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():
print("Wrong valence for atom {0:s}{1:d}".format(a.GetSymbol(),
a.GetIdx()))
Wrong valence for atom C 1
Wrong valence for atom O 3
HTH, cheers
p.
On 11/05/2020 13:33, Pablo Ramos wrote:
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 since valences do not match the ones
specified for Carbon and Oxygen beingHydrogens already explicit: C_val
= 4 ; O_val = 2
However, sanitizing this object creates automatically the missing
Hydrogens providing a valid smiles: [H]OC([H])([H])[H] and therefore
it assumes the smiles is correct.
Is there any way to specify that my Hydrogens are already explicit
during sanitazion so I get my error message?
Thank you so much J
Best regards,
*Pablo Ramos*
Ph.D. at Covestro Deutschland AG
covestro.com <http://www.covestro.com/>
*Telephone*
+49 214 6009 7356
Covestro Deutschland AG
COVDEAG-Chief Commer-PUR-R&D-EMEA-PMD
B103, R164
51365 Leverkusen, Germany
_pablo.ramos@covestro.com_
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