1.1 --- a/allpy/config.py	Tue Apr 03 12:06:26 2012 +0400
     1.2 +++ b/allpy/config.py	Tue Apr 03 12:20:13 2012 +0400
     1.3 @@ -15,7 +15,7 @@
     1.4  # pdb download url (XXXX is pdb code place)
     1.5  pdb_url = 'http://www.pdb.org/pdb/files/%s.pdb'
     1.6  pdb_path = '/tmp/%s.pdb'
     1.7 -timeout = 10 # time in sec. for BRON-KERBOSH algorithm
     1.8 +timeout = 10 # time in sec. for BRON-KERBOSCH algorithm
     1.9  
    1.10  
    1.11  # min part or new atoms in new alternative core
    1.12 @@ -26,5 +26,5 @@
    1.13  
    1.14  # blocks3d
    1.15  min_width = 4
    1.16 -timeout_2 = 10 # bron-kerbosh for blocks
    1.17 +timeout_2 = 10 # bron-kerbosch for blocks
    1.18  

     2.1 --- a/allpy/graph.py	Tue Apr 03 12:06:26 2012 +0400
     2.2 +++ b/allpy/graph.py	Tue Apr 03 12:20:13 2012 +0400
     2.3 @@ -27,11 +27,11 @@
     2.4      >>> g.fast_cliques()
     2.5      Fast algorithm started
     2.6      [frozenset([1, 2, 3])]
     2.7 -    >>> g.bron_kerbosh()
     2.8 -    Bron and Kerbosh algorithm started
     2.9 +    >>> g.bron_kerbosch()
    2.10 +    Bron and Kerbosch algorithm started
    2.11      [frozenset([1, 2, 3])]
    2.12      >>> g.cliques()
    2.13 -    Bron and Kerbosh algorithm started
    2.14 +    Bron and Kerbosch algorithm started
    2.15      [frozenset([1, 2, 3])]
    2.16  
    2.17      """
    2.18 @@ -77,7 +77,11 @@
    2.19                  self.set_edge(vertex, v, parent_graph[vertex][v])
    2.20  
    2.21      def bron_kerbosh(self, timeout=-1, minsize=1):
    2.22 -        """ Bron and Kerboch algorithm implementation
    2.23 +        """ Deprecated. Use bron_kerbosch() instead """
    2.24 +        return self.bron_kerbosch(timeout, minsize)
    2.25 +
    2.26 +    def bron_kerbosch(self, timeout=-1, minsize=1):
    2.27 +        """ Bron and Kerbosch algorithm implementation
    2.28  
    2.29          returns list of cliques
    2.30          clique is frozenset
    2.31 @@ -87,7 +91,7 @@
    2.32          if timeout == 0:
    2.33              raise TimeoutError()
    2.34          if config.debug:
    2.35 -            print 'Bron and Kerbosh algorithm started'
    2.36 +            print 'Bron and Kerbosch algorithm started'
    2.37          cliques = []
    2.38  
    2.39          class ExtendCall(object):
    2.40 @@ -228,7 +232,7 @@
    2.41  
    2.42          clique is frozenset
    2.43  
    2.44 -        try to execute bron_kerbosh
    2.45 +        try to execute bron_kerbosch
    2.46          if it raises TimeoutError, executes fast_cliques
    2.47          """
    2.48          cliques = []
    2.49 @@ -238,7 +242,7 @@
    2.50                      if len(neighbours_dict) < minsize - 1 and v in graph:
    2.51                          graph.drop_vertex(v)
    2.52                  try:
    2.53 -                    cliques += graph.bron_kerbosh(timeout, minsize)
    2.54 +                    cliques += graph.bron_kerbosch(timeout, minsize)
    2.55                  except TimeoutError:
    2.56                      cliques += graph.fast_cliques(minsize)
    2.57          cliques.sort(key=lambda clique: len(clique), reverse=True)

     3.1 --- a/allpy/structure.py	Tue Apr 03 12:06:26 2012 +0400
     3.2 +++ b/allpy/structure.py	Tue Apr 03 12:20:13 2012 +0400
     3.3 @@ -623,7 +623,7 @@
     3.4          GC is set of columns
     3.5  
     3.6          * max_delta -- threshold of distance spreading
     3.7 -        * timeout -- Bron-Kerbosh timeout (then fast O(n ln n) algorithm)
     3.8 +        * timeout -- Bron-Kerbosch timeout (then fast O(n ln n) algorithm)
     3.9          * minsize -- min size of each core
    3.10          * ac_new_atoms -- min part or new atoms in new alternative core
    3.11              current GC is compared with each of already selected GCs if
    3.12 @@ -725,8 +725,8 @@
    3.13          """ Return length-sorted list of reliable blocks
    3.14  
    3.15          * max_delta -- threshold of distance spreading (ignored if parts)
    3.16 -        * timeout -- Bron-Kerbosh timeout (couple cores) (ignored if parts)
    3.17 -        * timeout_2 -- Bron-Kerbosh timeout (blocks)
    3.18 +        * timeout -- Bron-Kerbosch timeout (couple cores) (ignored if parts)
    3.19 +        * timeout_2 -- Bron-Kerbosch timeout (blocks)
    3.20          * min_width -- min width of each core (ignored if parts)
    3.21          * ignore_one_ss -- ignore geometrical cores, owned by one secondary
    3.22              structure element in every sequence (ignored if parts)