allpy: 4a2341bc90b1 allpy/config.py

allpy

view allpy/config.py @ 275:4a2341bc90b1

base.Sequence major cleanup * moved base.Sequence.secstr_has to pdb (it appears that secondary structure it uses is from PDB, which is not a nice thing to do; secondary structure is an entity in itself and must have same names across different sources) * removed stupid base.Sequence.monomers, since base.Sequence is subclass of list * removed all methods that reimplement list behaviour * fixed headers of base.Sequence.from_slice

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Wed, 15 Dec 2010 20:06:27 +0300
parents	57c923c2e333
children	d7fc6865ce58

line source

1 delta = 2.0 # for geometrical core building

2 minsize = 20 # min size of returning cores

3 maxabsent = 0.15 # deprecated?

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

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

7 pdb_dir = '/tmp/%s.pdb'

8 timeout = 10 # time in sec. for BRON-KERBOSH algorithm

11 # min part or new atoms in new alternative core

12 ac_new_atoms = 0.5

14 # max number of cores (including main core)

15 ac_count = 5