allpy: 3d40d7b9a123 lib/sequence.py

allpy

lib::project::muscle_align project::save_fasta sequence::operator== fixes test -- alignment done

line source

1 #!/usr/bin/python

2 import monomer

3 from Bio.PDB import PDBParser, CaPPBuilder

4 from Bio.Seq import Seq

5 from allpy_pdb import Pdb

7 cappbuilder = CaPPBuilder()

9 class Sequence(object):

10 """

11 Mandatory data:

12 * name -- str with the name of sequence

13 * description -- str with description of the sequence

14 * monomers -- list of monomer objects (aminoacids or nucleotides)

15 * pdb_chain -- list of Bio.PDB.Chain's

17 TODO: class Protein: container of multiple Sequences,

18 class ProteinMononer: container of multiple Monomers

19 """

20 def __init__(self, name, monomers, description=""):

21 self.name = name

22 self.description = description

23 self.monomers = monomers

25 def __len__(self):

26 return len(self.monomers)

28 def __str__(self):

29 return ''.join([monomer.monomer_type.code1 for monomer in self.monomers])

31 def __eq__(self, other):

32 return len(self) == len(other) and \

33 all([a==b for a, b in zip(self.monomers, other.monomers)])

35 def pdb_chain_add(self, pdb_file, pdb_id, pdb_chain, pdb_model=0):

36 """

37 Reads Pdb chain from file

38 and align each Monomer with PDB.Residue (TODO)

39 """

40 name = Pdb.std_id(pdb_id, pdb_chain, pdb_model)

41 self.pdb_chain = PDBParser().get_structure(name, pdb_file)[pdb_model][pdb_chain]

42 peptide = cappbuilder.build_peptides(self.pdb_chain)

43 sequence = str(peptide[0].get_sequence()) # TRU?

44 print sequence

45 # FIXME: align and map