allpy: 675b402094be test/test.py

allpy

view test/test.py @ 151:675b402094be

day commit -- a lot of changes fasta.py: universal save_fasta() determine_long_line -- for determine length of fasta sequence string in user input everywhere: standart long_line=60 --> 70 blocK.sequences_chains: returns sequences in order as in project added monomer pdb_secstr to store secondary structure pdb adding: some improvements and fixes fix in from_pdb_chain: use all peptides, not only first Sequence.pdb_files added to store information about pdb file for each chain dssp bindings to get secondary structure /sec_str -- tool to map secondary structure on each sequence of alignment

author	boris (netbook) <bnagaev@gmail.com>
date	Tue, 26 Oct 2010 00:40:36 +0400
parents	89de20cda19c
children	fb3164f03984

line source

1 import sys

3 from allpy.lib.project import Project

4 from allpy.lib.block import Block

6 p = Project(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)