view allpy/config.py @ 896:6134ae1dfdae
fix error caused by applying secondary structure markup
This bug should be digged.
For some reason BioPython's DSSP failed to get secondary structure
information of a residue:
$ ./pair_cores/pair_cores.py -i test/aln1.fasta -y aaa -e True
...
('A', (' ', 51, ' '))
caused by dssp.__getitem__
| author |
Boris Nagaev <bnagaev@gmail.com> |
| date |
Fri, 23 Sep 2011 14:10:25 +0400 |
| parents |
52f311cae778 a89409bb4653 |
| children |
3cc7ef543da5 |
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
