As part of the work on improving the way RDKit handles organometallics that is in the latest release, there is MolOps::cleanUpOrganometallics, which attempts to do the bond transformations in a similar way to that gist. The intention was that this would be part of the default sanitization, but late in the day it was discovered that it didn't work well with compounds with 2 metal atoms and bridging chlorine atoms, such as 'F[Pd]1(Cl)Cl->[Pd](Cl)(Cl)<-Cl1'. It's my intention to fix that at some point in the near future, but in the meantime if you're working in C++ it is available for use with caveats. Worth a try in this case, perhaps. Dave
On Thu, May 4, 2023 at 9:51 AM Santiago Fraga <santi...@mestrelab.com> wrote: > Good morning Wim > Yes, I know that the original smiles has problems with the dative > bonds. > I am trying to load the molecule and then fix those bonds using this > solution: > https://gist.github.com/greglandrum/6cd7aadcdedb1ebcafa9537e8a47e3a4 > > And then generate a new molfile. I will try to apply your code to > see if I can improve the molecule > depiction. > > Regards > Santiago > > <http://www.mestrelab.com> > > SANTIAGO FRAGA > *Software Developer* > santi...@mestrelab.com <+santi...@mestrelab.com> > > *MESTRELAB RESEARCH S.L.* > PHONE *+34881976775* > FAX *+34981941079* > Feliciano Barrera, 9B-Bajo 15706 > Santiago de Compostela (SPAIN) > > Follow us: > [image: Mestrelab Twitter] <https://twitter.com/mestrelab> [image: > Mestrelab Linkedin] <https://www.linkedin.com/company/mestrelab-research> > [image: Canal de YouTube Mestrelab] > <https://www.youtube.com/channel/UCf3MVnd3XZflv0acvTv14ww> [image: > MestreBlog] <http://mestrelab.com/blog/> > > > > ------------------------------ > *De:* Wim Dehaen <wimdeh...@gmail.com> > *Enviado:* martes, 2 de mayo de 2023 21:37 > *Para:* Santiago Fraga <santi...@mestrelab.com> > *Cc:* Ling Chan <lingtrek...@gmail.com>; RDKit Discuss < > rdkit-discuss@lists.sourceforge.net> > *Asunto:* Re: [Rdkit-discuss] Molfile from smiles > > Hi all, > unfortunately I can't offer a "fix" but I can offer these minor comments: > -it seems like the SMILES has some parsing error. You can make uses of > RDKits extension for dative bonds in SMILES ("->") and replace the SMILES > with the below, which will parse, and give (what i assume is) the intended > structure: > > "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" > -more fundamentally, i think the reason this molecule is hard to render is > because, as a hexavalent iridium complex it is more fundamentally > 3-dimensional and therefore tougher to sketch. you can see here on > wikipedia Ir(ppy)3 even when manually sketched looks a bit funny: > > https://upload.wikimedia.org/wikipedia/commons/c/c8/Ir%28ppy%29_Schematic.png > -in general, organometallic species have various limitations when it comes > to their handling by cheminformatics packages. for this reason, some care > is needed when dealing with species like this to make sure you won't have > issues down the line. an overview of some rdkit related ones see this > presentation by prof jan jensen: > https://raw.githubusercontent.com/rdkit/UGM_2020/master/Presentations/JanJensen.pdf > > Finally, if i embed the molecule and then display its 2D projection, it > actually looks pretty good (despite a warning UFF doesnt recognize > iridium). See below: > [image: image.png] > This was generated using the following codeblock (in Python, not C++, > sorry for that): > > mol = > Chem.MolFromSmiles("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",sanitize=True) > mol = Chem.AddHs(mol) > AllChem.EmbedMolecule(mol,randomSeed=0xf00d) > mol = Chem.RemoveHs(mol) > display(mol) > > best wishes > wim > > On Tue, May 2, 2023 at 5:06 PM Santiago Fraga <santi...@mestrelab.com> > wrote: > > Thanks for your answer, Ling Chan. > But I am already using that option with the C++ API. > > Regards > Santiago > > <http://www.mestrelab.com> > > SANTIAGO FRAGA > *Software Developer* > santi...@mestrelab.com <+santi...@mestrelab.com> > > *MESTRELAB RESEARCH S.L.* > PHONE *+34881976775* > FAX *+34981941079* > Feliciano Barrera, 9B-Bajo 15706 > Santiago de Compostela (SPAIN) > > Follow us: > [image: Mestrelab Twitter] <https://twitter.com/mestrelab> [image: > Mestrelab Linkedin] <https://www.linkedin.com/company/mestrelab-research> > [image: Canal de YouTube Mestrelab] > <https://www.youtube.com/channel/UCf3MVnd3XZflv0acvTv14ww> [image: > 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> 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 > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- David Cosgrove Freelance computational chemistry and chemoinformatics developer http://cozchemix.co.uk
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