Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/hg/allpy/annotate/835efa2a8c71/allpy/dna.py
Дата изменения: Unknown
Дата индексирования: Thu Feb 28 03:57:12 2013
Кодировка:
allpy: allpy/dna.py annotate

allpy

annotate 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
rev   line source
bnagaev@240 1 import base
me@353 2 import data.codes
me@280 3
dendik@382 4 import dna
dendik@382 5
me@328 6 class Monomer(base.Monomer):
me@328 7 """DNA monomers: nucleotides."""
me@328 8 type = 'dna'
dendik@382 9 types = dna
me@280 10 by_code1 = {}
me@280 11 by_code3 = {}
me@280 12 by_name = {}
me@353 13 Monomer._initialize(data.codes.dna)
bnagaev@240 14
bnagaev@240 15 class Sequence(base.Sequence):
dendik@382 16 types = dna
dendik@382 17
dendik@382 18 class Alignment(base.Alignment):
dendik@382 19 types = dna
bnagaev@240 20
me@341 21 class Block(Alignment, base.Block):
me@341 22 pass
me@341 23
me@280 24 # vim: set ts=4 sts=4 sw=4 et: