view test/test.py @ 385:d7fc6865ce58
refactoring of pdb-related code
* remove (transiently) secstr from pdb.py
* refactoring of pdb loading
* create module protein_pdb with 4 classes with both properties
* make geometrical-core work (with errors and without saving to fasta)
| author |
boris <bnagaev@gmail.com> |
| date |
Wed, 02 Feb 2011 15:50:20 +0300 |
| parents |
fb3164f03984 |
| children |
faa7e19bffd9 |
line source
3 from allpy.alignment import Alignment
4 from allpy.block import Block
6 p = Alignment(open('test.fasta'))
7 print "alignment length: %i" % len(p)
8 print "sequence: %s" % str(p.sequences[0])
10 p.sequences[0].pdb_chain_add(open('1jcc.pdb'), '1jcc', 'B')
11 p.sequences[1].pdb_chain_add(open('1kfm.pdb'), '1kfm', 'A')
14 GCs = b.geometrical_cores(ac_new_atoms=0.00, ac_count=-1)
15 b.save_fasta(sys.stdout)
16 for i, GC in enumerate(GCs):
17 GC.save_xstring(sys.stdout, i)
20 #~ p.save_fasta(sys.stdout)
