1.1 --- a/pair_cores/pair_cores.py	Wed Feb 29 22:40:54 2012 +0400
     1.2 +++ b/pair_cores/pair_cores.py	Thu Mar 01 00:24:08 2012 +0400
     1.3 @@ -14,11 +14,12 @@
     1.4  import allpy.base
     1.5  from html import html_template
     1.6  from allpy.structure import CachedDownloadPdb, cached_download_pdb
     1.7 +from allpy.homology import MonomerHomology
     1.8  
     1.9  def homology_from_3d(markup_file, homology_file, max_delta, ignore_one_ss=False, alignment_file=None,
    1.10      out_alignment_file=None, out_pair_cores_file=None, out_html_file=None,
    1.11      pdb_getter=cached_download_pdb, out_pymol_file=None, min_width=4,
    1.12 -    out_high_blocks_file=None, out_high_blocks_html_file=None,
    1.13 +    out_high_blocks_file=None, out_high_blocks_html_file=None, blocks3d=False,
    1.14      blocks3d_timeout=-1):
    1.15      """ Turn pdb markup into homology_file
    1.16  
    1.17 @@ -34,6 +35,7 @@
    1.18      * min_width -- min width of each core
    1.19      * out_high_blocks_file -- output file with blocks of multiple sequences
    1.20      * out_high_blocks_html_file -- output HTML file with blocks of multiple sequences
    1.21 +    * blocks3d -- if old (graph-based) blocks algorithm is used
    1.22      * blocks3d_timeout -- Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)
    1.23      """
    1.24      if markup_file:
    1.25 @@ -78,9 +80,15 @@
    1.26          block.blocks_to_pymol(out_pymol_file, blocks)
    1.27      if out_high_blocks_file or out_high_blocks_html_file:
    1.28          high_blocks = []
    1.29 -        high_blocks = list(block.blocks3d(parts=blocks,
    1.30 -            timeout_2=blocks3d_timeout))
    1.31 -        del blocks # spoiled by blocks3d()
    1.32 +        if blocks3d:
    1.33 +            high_blocks = list(block.blocks3d(parts=blocks,
    1.34 +                timeout_2=blocks3d_timeout))
    1.35 +            del blocks # spoiled by blocks3d()
    1.36 +        else:
    1.37 +            homology = MonomerHomology()
    1.38 +            homology.read(homology_file.name, columns=True)
    1.39 +            homology.highest_blocks()
    1.40 +            high_blocks = block.blocks_from_homology(homology, min_width=min_width)
    1.41          if out_high_blocks_file:
    1.42              block.blocks_to_file(out_high_blocks_file, high_blocks)
    1.43          if out_high_blocks_html_file:
    1.44 @@ -106,6 +114,7 @@
    1.45  
    1.46      p.add_argument('--high-blocks',help='Output text file with high blocks',metavar='FILE',type=w)
    1.47      p.add_argument('--high-blocks-html',help='Output HTML file with high blocks',metavar='FILE',type=w)
    1.48 +    p.add_argument('--blocks3d',help='Use blocks3d algorithm for high blocks',action='store_true')
    1.49      p.add_argument('--blocks3d-timeout',help='Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)',
    1.50              metavar='int',type=timeout,default=config.timeout_2)
    1.51      args = p.parse_args()
    1.52 @@ -115,7 +124,7 @@
    1.53          out_pymol_file=args.p,min_width=args.w,
    1.54          out_high_blocks_file=args.high_blocks,
    1.55          out_high_blocks_html_file=args.high_blocks_html,
    1.56 -        blocks3d_timeout=args.blocks3d_timeout)
    1.57 +        blocks3d=args.blocks3d, blocks3d_timeout=args.blocks3d_timeout)
    1.58  
    1.59  if __name__ == '__main__':
    1.60          main()