[Biopython] is_aa() returning true on nonstandard amino acids

[João Rodrigues]

Hi Ahmad,


I was really happy that I found out about is_aa, however, I just found out
> that it returns false positives on a lot of modified residues
> like S-NITROSO-CYSTEINE (SCN) and a few others.
>
> Is it supposed to do that? Is there another method for standard amino
> acids only?
>


It is supposed to do that yes, but you can use is_aa(residue,
standard=True) to check only for the 20 canonical amino acids. The default
behaviour (standard=False) checks against a list of residues from SCOP that
include modifications.



> Also sorry to hijack my own thread, but I was trying to sample some random
> structures with certain constraints using the PDB's advanced search. I
> specifically chose no ligands or modified residues, yet  I still get those
> in my structures, any idea why?
>


If this is related to the RCSB PDB Advanced Search, you should ask them :)
But check their definition of ligand and/or modified amino acids:

Searches for structures that have chemical components which are not part of
> a polymeric entity (ligands)
> Ligands represent small molecules, carbohydrates, ions, solvents, etc.
> that are not part of a polymer


Searches for structures that have modified residues.
> Modified residues are non-standard polymeric components (i.e. non-standard
> amino-acids in a protein or non-standard nucleotides in a nucleic acid)




> Finally, noob question, is_aa doesn't work unless I do "from
> Bio.PDB.Polypeptide import is_aa" or "from Bio.PDB.Polypeptide import *",
> but doesn't work if I do "from Bio.PDB import Polypeptide", doesn't the
> class come with all its methods?
>

What is confusing you is that the Polypeptide *module* has a Polypeptide
*class*. The is_aa method is not part of any class actually, just of the
module. However, it does work for me if I do 'from Bio.PDB import
Polypeptide', I just have to do Polypeptide.is_aa afterwards (instead of
directly is_aa).
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20170421/a396337b/attachment.html>