[Biopython] is_na()?

[João Rodrigues]

That list also has all the nucleic acids so it's a matter of parsing it and
using only a portion of it.

Cheers,

João


2013/10/17 Willis, Jordan R <jordan.r.willis at vanderbilt.edu>

> I would just get the ID of the residue and ask if it's in the standard
> amino acid library. If you wanna use all Bio.PDB the Polypeptide class has
> a three_to_one function that only contains the naturally occurring 20 AA's
> by their 3 letter code. Do something like:
>
> from Bio.PDB.PDBParser import PDBParser
> from Bio.PDB.Polypeptide import three_to_one
> structure = PDBParser().get_structure('XXXX', 'you_structure.pdb')
> residues = structure.get_residues()
> for resi in residues:
>     try:
>         three_to_one(resi.get_resname())
>     except KeyError:
>         print "residue {0} {1} on chain {2} is not a standard amino
> acid".format(resi.get_id()[1],resi.get_resname(),resi.get_parent().get_id())
>
>
>
> On Oct 17, 2013, at 5:07 AM, David Dufour Rausell <ddufour at pcb.ub.cat>
>  wrote:
>
> > Hello again,
> >
> > I forgot to mention that I'm working with PDB files, so I'm using the
> Bio.PDB module. I'm thinking in extracting the sequence from each chain and
> check if it is made by RNA residues, but any other idea will be very
> welcome.
> >
> > Thanks!
> >
> > David Dufour Rausell
> >
> > Genome Biology Group  - Centre Nacional d'Anàlisis Genòmic (CNAG)
> > Structural Genomics Group - Centre de Regulació Genòmica (CRG)
> >
> > Parc Cientific de Barcelona - Torre I - Baldiri Reixac, 4 - 2a.p - 08028
> - Barcelona
> > Tel +34 93 4020542
> > email ddufour at pcb.ub.cat
> >
> > On Oct 17, 2013, at 10:33 AM, David Dufour Rausell wrote:
> >
> >> Hello,
> >>
> >> I would like to know if there is a function like is_aa(residue) but to
> test if a residue is RNA? Basically, what I want to know if a chain is RNA
> or not. Thanks in advance.
> >>
> >>
> >> David Dufour Rausell
> >>
> >> Genome Biology Group  - Centre Nacional d'Anàlisis Genòmic (CNAG)
> >> Structural Genomics Group - Centre de Regulació Genòmica (CRG)
> >>
> >> Parc Cientific de Barcelona - Torre I - Baldiri Reixac, 4 - 2a.p -
> 08028 - Barcelona
> >> Tel +34 93 4020542
> >> email ddufour at pcb.ub.cat
> >>
> >>
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> >
> >
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> >
>
>
>
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