view allpy/config.py @ 615:6e93a74d1917
allpy/structure.py: move superimpose(+fix) and save_pdb to AlignmentMixin
move superimpose and save_pdb from BlockMixin to AlignmentMixin
fix of superimpose:
* add extra_columns parameter (allow columns with gaps or without structure)
* add documentation
| author |
boris (kodomo) <bnagaev@gmail.com> |
| date |
Fri, 29 Apr 2011 16:04:51 +0400 |
| parents |
71910cefe37a |
| children |
b1d9fb2a7e2a |
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
