allpy
changeset 520:1785e40b2a2d
blocks3d(): add primary_cliques parameter
if primary_cliques parameter is set,
blocks3d() returns self-overlapping raw cliques (as blocks)
instead of set of self-non-overlapping blocks (default)
it could be used for debugging and testing
| author | boris (kodomo) <bnagaev@gmail.com> |
|---|---|
| date | Sat, 26 Feb 2011 18:05:10 +0300 |
| parents | c19216f2d7b4 |
| children | a3df15a42f9d |
| files | allpy/structure.py |
| diffstat | 1 files changed, 5 insertions(+), 1 deletions(-) [+] |
line diff
1.1 --- a/allpy/structure.py Fri Feb 25 18:00:20 2011 +0300 1.2 +++ b/allpy/structure.py Sat Feb 26 18:05:10 2011 +0300 1.3 @@ -242,13 +242,15 @@ 1.4 1.5 def blocks3d(self, max_delta=config.delta, 1.6 timeout=config.timeout, timeout_2=config.timeout_2, 1.7 - min_width=config.min_width): 1.8 + min_width=config.min_width, primary_cliques=False): 1.9 """ Returns length-sorted list of reliable blocks 1.10 1.11 * max_delta -- threshold of distance spreading 1.12 * timeout -- Bron-Kerbosh timeout (couple cores) 1.13 * timeout_2 -- Bron-Kerbosh timeout (blocks) 1.14 * min_width -- min width of each core 1.15 + * primary_cliques -- if True, return cliques 1.16 + instead of not-self-intersected blocks 1.17 """ 1.18 result = [] 1.19 Block = self.__class__ 1.20 @@ -312,6 +314,8 @@ 1.21 return cmp(width1, width2) 1.22 # sort blocks 1.23 clique_blocks.sort(cmp=cmp_blocks, reverse=True) 1.24 + if primary_cliques: 1.25 + return clique_blocks 1.26 used_monomers = set() 1.27 for clique_block in clique_blocks: 1.28 monomers = set(clique_block.monomers())