1.1 --- a/pair_cores/pair_cores.py	Wed Feb 29 15:13:12 2012 +0400
     1.2 +++ b/pair_cores/pair_cores.py	Wed Feb 29 15:16:46 2012 +0400
     1.3 @@ -7,6 +7,8 @@
     1.4  import argparse
     1.5  from copy import copy
     1.6  
     1.7 +from allpy import config
     1.8 +from allpy.argparse_validators import timeout
     1.9  from protein_pdb import Alignment, Block, Monomer, Sequence
    1.10  from allpy import processors, markups
    1.11  import allpy.base
    1.12 @@ -15,7 +17,9 @@
    1.13  
    1.14  def homology_from_3d(markup_file, homology_file, max_delta, ignore_one_ss=False, alignment_file=None,
    1.15      out_alignment_file=None, out_pair_cores_file=None, out_html_file=None,
    1.16 -    pdb_getter=cached_download_pdb, out_pymol_file=None, min_width=4):
    1.17 +    pdb_getter=cached_download_pdb, out_pymol_file=None, min_width=4,
    1.18 +    out_high_blocks_file=None, out_high_blocks_html_file=None,
    1.19 +    blocks3d_timeout=-1):
    1.20      """ Turn pdb markup into homology_file
    1.21  
    1.22      * markup_file -- file with pdb markup of alignment
    1.23 @@ -28,6 +32,9 @@
    1.24      * pdb_getter -- see structure.SequenceMixin.auto_pdb
    1.25      * out_pymol_file -- output file with PyMol superimposing script
    1.26      * min_width -- min width of each core
    1.27 +    * out_high_blocks_file -- output file with blocks of multiple sequences
    1.28 +    * out_high_blocks_html_file -- output HTML file with blocks of multiple sequences
    1.29 +    * blocks3d_timeout -- Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)
    1.30      """
    1.31      if markup_file:
    1.32          input_file = markup_file
    1.33 @@ -60,6 +67,7 @@
    1.34      blocks = block.pair_core_parts(max_delta=max_delta, timeout=0,
    1.35          min_width=min_width, ignore_one_ss=ignore_one_ss)
    1.36      alignment.blocks_to_homology(homology_file, blocks)
    1.37 +    homology_file.close()
    1.38      if out_alignment_file:
    1.39          block.to_file(out_alignment_file)
    1.40      if out_pair_cores_file:
    1.41 @@ -68,6 +76,16 @@
    1.42          block.blocks_to_html(out_html_file, blocks, open(html_template).read())
    1.43      if out_pymol_file:
    1.44          block.blocks_to_pymol(out_pymol_file, blocks)
    1.45 +    if out_high_blocks_file or out_high_blocks_html_file:
    1.46 +        high_blocks = []
    1.47 +        high_blocks = list(block.blocks3d(parts=blocks,
    1.48 +            timeout_2=blocks3d_timeout))
    1.49 +        del blocks # spoiled by blocks3d()
    1.50 +        if out_high_blocks_file:
    1.51 +            block.blocks_to_file(out_high_blocks_file, high_blocks)
    1.52 +        if out_high_blocks_html_file:
    1.53 +            block.blocks_to_html(out_high_blocks_html_file, high_blocks,
    1.54 +                open(html_template).read())
    1.55  
    1.56  def main():
    1.57      r = argparse.FileType('r')
    1.58 @@ -85,15 +103,20 @@
    1.59      p.add_argument('-H',help='Output HTML file',metavar='FILE',type=w)
    1.60      p.add_argument('-p',help='Output PyMol file',metavar='FILE',type=w)
    1.61      p.add_argument('-w',help='Min width of pair core',metavar='WIDTH',type=int,default=4)
    1.62 +
    1.63 +    p.add_argument('--high-blocks',help='Output text file with high blocks',metavar='FILE',type=w)
    1.64 +    p.add_argument('--high-blocks-html',help='Output HTML file with high blocks',metavar='FILE',type=w)
    1.65 +    p.add_argument('--blocks3d-timeout',help='Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)',
    1.66 +            metavar='int',type=timeout,default=config.timeout_2)
    1.67      args = p.parse_args()
    1.68      homology_from_3d(markup_file=args.m, homology_file=args.y, max_delta=args.d, ignore_one_ss=args.e,
    1.69          alignment_file=args.i, out_alignment_file=args.o, out_pair_cores_file=args.b,
    1.70          out_html_file=args.H, pdb_getter=CachedDownloadPdb(cache_dir=args.c),
    1.71 -        out_pymol_file=args.p,min_width=args.w)
    1.72 +        out_pymol_file=args.p,min_width=args.w,
    1.73 +        out_high_blocks_file=args.high_blocks,
    1.74 +        out_high_blocks_html_file=args.high_blocks_html,
    1.75 +        blocks3d_timeout=args.blocks3d_timeout)
    1.76  
    1.77  if __name__ == '__main__':
    1.78 -    try:
    1.79          main()
    1.80 -    except Exception, e:
    1.81 -        print e
    1.82