Hi Jean-Marc, There difference is due to bond orientation (if my inchi analysis skills are correct). See the bold bond layer below (14-7+ vs 14-7-).
m1 -> InChI=1S/C20H26O4/c1-12(2)17-11-18(22)14(4)7-5-6-13(3)8-16(21)9-15-10-19(17)24-20(15)23/h6-7,10,12,17,19H,5,8-9,11H2,1-4H3/*b13-6-,14-7+*/t17-,19-/m1/s1 m2 -> InChI=1S/C20H26O4/c1-12(2)17-11-18(22)14(4)7-5-6-13(3)8-16(21)9-15-10-19(17)24-20(15)23/h6-7,10,12,17,19H,5,8-9,11H2,1-4H3/*b13-6-,14-7-*/t17-,19-/m1/s1 Not sure why it happens, but I've seen it multiple times... Best, Christos Christos Kannas Chem[o]informatics Researcher & Software Developer [image: View Christos Kannas's profile on LinkedIn] <http://cy.linkedin.com/in/christoskannas> On Tue, 18 Dec 2018 at 17:36, JEAN-MARC NUZILLARD < jm.nuzill...@univ-reims.fr> wrote: > Thank you for your answer but alatis might not be adapted to my current > problem. > > Attempting to understand what was changed by the embedding step I wrote: > > inchi1 = > > "InChI=1S/C20H26O4/c1-12(2)17-11-18(22)14(4)7-5-6-13(3)8-16(21)9-15-10-19(17)24-20(15)23/h6-7,10,12,17,19H,5,8-9,11H2,1-4H3/b13-6-,14-7+/t17-,19-/m1/s1" > m1 = Chem.MolFromInchi(inchi1) > m1 = Chem.AddHs(m1) > m2 = Chem.Mol(m1) > AllChem.EmbedMolecule(m2) > sm1 = Chem.MolToSmiles(m1) > sm2 = Chem.MolToSmiles(m2) > print(sm1) > print(sm2) > print(sm1 == sm2) > inc1 = Chem.MolToInchi(m1) > inc2 = Chem.MolToInchi(m2) > print(inc1) > print(inc2) > print(inc1 == inc2) > > Molecules m1 and m2 have identical SMILES representations > but different InChI representations, which I find odd. > > All the best, > > Jean-Marc > > > > > Le 18/12/2018 00:40, Dimitri Maziuk via Rdkit-discuss a écrit : > > On 12/17/18 4:50 PM, JEAN-MARC NUZILLARD wrote: > >> Is there any more deterministic procedure than the one of trying until > >> success is obtained? > >> > >> How do I determine the InChI string of a conformer obtained after > >> multiple embedding? > > > > This representation keeps 3D config: http://alatis.nmrfam.wisc.edu/ > > > > Generally speaking the problem with InChI is that the only *required* > > layer is the formula. Therefore *an* InChI string cannot be used to > > differentiate conformers, you need the InChI string with all the > > relevant layers and all the protons. > > > > https://www.nature.com/articles/sdata201773 > > > > _______________________________________________ > > 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
