1.1 --- a/allpy/config.py	Sat Mar 26 01:09:05 2011 +0300
     1.2 +++ b/allpy/config.py	Sat Mar 26 01:13:56 2011 +0300
     1.3 @@ -8,6 +8,8 @@
     1.4  min_match = 5
     1.5  max_waste_in_pdb = 5
     1.6  
     1.7 +min_core_size = 10
     1.8 +
     1.9  # pdb download url (XXXX is pdb code place)
    1.10  pdb_url = 'http://www.pdb.org/pdb/files/%s.pdb'
    1.11  pdb_path = '/tmp/%s.pdb'

     2.1 --- a/allpy/structure.py	Sat Mar 26 01:09:05 2011 +0300
     2.2 +++ b/allpy/structure.py	Sat Mar 26 01:13:56 2011 +0300
     2.3 @@ -375,7 +375,8 @@
     2.4          return GCs
     2.5  
     2.6      def pair_core_parts(self, max_delta=config.delta,
     2.7 -    timeout=config.timeout, min_width=config.min_width):
     2.8 +    timeout=config.timeout, min_width=config.min_width,
     2.9 +    min_core_size=config.min_core_size):
    2.10          """ Return list of continuous parts of gc for each sequence pair
    2.11  
    2.12          part is block
    2.13 @@ -388,7 +389,7 @@
    2.14                      block = copy(self)
    2.15                      block.sequences = [seq1, seq2]
    2.16                      cores = block.geometrical_cores(max_delta=max_delta,
    2.17 -                        timeout=timeout, minsize=min_width,
    2.18 +                        timeout=timeout, minsize=min_core_size,
    2.19                          ac_new_atoms=0.0, ac_count=0)
    2.20                      for core in cores:
    2.21                          core_block = copy(block)