Thanks Brian. Didn't know that existed! Very useful.
As you mention, it is a lot slower to do the check.
Tim
On Mon, Sep 27, 2021 at 1:30 PM Brian Cole wrote:
> Good Morning Tim,
>
> The RDKit EnumerateStereoisomers function accomplishes this through the
> ‘tryEmbedding’ flag:
>
be interesting to know what rdkit makes of a molecule like the
first one on the left.
Does it ‘read’ the stereochemistry correctly?
brg
Giovanni
From: Tim Dudgeon
Sent: 27 September 2021 14:04
To: RDKit Discuss
Subject: [Rdkit-discuss] validating stereochemistry
*** CAUTION : External e-mail ***
I
Good Morning Tim,
The RDKit EnumerateStereoisomers function accomplishes this through the
‘tryEmbedding’ flag:
https://github.com/rdkit/rdkit/blob/d20e5cadc81bf6c7b4e590124866f178f2f2fe28/rdkit/Chem/EnumerateStereoisomers.py#L8
It attempts to generate a 3D conformer for the given stereo
I have Python code to enumerate undefined chiral centres in a molecule.
Mostly this works fine, but for some constrained structures this can
generate stereochemistry that makes no sense. For
instance consider NC1CC2CCC1C2:
[image: #1 (2).png]
These two make sense:
[image: #2.png]
[image: #3.png]
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