Hi Paolo,
This is exactly what I have tried to do but unsuccessfully because I was
just increasing the number of explicit Hs by
nbr.SetNumExplicitHs(nbr.GetNumExplicitHs()
+ 1).
In fact, my logic was to increase the number of Hs by 1 for each atom
removed and I am still puzzled on why that should be increased by 2 for
aromatic bonds (int(GetBondTypeAsDouble) == 2). Could you elaborate that
for me?
Giammy
On Thu, 7 Apr 2022 at 10:38, Paolo Tosco <paolo.tosco.m...@gmail.com> wrote:
> Hi Gianmarco,
>
> this issue has been discussed before.
> Removing bonds with RWMol.RemoveBond() will not adjust the implicit H
> count of the atom at the two ends of the bond.
> While this is not important for the atom that is going to be removed, the
> count on the atom that stays needs to be adjusted. In particular, you need
> to add as many implicit Hs as the order of the bond that you have removed.
> See below for such an algorithm:
>
> with Chem.RWMol(mol) as rwmol:
> for b in rwmol.GetBonds():
> for a in (b.GetBeginAtom(), b.GetEndAtom()):
> if a.GetDegree() == 1:
> oa = b.GetOtherAtom(a)
> if oa.GetDegree() > 1:
> oa.SetNumExplicitHs(oa.GetNumExplicitHs() +
> int(b.GetBondTypeAsDouble()))
> rwmol.RemoveBond(a.GetIdx(), oa.GetIdx())
> rwmol.RemoveAtom(a.GetIdx())
> break
>
> Chem.SanitizeMol(rwmol)
>
> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>
> rwmol
>
> [image: image.png]
>
> Using Chem.RWMol as a context manager will allow you commit the changes
> only when you are done, so you won't invalidate atom and bond iterators
> along the way.
>
> Cheers,
> p.
>
> On Thu, Apr 7, 2022 at 10:51 AM Gianmarco Ghiandoni <ghiandon...@gmail.com>
> wrote:
>
>> Hi all,
>>
>> I am writing a function that removes atoms with only one bond and can be
>> applied recursively in order to find the scaffold of a molecule. The
>> function works in most cases but I have observed that, when aromatic rings
>> are involved, it produces a loss of information. This is an example:
>>
>> from rdkit import Chem
>> smiles =
>> "CCN1CCC(N(CCCCCCc2ccc(C(F)(F)F)cc2)C(=O)Cn2c(CCc3cccc(F)c3F)cc(=O)c3ccccc32)CC1"
>> Chem.MolFromSmiles(smiles.replace('@',''))
>>
>> [image: image.png]
>> mol = Chem.MolFromSmiles(smiles.replace('@', ''))
>> rwmol = Chem.RWMol(mol)
>>
>> # Note that in this case, I am iterating through the atoms only once
>> # but the idea is to repeat this iteration until all single-bonded
>> # atoms have been removed
>> for a in list(rwmol.GetAtoms()):
>> if len(a.GetBonds()) == 1:
>> nbr = a.GetNeighbors()[0]
>> rwmol.RemoveBond(a.GetIdx(), nbr.GetIdx())
>> rwmol.RemoveAtom(a.GetIdx())
>> rwmol
>>
>> [image: image.png]
>> If you check the top aromatic ring in the starting molecule and the
>> result after the first iteration, you can already see that the removal
>> messes up the aromatic configuration of the ring after removing the two
>> fluorines. If I try to Chem.SanitizeMol, at the end of the loop, it will
>> not fix the problem (KekulizeException: Can't kekulize mol. Unkekulized
>> atoms: 21 30 31 32 33 34 35 36 37). I have also done some attempts with
>> using different sanitiseOps or by increasing the number of hydrogens on the
>> atoms attached to those I remove but I could not figure out a solution -
>> and clearly, if I carry on removing atoms recursively (i.e., I reapply the
>> removal again), then the molecule gets messed up completely:
>>
>> [image: image.png]
>>
>> Can anyone help me with understanding what's missing?
>>
>> Thanks,
>>
>> Giammy
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
--
*Gianmarco*
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