Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/hg/allpy/file/835efa2a8c71/allpy/dna.py
Дата изменения: Unknown
Дата индексирования: Sun Feb 3 18:54:07 2013
Кодировка:
allpy: 835efa2a8c71 allpy/dna.py

allpy

view allpy/dna.py @ 817:835efa2a8c71

optimization of rasmol_homology: keep structure loaded of two sequences only One of steps of this program is superimposition of all sequences with main sequence and saving of all structures to pdb file. Loaded structure of all sequences is not needed to do this. At every moment only structure of main sequence and of superimposing sequence. This optimization results in essential memory saving. Output files should be the same to previous revision. To implement this optimization methods supeimpose and save_pdb of alignment were replaced with methods with same names of sequence. So some code is same as code of methods of alignment. Note: behaves as before, with superimpose and save_pdb methods of alignment. Model was returned by these methods but never used while generating spt script. This can result in collisions of rasmol selections when number of sequences is greater than max number of chains of one model.
author boris (kodomo) <bnagaev@gmail.com>
date Fri, 15 Jul 2011 02:23:27 +0400
parents 5639138f619a
children 5f9e9c4e9ed6 e461a5529338
line source
1 import base
2 import data.codes
4 import dna
6 class Monomer(base.Monomer):
7 """DNA monomers: nucleotides."""
8 type = 'dna'
9 types = dna
10 by_code1 = {}
11 by_code3 = {}
12 by_name = {}
13 Monomer._initialize(data.codes.dna)
15 class Sequence(base.Sequence):
16 types = dna
18 class Alignment(base.Alignment):
19 types = dna
21 class Block(Alignment, base.Block):
22 pass
24 # vim: set ts=4 sts=4 sw=4 et: