Thanks for your answer, Ling Chan. But I am already using that option with the C++ API.
Regards Santiago [http://www.mestrelab.com/mestrelab/wp-content/uploads/signs/line3.jpg] [http://www.mestrelab.com/mestrelab/wp-content/uploads/signs/M-red-200pxb.jpg]<http://www.mestrelab.com> SANTIAGO FRAGA Software Developer santi...@mestrelab.com<mailto:%20santi...@mestrelab.com> MESTRELAB RESEARCH S.L. PHONE +34881976775 FAX +34981941079 Feliciano Barrera, 9B-Bajo 15706 Santiago de Compostela (SPAIN) Follow us: [Mestrelab Twitter]<https://twitter.com/mestrelab> [Mestrelab Linkedin] <https://www.linkedin.com/company/mestrelab-research> [Canal de YouTube Mestrelab] <https://www.youtube.com/channel/UCf3MVnd3XZflv0acvTv14ww> [MestreBlog] <http://mestrelab.com/blog/> ________________________________ De: Ling Chan <lingtrek...@gmail.com> Enviado: martes, 2 de mayo de 2023 4:15 Para: Santiago Fraga <santi...@mestrelab.com> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net> Asunto: Re: [Rdkit-discuss] Molfile from smiles 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<mailto: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<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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