Thanks for the detailed response!
Best,
Navid
On Wed, Sep 16, 2020 at 4:49 AM Téletchéa Stéphane <
stephane.teletc...@univ-nantes.fr> wrote:
> Le 16/09/2020 à 06:34, Navid Shervani-Tabar a écrit :
>
> Thanks, Stéphane! Can you by any chance point me to an example with either
> of them? (It seems biopython is more relevant for my purpose, which is to
> load positions and dihedral angles for a large dataset and add conformation
> type as a label to each one, but I can't find anything in its tutorials).
> Thanks again!
>
> Best,
> Navid
>
> Dear Navid,
>
> If you want to use command-line, then biopython may do the trick.
> I also forgot to talk also about MDanalysis for which a binding to rdkit
> was developped this year
> (https://www.mdanalysis.org/2020/08/29/gsoc-report-cbouy/).
>
> The problem with biopython is that its documentation is targeting
> bioinformaticians,
> and thus not always clear :-)
>
> If you go for it (and I recommend it), then you can look at the Bio.PDB
> module which has his own documentation:
>
> https://biopython.org/docs/1.75/api/Bio.PDB.html
>
> What you want to do is bulding a polypeptide chain "from scratch" from a
> sequence:
>
> https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ
> https://biopython.org/docs/1.75/api/Bio.PDB.StructureBuilder.html
>
> Briefly:
> 1 - create a CaPPBuilder or a structure object if you want to start from
> scratch
>
> from Bio.PDB.Polypeptide import PPBuilder
>
> ppb = CaPPBuilder()
>
> See also https://biopython.org/docs/1.75/api/Bio.PDB.Structure.html
>
> 2 - load an existing pdb file (the one containing your dihedral angles):
>
> parser = PDB.PDBParser()
> newpdb = parser.get_structure('theNew', filename)
> pp=ppb.build_peptides(newpdb)
>
> (get the resulting sequence)
> seq=pp[0].get_sequence()
>
> 3 - write out the new pdb
>
> io = PDBIO()io.set_structure(s)io.save("out.pdb")
>
> If more is required, look at the reference papers and/or ask the (low
> traffic) biopython mailing list.
>
> Best,
>
> Stéphane
>
> PS: keeping the discussion on the list since it may help others (and they'll
> probably complete my answer).
>
> --
> Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein
> Design In Silico
> UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes
> cedex 03, France
> Tél : +33 251 125 636 / Fax : +33 251 125 632http://www.ufip.univ-nantes.fr/
> - http://www.steletch.org
>
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