allpy: 9ad22a1848fc test/test.py

allpy

view test/test.py @ 310:9ad22a1848fc

Added calls to super to all classes in allpy.base The calls are not exactly correct. This WILL fail in certain inheritance situations. There are two bad situations: * inheritance from object; __init__ of object does not accept any arguments, so it is not compatible with interface of any of our classes * inheritance of Block(Alignment). The situation here is relatively easy to fix: we should force compatibility of function interfaces for Block and Alignment.

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Thu, 16 Dec 2010 21:08:03 +0300
parents	fb3164f03984
children	faa7e19bffd9

line source

1 import sys

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')

13 b = Block(p)

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)

19 #~ p.muscle_align()

20 #~ p.save_fasta(sys.stdout)