allpy: 8a81996f8bda allpy/config.py

allpy

structure.py: add join parameter to pair_cores_parts() with join parameter all parts are joined to intersecting parts

author	boris (kodomo) <bnagaev@gmail.com>
date	Sat, 26 Mar 2011 01:24:21 +0300
parents	7eeae2471e69
children	49582a92418a

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 = 20

7 min_match = 5

8 max_waste_in_pdb = 5

10 min_core_size = 10

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

19 ac_new_atoms = 0.5

21 # max number of cores (including main core)

22 ac_count = 5

24 # blocks3d

25 min_width = 3

26 timeout_2 = 10 # bron-kerbosh for blocks