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 > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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