Dear RDKit Users,
For your information (and to make a bit of advertisement):
We have recently developed and published an extension of the ETKDG conformer
generator to improve sampling of small and large rings, which is available in
the 2020.03 release of the RDKit.
Shuzhe Wang, Jagna Witek,
Dear Pablo,
You might do something along these lines:
from rdkit import Chem
smi = "[H]C([H])O"
params = Chem.SmilesParserParams()
params.sanitize = True
params.removeHs = False
mol = Chem.MolFromSmiles(smi, params)
for a in mol.GetAtoms():
if a.GetNumImplicitHs():
Hi Pablo,
SMILES by definition has implicit hydrogens (enough to satisfy the typicial
valence) for atoms that are not within brackets.
It doesn't matter if you write C, C[H], [H]C[H], or [H]C([H])([H])[H]; they
are all methane. The number of hydrogens that are returned by
GetNumImplicitHs() and
Dear all,
I am trying to catch an error every time that a smiles associated to a mol
object does not exist. To do this, I want to use sanitize function: if the
smiles is incorrect I will get my error.
My smiles with explicit hydrogens is the next one: [H]C([H])O
I want it to provide an error
Dear Paolo,
Thank you very much. I'll test this and revert to you.
Have a nice day.
Best regards,
Quoc-Tuan
> Le 10 mai 2020 à 13:09, Paolo Tosco mailto:paolo.tosco.m...@gmail.com > a écrit :
>
>
> Dear Quoc-Tuan,
>
> I think I have come with a reasonably fast algorithm that seems to
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