allpy: 9369dbad919d test/test.py

allpy

view test/test.py @ 251:9369dbad919d

Incompatible changes to Monomer interfaces. This branch does not work! - (!!) only changed allpy._monomer, not uses - (!!) removed (temporarily) classes for specific monomer types (DNAMonomer, etc) - refurbished allpy.data.AAcodes to allpy.data.codes with much cleaner interface - refurbished allpy._monomer for simplicity and more friendly interface Now it will (someday) be possible to say: a = Monomer.from_name("alanine") b = protein.Monomer.from_code1("a") c = protein.MonomerType.from_code3("ala") d = dna.Monomer.from_code3("DA") but impossible to say: d = protein.Monomer.from_code3("DA")

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Mon, 13 Dec 2010 20:12:11 +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)