Dear All,
Thanks to find a solution. But, that’s true, it’s clearly a “bug” in the
processus of embegging.
I observe this issue only few of those “@” or “@@” cases.
Examples:
C[C@H]1CCCC[C@H]1C works
CC[C@H](C)O failed
Thanks for helping,
Guillaume
De : Greg Landrum <greg.land...@gmail.com>
Date : samedi, 28 septembre 2019 à 07:22
À : RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
Cc : Guillaume GODIN <guillaume.go...@firmenich.com>
Objet : Re: [Rdkit-discuss] Issue with Chirality
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
<dan.nealschnei...@schrodinger.com<mailto:dan.nealschnei...@schrodinger.com>>
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
Erreur ! Nom du fichier non spécifié.<https://www.schrodinger.com/>
On Wed, Sep 25, 2019 at 1:45 AM Guillaume GODIN
<guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>> 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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