Hi Ivan,
I agree that there is a bug here, but I think the problem is actually that
the double bond is being assigned stereochemistry at all in this case.
In [2]: m = Chem.MolFromSmiles('[H]/C=C/F')
In [3]: m.Debug()
Atoms:
0 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 0 chi: 0
2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 0 chi: 0
3 9 F chg: 0 deg: 1 exp: 1 imp: 0 hyb: 4 arom?: 0 chi: 0
Bonds:
0 0->1 order: 1 dir: 4 conj?: 0 aromatic?: 0
1 1->2 order: 2 stereo: 3 stereoAts: (0 3) conj?: 0 aromatic?: 0
2 2->3 order: 1 dir: 4 conj?: 0 aromatic?: 0
Given that the two substituents on the first C are the same, the double
bond shouldn't be marked as STEREOE at all.
I'll get this fixed.
-greg
On Wed, Nov 6, 2019 at 4:34 PM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:
> Hi,
>
> For reasons to complicated to get into here, I ended up with a molecule
> containing a =CH2 in which one of the hydrogens was explicit and had E/Z
> stereo info. For example, consider [H]/C=C/F.
>
> I was surprised that RemoveHs() refused to remove the hydrogen, although
> later I found that that's the documented behavior, and generally it makes
> sense as a way to prevent the loss of stereochemical information.
>
> For example, compare these two:
>
> In [7]: Chem.MolToSmiles(Chem.RemoveHs(Chem.MolFromSmiles('[H]/C=C/F')))
> Out[7]: '[H]/C=C/F'
>
> In [8]: Chem.MolToSmiles(Chem.RemoveHs(Chem.MolFromSmiles('[H]C=C/F')))
> Out[8]: 'C=CF'
>
> A chemist would say that these two are obviously the same molecule, and
> arguably the second representation is better, because a double bond ending
> in =CH2 can't have geometric isomers. Maybe it's unreasonable to expect
> RDKit to make that kind of inference, but still I wonder, what would be a
> good automated way to get from [H]/C=C/F to C=CF?
>
> One idea is to add a "=CH2 cleanup" step, perhaps implemented by applying
> this reaction:
>
> [H][C&h1:1]=[*:2]>>[CH2:1]=[*:2]
>
> but perhaps there's a better way?
>
> Best,
> Ivan
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