    1.62