It would be useful to know what problem you are trying to solve here. OB does not support canonical Kekule SMILES, if you expect different resonance forms to give the same canonical Kekule SMILES. Of course, you can just write out an canonical aromatic SMILES, read it back in, and then write it out in Kekule form (no need for canonical option).
Regarding the second question, I don't know where you got that SMILES from, but if you go to https://www.simolecule.com/cdkdepict/depict.html, and paste the SMILES into the SMILES box, and the SMARTS pattern into the SMARTS box, you will not see a match either. Both software by default apply the Daylight aromaticity model (as best they can) leading to the bridging O and C being aromatic. $ obabel -:"O=C(NCCN(C)C)c1cccc2C(=O)c3ccccc3(Oc12)" -osmi O=C(NCCN(C)C)c1cccc2c(=O)c3ccccc3oc12 Note the lowercase 'o' and 'c' - this is why the SMARTS won't match. I don't recommend it unless you know what you're doing, but OB can preserve whatever aromaticity is in the input using the "a" input option to SMILES: $ obabel -:"O=C(NCCN(C)C)c1cccc2C(=O)c3ccccc3(Oc12)" -osmi -aa O=C(NCCN(C)C)c1cccc2C(=O)c3ccccc3Oc12 Note that the uppercase 'O' and 'C' is preserved. Here's proof that it matches the SMARTS: $ obabel -:"O=C(NCCN(C)C)c1cccc2C(=O)c3ccccc3(Oc12)" -s "c1cccc2Cc3ccccc3(Oc12)" -osmi 0 molecules converted $ obabel -:"O=C(NCCN(C)C)c1cccc2C(=O)c3ccccc3(Oc12)" -s "c1cccc2Cc3ccccc3(Oc12)" -osmi -aa O=C(NCCN(C)C)c1cccc2C(=O)c3ccccc3Oc12 Regards, Noel On Fri, 17 Feb 2023 at 18:50, Thomas <odioidenti...@gmail.com> wrote: > Thank you Noel. > I wanted to get the canonical SMILES, without changing the aromaticity of > the input SMILES: > > mol = pybel.readstring('smi', 'O=C(NCCN(C)C)C1=CC=CN2C(=O)c3ccccc3(N=C12)') > mol.write(opt={"k": True, 'c':True}) > 'CN(CCNC(=O)C1=CC=CN2C1=NC1C=CC=CC=1C2=O)C\t\n' > mol.write(opt={'c':True}) > 'CN(CCNC(=O)c1cccn2c1nc1ccccc1c2=O)C\t\n' > > Furthermore, can you explain me this: > > mol = pybel.readstring('smi', "O=C(NCCN(C)C)c1cccc2C(=O)c3ccccc3(Oc12)") > sma = pybel.Smarts("c1cccc2Cc3ccccc3(Oc12)") > sma.obsmarts.Match(mol.OBMol, True) > False > > Thank you again > Thomas > > Il giorno ven 17 feb 2023 alle ore 18:37 Noel O'Boyle < > baoille...@gmail.com> ha scritto: > >> Hi Thomas, >> >> OB does not sanitize molecules when reading from SMILES (or any other >> format). By default it writes aromatic SMILES though, but it sounds like >> you want Kekule SMILES - see the obabel -Hsmi for the list of options. In >> this case you want 'k': >> >> $ obabel -:"O=C1C=COC(=C1(O))C" -xk -osmi >> O=C1C=COC(=C1O)C >> >> In Python, this is something like mol.write(opt={"k:" True}). >> >> Neither does it add Hs. A SMILES string exactly specifies the number of >> Hs on each atom; this is preserved on reading/writing. If you could provide >> information on a specific case, we could explain what's happening more >> clearly. >> >> Regards >> Noel >> >> >> On Fri, 17 Feb 2023 at 16:18, Thomas <odioidenti...@gmail.com> wrote: >> >>> Is there an option to avoid sanitization of a molecule when reading from >>> SMILES? >>> For example I'd like the SMILES to remain unchanged if I read and write >>> it: >>> >>> mol = pybel.readstring('smi', 'O=C1C=COC(=C1(O))C') >>> mol.write() >>> O=c1ccoc(c1O)C >>> >>> Beside kekulization issues, other unwanted sanitizations are the >>> addition of Hs if I generate the molecule from SMILES fragments (partial >>> SMILES) >>> >>> Thank you >>> Thomas >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >> _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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