allpy: ee2c10aa74b8 allpy/protein.py

allpy

view allpy/protein.py @ 610:ee2c10aa74b8

paired_cores/score.py: change method of score evaluation Boundary positions of blocks are not considered. Columns represented with one sequence or pure gap columns are not considered. Calculate weighted average of number of connected components in columns. Weight of column = l / sum(l) (l = number of sequnces representing column)

author	boris (kodomo) <bnagaev@gmail.com>
date	Tue, 05 Apr 2011 23:11:41 +0400
parents	387f692e2356
children	4a9b4503a027

line source

1 import base

2 import data.codes

4 import protein

6 class Monomer(base.Monomer):

7 """Protein monomers: aminoacids."""

8 type = 'protein'

9 types = protein

10 by_code1 = {}

11 by_code3 = {}

12 by_name = {}

13 Monomer._initialize(data.codes.protein)

15 class Protein(list):

16 """User defined protein; list of protein_sequences."""

17 pass

19 class Sequence(base.Sequence):

20 types = protein

22 class Alignment(base.Alignment):

23 types = protein

25 class Block(Alignment, base.Block):

26 pass

28 # vim: set ts=4 sts=4 sw=4 et: