1.1 --- a/blocks3d/blocks3d.py	Tue Apr 03 12:02:57 2012 +0400
     1.2 +++ b/blocks3d/blocks3d.py	Tue Apr 03 12:06:26 2012 +0400
     1.3 @@ -22,7 +22,7 @@
     1.4  p = argparse.ArgumentParser(
     1.5  description='Blocks3D',
     1.6  epilog='''1) Distance spreading [angstrom]
     1.7 -2) -1 timeout means running Bron-Kerbosh algorithm without timeout''',
     1.8 +2) -1 timeout means running Bron-Kerbosch algorithm without timeout''',
     1.9  formatter_class=argparse.ArgumentDefaultsHelpFormatter,
    1.10  )
    1.11  
    1.12 @@ -36,8 +36,8 @@
    1.13  p.add_argument('-d',help='Distance spreading',metavar='float',type=f_nng,default=c.delta)
    1.14  p.add_argument('-e',help='Ignore cores, owned by one SS element',type=bool, default=False)
    1.15  p.add_argument('-m',help='Min block width',metavar='int',type=pos,default=c.min_width)
    1.16 -p.add_argument('-t',help='Bron-Kerbosh (couple cores) timeout (-1 - unlimited)',metavar='int',type=timeout,default=0)
    1.17 -p.add_argument('-T',help='Bron-Kerbosh (blocks) timeout (-1 - unlimited)',metavar='int',type=timeout,default=c.timeout_2)
    1.18 +p.add_argument('-t',help='Bron-Kerbosch (couple cores) timeout (-1 - unlimited)',metavar='int',type=timeout,default=0)
    1.19 +p.add_argument('-T',help='Bron-Kerbosch (blocks) timeout (-1 - unlimited)',metavar='int',type=timeout,default=c.timeout_2)
    1.20  
    1.21  args = p.parse_args()
    1.22  

     2.1 --- a/geometrical_core/geometrical-core	Tue Apr 03 12:02:57 2012 +0400
     2.2 +++ b/geometrical_core/geometrical-core	Tue Apr 03 12:06:26 2012 +0400
     2.3 @@ -22,7 +22,7 @@
     2.4  p = argparse.ArgumentParser(
     2.5  description='Geometrical Core building tool.',
     2.6  epilog='''1) Distance spreading [angstrom]
     2.7 -2) -1 timeout means running Bron-Kerbosh algorithm without timeout
     2.8 +2) -1 timeout means running Bron-Kerbosch algorithm without timeout
     2.9  3) Alternative core new aa part: read documentation for more information
    2.10  4) Superposition core: main core is 0, first alternative is 1 etc. ''',
    2.11  formatter_class=argparse.ArgumentDefaultsHelpFormatter,
    2.12 @@ -43,7 +43,7 @@
    2.13  p.add_argument('-e',help='Ignore cores, owned by one SS element',type=bool, default=False)
    2.14  p.add_argument('-m',help='Min core size',
    2.15      metavar='int',type=pos,default=c.minsize)
    2.16 -p.add_argument('-t',help='Bron-Kerbosh algorithm timeout',
    2.17 +p.add_argument('-t',help='Bron-Kerbosch algorithm timeout',
    2.18      metavar='int',type=timeout,default=c.timeout)
    2.19  p.add_argument('-n',help='Alternative core new aa part',
    2.20      metavar='float',type=part,default=c.ac_new_atoms)

     3.1 --- a/pair_cores/pair_cores.py	Tue Apr 03 12:02:57 2012 +0400
     3.2 +++ b/pair_cores/pair_cores.py	Tue Apr 03 12:06:26 2012 +0400
     3.3 @@ -38,8 +38,8 @@
     3.4      * out_high_blocks_html_file -- output HTML file with blocks of multiple sequences
     3.5      * out_high_blocks_pymol_file -- output PyMol file with blocks of multiple sequences
     3.6      * blocks3d -- if old (graph-based) blocks algorithm is used
     3.7 -    * blocks3d_timeout -- Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)
     3.8 -    * pair_timeout -- Bron-Kerbosh (pair cores) timeout (-1 - unlimited)
     3.9 +    * blocks3d_timeout -- Bron-Kerbosch (blocks3d) timeout (-1 - unlimited)
    3.10 +    * pair_timeout -- Bron-Kerbosch (pair cores) timeout (-1 - unlimited)
    3.11      """
    3.12      if markup_file:
    3.13          input_file = markup_file
    3.14 @@ -126,9 +126,9 @@
    3.15      p.add_argument('--high-blocks-html',help='Output HTML file with high blocks',metavar='FILE',type=w)
    3.16      p.add_argument('--high-blocks-pymol',help='Output PyMol file with high blocks',metavar='FILE',type=w)
    3.17      p.add_argument('--blocks3d',help='Use blocks3d algorithm for high blocks',action='store_true')
    3.18 -    p.add_argument('--blocks3d-timeout',help='Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)',
    3.19 +    p.add_argument('--blocks3d-timeout',help='Bron-Kerbosch (blocks3d) timeout (-1 - unlimited)',
    3.20              metavar='int',type=timeout,default=config.timeout_2)
    3.21 -    p.add_argument('--pair-timeout',help='Bron-Kerbosh (pair cores) timeout (-1 - unlimited)',
    3.22 +    p.add_argument('--pair-timeout',help='Bron-Kerbosch (pair cores) timeout (-1 - unlimited)',
    3.23              metavar='int',type=timeout,default=0)
    3.24      args = p.parse_args()
    3.25      homology_from_3d(markup_file=args.m, homology_file=args.y, max_delta=args.d, ignore_one_ss=args.e,