Dear Sereina, No, I have just a table of 3D coordinates (generated by cclib). This is equivalent to having an xyz file. I know that this conversion is possible with OpenBabel, but I would like to avoid using it for this particular purpose. It seems that the simplest way is to hardcode generation of SDF myself.
Thanks, Michal On 4 November 2013 13:52, sereina riniker <sereina.rini...@gmail.com> wrote: > Hi Michal, > > Well, if you have your 3D coordinates as a PDB file, you can read them in > with the new PDB parser and assign the bond orders based on a template > (generated from the SMILES of your molecule): > tmp = Chem.MolFromPDBFile(yourfilename) > template = Chem.MolFromSmiles(yoursmiles) > mol = AllChem.AssignBondOrdersFromTemplate(template, tmp) > > I don't know if this is what you were looking for. > > Best, > Sereina > > > > 2013/11/4 Michal Krompiec <michal.kromp...@gmail.com> >> >> Hello, >> Is it possible to construct a Mol (or EditableMol) object out of a >> list of 3D coordinates? I am trying to write a bridge between cclib >> and RDKit, and I need a function to convert 3D geometries to SDF. >> Thanks, >> Michal >> >> >> ------------------------------------------------------------------------------ >> Android is increasing in popularity, but the open development platform >> that >> developers love is also attractive to malware creators. Download this >> white >> paper to learn more about secure code signing practices that can help keep >> Android apps secure. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
