Hi Alfredo,
if that's really what you want to do, the following Python function should
help:
from rdkit import Chem
bilastine =
Chem.AddHs(Chem.MolFromSmiles("O=C(O)C(c1ccc(cc1)CCN4CCC(c2nc3c3n2CCOCC)CC4)(C)C"))
bilastine
[image: image.png]
def removeHsBondedToSp3Carbon(mol):
bonds = []
atoms = []
for b in mol.GetBonds():
ba = b.GetBeginAtom()
ea = b.GetEndAtom()
for a in (ba, ea):
oa = b.GetOtherAtom(a)
if (a.GetAtomicNum() == 1 and oa.GetAtomicNum() == 6 and
oa.GetHybridization() == Chem.HybridizationType.SP3):
bonds.append(b.GetIdx())
atoms.append(a.GetIdx())
break
if bonds:
mol = Chem.RWMol(mol)
for bi in sorted(bonds, reverse=True):
b = mol.GetBondWithIdx(bi)
mol.RemoveBond(b.GetBeginAtomIdx(), b.GetEndAtomIdx())
for ai in sorted(atoms, reverse=True):
mol.RemoveAtom(ai)
return mol.GetMol()
bilastine_no_h = removeHsBondedToSp3Carbon(bilastine)
bilastine_no_h
[image: image.png]
Cheers,
p.
On Tue, Oct 19, 2021 at 8:08 PM Alfredo Quevedo
wrote:
> Dear all,
>
> I am trying to figure out if there is a way to remove all hydrogens bond
> to sp3 carbons in my molecule?
>
> thanks in advance for the help,
>
> kind regards
>
> Alfredo
>
>
>
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