Jason, I can see the image :-)
Yingfeng On Mon, Dec 17, 2018 at 10:01 AM Jason Biggs <jasondbi...@gmail.com> wrote: > Is this the same issue as https://github.com/rdkit/rdkit/issues/1852? > where the input string specifies a trans double bond in a ring but > EmbedMolecule returns a cis configuration? I get different SMILES string > before and after embedding, > > C/C1=C/C/C=C(\C)C(=O)C[C@H](C(C)C)[C@H]2C=C(CC(=O)C1)C(=O)O2 > C/C1=C/C/C=C(/C)C(=O)C[C@H](C(C)C)[C@H]2C=C(CC(=O)C1)C(=O)O2 > > Getting the two highlighted atoms trans to each other seems difficult, and > the embedder doesn't check and reject for double-bond stereo like it does > for chiral centers. > > > [image: image.png] > > (does this copy/pasted image come across in the mailing list?) > > > Jason Biggs > > > > On Mon, Dec 17, 2018 at 7:24 AM JEAN-MARC NUZILLARD < > jm.nuzill...@univ-reims.fr> wrote: > >> Dear all, >> >> I tried to transform an InChI into a Mol and back to InChi. >> >> The following code: >> >> 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" >> m = Chem.MolFromInchi(inchi1) >> m = Chem.AddHs(m) >> AllChem.EmbedMolecule(m) >> inchi2 = Chem.MolToInchi(m) >> print(inchi1) >> print(inchi2) >> print("EQUAL" if inchi1 == inchi2 else "DIFFERENT") >> >> returns DIFFERENT. >> >> Removing the EmbedMolecule step returns EQUAL. >> >> How could I change that? >> >> >> All the best, >> >> Jean-Marc >> >> >> _______________________________________________ >> 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 >
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