1.1 --- a/utils/rasmol_homology.py	Sat Jul 16 17:07:19 2011 +0400
     1.2 +++ b/utils/rasmol_homology.py	Sat Jul 16 19:59:16 2011 +0400
     1.3 @@ -3,6 +3,8 @@
     1.4  import optparse
     1.5  from allpy import protein, structure, markups, homology
     1.6  
     1.7 +flank_size = 5 #flanks' size
     1.8 +
     1.9  class Alignment(protein.Alignment, structure.AlignmentMixin):
    1.10      pass
    1.11  class Block(protein.Block, structure.BlockMixin):
    1.12 @@ -80,15 +82,23 @@
    1.13  process_sequence(main_sequence, len(alignment.sequences)-1)
    1.14  main_sequence.pdb_unload()
    1.15  
    1.16 +def sequence2name(sequence):
    1.17 +    return 'str_%s' % sequence.name.replace('/','_').replace(':','_')
    1.18 +
    1.19 +sequence_names = []
    1.20  for sequence, chain_model in idmap.items():
    1.21      chain, model = chain_model
    1.22 -    write('define str_%s *:%s' % (sequence.name, chain))
    1.23 +    write('define %s *:%s' % (sequence2name(sequence), chain))
    1.24 +    sequence_names.append(sequence2name(sequence))
    1.25  
    1.26  write('select all')
    1.27  write('color chain')
    1.28  write('restrict none')
    1.29  write('background [230, 240, 250]')
    1.30  write('select none')
    1.31 +write('select %s' % ', '.join(sequence_names))
    1.32 +write('backbone')
    1.33 +write('pause')
    1.34  
    1.35  for num, block in enumerate(blocks, 1):
    1.36      name = 'block_%s' % num
    1.37 @@ -100,24 +110,30 @@
    1.38          warn("Skipping %s of depth %s" % (name, len(block.sequences)))
    1.39          continue
    1.40  
    1.41 +    with_flanks = []
    1.42      parts = []
    1.43      for sequence in block.sequences:
    1.44          chain, model = idmap[sequence]
    1.45          resi_from = monomer2id[block.columns[0][sequence]]
    1.46          resi_to = monomer2id[block.columns[-1][sequence]]
    1.47 +        with_flanks.append('%i-%i:%s' % (resi_from-flank_size, resi_to+flank_size, chain))
    1.48          parts.append('%i-%i:%s' % (resi_from, resi_to, chain))
    1.49  
    1.50      selection = ','.join(parts)
    1.51 -    sequences = ', '.join(seq.name for seq in block.sequences)
    1.52 +    sequences = ', '.join(sequence2name(seq) for seq in block.sequences)
    1.53      column_from = alignment.markups['number'][block.columns[0]]
    1.54      column_to = alignment.markups['number'][block.columns[-1]]
    1.55  
    1.56      write('')
    1.57 -    write('backbone')
    1.58 +    write('define with_flanks_%i %s' % (num, ','.join(with_flanks)))
    1.59      write('define %s %s' % (name, selection))
    1.60 +    write('select with_flanks_%i' % num)
    1.61 +    write('backbone 60')
    1.62      write('select %s' % (name))
    1.63      write('echo %s %s %i-%i' % (name, sequences, column_from, column_to))
    1.64 -    write('backbone 100')
    1.65 +    write('backbone 150')
    1.66      write('pause')
    1.67 +    write('select with_flanks_%i' % num)
    1.68 +    write('backbone ')
    1.69  
    1.70  # vim: set et ts=4 sts=4 sw=4: