Based on this, your input SD file does not describe the deprotonated form. You should take a look at the spec for SDF regarding charged atoms and check your file against it.
On Sun, 25 Apr 2021, 13:28 David van der Spoel, <david.vandersp...@icm.uu.se> wrote: > On 2021-04-25 14:09, Peter Jarowski wrote: > > Hi David: > > > > I would suggest you avoid inchi entirely for this as it has its own > > rules regarding canonical protonation state and connectivity (tautomer). > > > > Stick with SMILES. There is no benefit to inchi unless you are > > concerned with clashing because you have a very large database. > > > > SMILES will represent your molecule as you want, you can use explicite > > hydrogens if you need to as well. > Thanks for the suggestion, but: > > % obabel -osmi -isdf perfluorotridecanoic-acid.sdf > > FC(F)(C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(=O)O > 3018355 > > % obabel -osmi -isdf perfluorotridecanoate.sdf > > FC(F)(C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(=O)O > > > Identical. With the -xt h flag I get no string whatsoever. > % obabel -osmi -xt h -isdf perfluorotridecanoic-acid.sdf > 3018355 > > If I drop the smiles string for the charged compound into Pubchem I get > the acid back, so there is still information missing. > > Maybe I'm still doing something wrong. The position of the hydrogens is > crucial because the identifiers are coupled to quantum chemistry > calculations. > > > > > Best, > > > > Peter > > > > On Sun, 25 Apr 2021 at 12:52, David van der Spoel > > <david.vandersp...@icm.uu.se <mailto:david.vandersp...@icm.uu.se>> > wrote: > > > > Hi, > > > > I would like to generate an Inchi fro my compound but without adding > > hydrogens. Is there a flag for that? > > > > Here is an example for an acid and its deprotonated form that > > yields the > > same InChi: > > % obabel -oinchi -isdf perfluorotridecanoic-acid.sdf > > > > InChI=1S/C13HF25O2/c14-2(15,1(39)40)3(16,17)4(18,19)5(20,21)6(22,23)7(24,25)8(26,27)9(28,29)10(30,31)11(32,33)12(34,35)13(36,37)38/h(H,39,40) > > % obabel -oinchi -isdf perfluorotridecanoate.sdf > > > > InChI=1S/C13HF25O2/c14-2(15,1(39)40)3(16,17)4(18,19)5(20,21)6(22,23)7(24,25)8(26,27)9(28,29)10(30,31)11(32,33)12(34,35)13(36,37)38/h(H,39,40) > > > > -- > > David van der Spoel, Ph.D., > > Professor of Computational Molecular Biophysics > > Uppsala University. > > http://virtualchemistry.org <http://virtualchemistry.org> > > > > > > > > > > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så > > innebär det att vi behandlar dina personuppgifter. För att läsa > > mer om hur vi gör det kan du läsa här: > > http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > <http://www.uu.se/om-uu/dataskydd-personuppgifter/> > > > > E-mailing Uppsala University means that we will process your > > personal data. For more information on how this is performed, > > please read here: > > http://www.uu.se/en/about-uu/data-protection-policy > > <http://www.uu.se/en/about-uu/data-protection-policy> > > > > > > _______________________________________________ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > <mailto:OpenBabel-discuss@lists.sourceforge.net> > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > <https://lists.sourceforge.net/lists/listinfo/openbabel-discuss> > > > > -- > > Peter Jarowski, Ph. D. > > CEO / Co-founder > > ChemAlive SA - Quantum Chemistry for All > > > > Twitter: @SAChemAlive <https://twitter.com/SAChemAlive> > > LinkedIn: https://www.linkedin.com/company/chemalive-sa/ > > <https://www.linkedin.com/company/chemalive-sa/> > > Web: http://www.chemalive.com <http://www.chemalive.com> > > > > Try our Interface: https://www.app.chemalive.com > > <https://demo.chemalive.com/> > > > > <http://www.chemalive.com/C/interfaceC.html> > > MassChallenge Switzerland <http://switzerland.masschallenge.org/> Gold > > Winners > > Stage 3 Climate-KIC <http://www.climate-kic.org/> Winners > > > -- > David van der Spoel, Ph.D., > Professor of Computational Molecular Biophysics > Uppsala University. > http://virtualchemistry.org > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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