On 2021-04-25 18:04, Noel O'Boyle wrote:
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.
Yes, there was an error in the charged sdf. However, the uncharged still does not show my hydrogen, so I do not trust it.
On Sun, 25 Apr 2021, 13:28 David van der Spoel, <david.vandersp...@icm.uu.se <mailto: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> <mailto: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> <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/> > <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> > <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> > <mailto: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> > <https://lists.sourceforge.net/lists/listinfo/openbabel-discuss <https://lists.sourceforge.net/lists/listinfo/openbabel-discuss>> > > -- > Peter Jarowski, Ph. 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-- 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
