[BioPython] Comment/Suggestion about Bio.PDB.Polypeptide class. How to keep gaps information ?

[Julie Bernauer]

On Tue, 2005-05-24 at 20:26 +0200, thamelry at binf.ku.dk wrote:
> Hi Julie,
> [...]
> I'll try to add this, but I'm busy at the moment (4 articles in the
> pipeline), but you're welcome to give it a try and send me your code :-).

Hi Thomas,

Thank you for your quick answer.

Here is a quick and dirty hack that works for me, just see whether you
may use it:

class BrokenPolypeptide(list):
    """
    A broken polypeptide is simply a list of polypeptide objects.
    """
    def get_sequence(self):
        """
        Return the AA sequence, filling gap or unknown residue with X.

        @return: polypeptide sequence
        @rtype: L{Seq}
        """
        s=""
        if self == []:
            end=0
        else :
            end=self[0][-1].get_id()[1]
        for peptide in self:
            start=peptide[0].get_id()[1]
            gaplength=start-end
            for indexgap in range(0, gaplength):
                s=s+'X'
            for res in peptide:
                resname=res.get_resname()
                if to_one_letter_code.has_key(resname):
                    resname=to_one_letter_code[resname]
                else:
                    resname='X'
                s=s+resname
            end=peptide[-1].get_id()[1]
        seq=Seq(s, ProteinAlphabet)
        return seq

HTH, regards,

J.

-- 
Julie BERNAUER
Equipe de Génomique Structurale          http://www.genomics.eu.org
IBBMC - UMR 8619 - U.P.S. Bât.430          Tel. : +33 1 69 15 31 57
91405 Orsay - FRANCE                       Fax. : +33 1 69 85 37 15