view allpy/config.py @ 610:ee2c10aa74b8
paired_cores/score.py: change method of score evaluation
Boundary positions of blocks are not considered.
Columns represented with one sequence or pure gap columns are not considered.
Calculate weighted average of number of connected components in columns.
Weight of column = l / sum(l)
(l = number of sequnces representing column)
| author |
boris (kodomo) <bnagaev@gmail.com> |
| date |
Tue, 05 Apr 2011 23:11:41 +0400 |
| parents |
7a72febf12f6 |
| children |
71910cefe37a |
line source
1 delta = 2.0 # for geometrical core building
2 minsize = 20 # min size of returning cores
3 maxabsent = 0.15 # deprecated?
5 # defaults for set_pdb_chain
6 min_continuous_match = 5
12 # pdb download url (XXXX is pdb code place)
13 pdb_url = 'http://www.pdb.org/pdb/files/%s.pdb'
14 pdb_path = '/tmp/%s.pdb'
15 timeout = 10 # time in sec. for BRON-KERBOSH algorithm
18 # min part or new atoms in new alternative core
21 # max number of cores (including main core)
26 timeout_2 = 10 # bron-kerbosh for blocks
