Hello Santiago, In case you are still looking for an answer, somewhere in my notes I wrote the following.
to get a better depiction of complicated topology, do this before rendering. from rdkit.Chem import rdDepictor rdDepictor.SetPreferCoordGen(True) Sometimes it helps. Good luck. Ling Santiago Fraga <santi...@mestrelab.com> 於 2023年4月21日週五 上午2:17寫道： > Good morning > > I am trying to generate a molfile from smiles, using the RDKit > C++ implementation. > But in some cases the result molfile is like the one in the > attached image. > > My code is something like this: > > string molecule = > "C1=CC2=[N](C=C1)[Ir]134(C5=CC=CC=C25)C2=CC=CC=C2C2=[N]1C=CC=C2.C1=CC(C2=CC=CC=C32)=[N]4C=C1"; > RDKit::ROMol* mol = RDKit::SmilesToMol(molecule, 0, false, nullptr); > mol->updatePropertyCache(false); > RDDepict::preferCoordGen = true; > RDDepict::compute2DCoords(*mol); > string molfile = RDKit::MolToMolBlock(*mol, true, -1, false, true) > > > How could I fix the molfile? > > Regards > Santiago > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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