allpy: faa7e19bffd9 allpy/protein.py

allpy

Removed obsolete protein.Alignment.muscle_realign, updated calls to it everywhere

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Tue, 08 Feb 2011 15:01:22 +0300
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: