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
>
>
> _______________________________________________
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>
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