allpy: 43b5207a70d7 allpy/config.py

allpy

view allpy/config.py @ 1081:43b5207a70d7

Bugfixed the previous commit (decency verification), (see #98) * Removed the decency verification function itself, it does not seem to be necessary YET * Moved the check on alignment quality within processors.FixOrdering, which is the one that actually fails and is hard to debug if sequences have the same identification. * Added a specific testcase for this situation.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Wed, 30 May 2012 13:35:04 +0400
parents	3cc7ef543da5
children	6c7e74a75d13

line source

1 debug = False

3 delta = 2.0 # for geometrical core building

4 minsize = 20 # min size of returning cores

5 maxabsent = 0.15 # deprecated?

7 # defaults for set_pdb_chain

8 min_continuous_match = 5

9 min_match = 20

10 max_waste_in_pdb = 5

12 min_core_size = 10

14 # pdb download url (XXXX is pdb code place)

15 pdb_url = 'http://www.pdb.org/pdb/files/%s.pdb'

16 pdb_path = '/tmp/%s.pdb'

17 timeout = 10 # time in sec. for BRON-KERBOSCH algorithm

20 # min part or new atoms in new alternative core

21 ac_new_atoms = 0.5

23 # max number of cores (including main core)

24 ac_count = 5

26 # blocks3d

27 min_width = 4

28 timeout_2 = 10 # bron-kerbosch for blocks