Many thanks again, Wim I was just moving in that direction, modifying directly the resulting molfile.
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: Wim Dehaen <wimdeh...@gmail.com> Enviado: martes, 11 de abril de 2023 11:25 Para: Santiago Fraga <santi...@mestrelab.com> Cc: rdkit-discuss@lists.sourceforge.net <rdkit-discuss@lists.sourceforge.net> Asunto: Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile Sorry for not reading your question properly. I am personally not aware of a way to export molfiles in this way in rdkit, but I might just be unaware. I think the easiest solution would be probably changing the molblock string post hoc by reading the M ISO line. for example like this in python: ``` mol=Chem.MolFromSmiles("c1c2cccc1[3H].[2H]2") def MolToMolfileDT(mol,path): mb=Chem.MolToMolBlock(mol).split("\n") iso=[x for x in mb[-3].split(" ") if len(x)>0] if iso[1]=="ISO": #check if theres isotope info for i in range(int(iso[2])): isotope=int(iso[4+2*i]) idx=int(iso[3+2*i])+3 if isotope in [2,3]: #only D and T mb[idx]=mb[idx].replace("H",{2:"D",3:"T"}[isotope]) #replace only H (to not have issues like [3Li]) with open(path, "w") as molfile: molfile.write("\n".join(mb)) return MolToMolfileDT(mol,"mol.mol")``` this returns: RDKit 2D 8 8 0 0 0 0 0 0 0 0999 V2000 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 2.5981 0.0000 T 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -2.5981 0.0000 D 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 6 1 1 0 8 2 1 0 M ISO 2 7 3 8 2 M END best wishes wim On Tue, Apr 11, 2023 at 9:14 AM Santiago Fraga <santi...@mestrelab.com<mailto:santi...@mestrelab.com>> wrote: Many thanks for your examples, Wim. But I was checking the option to save the labels D and T in the molfile for the hydrogen isotopes, as other tools can do. 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:+santi...@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: Wim Dehaen <wimdeh...@gmail.com<mailto:wimdeh...@gmail.com>> Enviado: lunes, 10 de abril de 2023 18:07 Para: Santiago Fraga <santi...@mestrelab.com<mailto:santi...@mestrelab.com>> Cc: rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net> <rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>> Asunto: Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile rdkit outputs a molfile with correct isotope labels for me using just: mol=Chem.MolFromSmiles("[3H]c1ccccc1[2H]") Chem.MolToMolFile(mol,"test.mol") or labelling the atoms post hoc: mol=Chem.MolFromSmiles("c1ccccc1") mol=Chem.AddHs(mol) mol.GetAtomWithIdx(6).SetIsotope(3) mol.GetAtomWithIdx(7).SetIsotope(2) mol=Chem.RemoveHs(mol) Chem.MolToMolFile(mol,"test2.mol") I hope this helps best wishes wim On Mon, Apr 10, 2023 at 4:43 PM Santiago Fraga <santi...@mestrelab.com<mailto:santi...@mestrelab.com>> wrote: Good afternoon! I am a relatively new user of RDKit, and mainly the C++ API. I am trying to save in a molfile the labels D and T for the hydrogen isotopes. Like in the following molfile: MJ230401 8 8 0 0 0 0 0 0 0 0999 V2000 -0.3572 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0716 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0716 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3572 -1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3572 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3572 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3572 1.2375 0.0000 T 0 0 0 0 0 0 0 0 0 0 0 0 1.0717 0.4125 0.0000 D 0 0 0 0 0 0 0 0 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 6 8 1 0 0 0 0 1 7 1 0 0 0 0 M END I am trying to set directly the labels in the hydrogen atoms: atom->setProp<string>("atomLabel", "D"); or atom->setProp<string>("_displayLabel", "D"); But when the molfile is generated the labels are not transferred. It seems also that when reading a mofile including the labels, they are discarded. Many thanks in advance Santiago Fraga _______________________________________________ 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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