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
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