As Dan said: you should be adding Hs to the molecule before generating
conformations. That clears up the problem:
In [17]: AllChem.EmbedMolecule(Chem.MolFromSmiles('CC[C@H](C)O'))
Out[17]: -1
In [18]: AllChem.EmbedMolecule(Chem.AddHs(Chem.MolFromSmiles('CC[C@H](C)O')))
Out[18]: 0
I would have actually expected that you could get a conformer with the Hs
and think there's likely a bug connected to the way chiral centers are
handed in the conformer generation code (embedding the non-chiral SMILES
CCC(C)O works just fine) that's causing this failure, but that doesn't
change the fact that it's always better to add Hs before generating
conformations.
-greg
On Fri, Sep 27, 2019 at 10:12 PM Dan Nealschneider <
[email protected]> wrote:
> Guillaume-
> You may want to add hydrogens before embedding. Not sure *specifically*
> why it's required in this case - maybe the stereo center needs a hydrogen
> in order to pop it into 3d?
>
> *dan nealschneider* | senior developer
> [image: Schrodinger Logo] <https://www.schrodinger.com/>
>
>
> On Wed, Sep 25, 2019 at 1:45 AM Guillaume GODIN <
> [email protected]> wrote:
>
>> Dear All,
>>
>>
>>
>> One question why this is not working ?
>>
>>
>>
>> def mol3D(mol):
>>
>> tot = AllChem.EmbedMolecule(mol)
>>
>> try:
>>
>> X = AllChem.Get3DDistanceMatrix(mol)
>>
>> except:
>>
>> print('err')
>>
>> print(tot)
>>
>> n = mol.GetNumAtoms()
>>
>> X = np.zeros(n,n)
>>
>> return X
>>
>>
>>
>> mol = Chem.MolFromSmiles('CC[C@H](C)O')
>>
>> X = mol3D(mol)
>>
>>
>>
>> Result:
>>
>>
>>
>> err
>>
>> -1
>>
>>
>> ---------------------------------------------------------------------------
>>
>> ValueError Traceback (most recent call
>> last)
>>
>> <ipython-input-17-f18aabd854d2> in mol3D(mol)
>>
>> * 3* try:
>>
>> ----> 4 X = AllChem.Get3DDistanceMatrix(mol)
>>
>> * 5* except:
>>
>>
>>
>> ValueError: Bad Conformer Id
>>
>>
>>
>> During handling of the above exception, another exception occurred:
>>
>>
>>
>> Thanks in advance,
>>
>>
>>
>> Guillaume
>>
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