1.1 --- a/allpy/allpy_pdb.py	Thu Feb 03 13:51:39 2011 +0300
     1.2 +++ b/allpy/allpy_pdb.py	Thu Feb 03 13:56:57 2011 +0300
     1.3 @@ -183,8 +183,8 @@
     1.4          cost is calculated as 1 / (delta + 1)
     1.5              delta in [0, +inf) => cost in (0, 1]
     1.6          """
     1.7 -        nodes = self.columns
     1.8 -        lines = {}
     1.9 +        vertices = self.columns
    1.10 +        edges = {}
    1.11          for i, column1 in enumerate(self.columns):
    1.12              for j, column2 in enumerate(self.columns):
    1.13                  if i < j:
    1.14 @@ -202,15 +202,15 @@
    1.15                      if len(distances) >= 2:
    1.16                          delta = max(distances) - min(distances)
    1.17                          if delta <= max_delta:
    1.18 -                            line = Graph.line(column1, column2)
    1.19 -                            lines[line] = 1.0 / (1.0 + delta)
    1.20 -        graph = Graph(nodes, lines)
    1.21 -        cliques = graph.fast_cliques(minsize=minsize)
    1.22 +                            edge = Graph.edge(column1, column2)
    1.23 +                            edges[edge] = 1.0 / (1.0 + delta)
    1.24 +        graph = Graph(vertices, edges)
    1.25 +        cliques = graph.cliques(minsize=minsize, timeout=timeout)
    1.26          GCs = []
    1.27          for clique in cliques:
    1.28              for GC in GCs:
    1.29 -                new_nodes = clique - GC
    1.30 -                if len(new_nodes) < ac_new_atoms * len(clique):
    1.31 +                new_vertices = clique - GC
    1.32 +                if len(new_vertices) < ac_new_atoms * len(clique):
    1.33                      break
    1.34              else:
    1.35                  GCs.append(clique)