[Biopython] is_na()?

[Willis, Jordan R]

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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