Hi Gianmarco,
it is not for aromatic bonds that you need to increase by 2, it is for
double bonds (or triple bonds) - there is no chance that an atom in a ring
can ever be terminal, as its degree is at least 2.
In your molecule you have two carbonyl groups. In those the oxygen is
doubly bonded to the parent carbon, so when you chop the oxygen off, you
need to add two implicit Hs to the parent carbon.
If you don't, the quinolone ring will fail to kekulize.
This is an example with a terminal triple bond where you need to add 3 Hs
to the parent carbon:
[image: image.png]
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]
Cheers,
p.
On Thu, Apr 7, 2022 at 12:12 PM Gianmarco Ghiandoni <ghiandon...@gmail.com>
wrote:
> 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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