I would call it a "feature"...
I guess running conformer optimization (i.e. ETKDG, UFF, MMFF94) after the
embedding would be a good practice...
> I think I do vaguely remember that InChI gives precedence to 3D
coordinates if present over anything else for the determination of
stereochemistry.
I
I think I do vaguely remember that InChI gives precedence to 3D coordinates if
present over anything else for the determination of stereochemistry. And I
think that is what happens here: the Allchem embedding of the molecule adds 3D
coordinates which are not present for the original molecule
On 12/18/18 1:57 PM, JEAN-MARC NUZILLARD wrote:
> Dimitri, how can alatis help me to find a first draft of 3D structure
> for a few ten thousands of compounds from InChI strings?
It won't, you have to feed it a 3D structure. However its InChI string
and/or MOL block will give you the same 3D
Thank you Christos for confirming what I suspected about double bond
geometry
and thank you Jason for finding some logics in my observation.
Dimitri, how can alatis help me to find a first draft of 3D structure
for a few ten thousands of compounds from InChI strings?
All the best,
Jean-Marc
On 12/18/18 11:34 AM, JEAN-MARC NUZILLARD wrote:
> Molecules m1 and m2 have identical SMILES representations
> but different InChI representations, which I find odd.
*shrug* this is precisely why they came up with alatis: take a molecule
in any input format, round-trip it through any
see https://github.com/rdkit/rdkit/issues/1852, and
https://sourceforge.net/p/rdkit/mailman/message/36309813/
You can see it in the smiles if you remove stereo after embedding, then
re-detect stereo from the conformation.
inchi1 =
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 ->
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 =
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