Re: [Rdkit-discuss] Distinguishing bridgeheads from ring-fusions with SMARTS

[S J. S. <swa...@gm...>]

Perhaps using ring perception instead would work better?

On Fri, Aug 25, 2023 at 10:22 AM Andreas Luttens <and...@gm...>
wrote:

> Dear Wim,
>
> Thanks for your reply!
>
> Apologies for the delay, finally got time to pick up this project again.
>
> Your suggestion works great, though I have found some cases where it
> breaks. For instance the molecule:
>
> mol = Chem.MolFromSmiles("C1CC2C3C2C1C3")
>
> It seems, in this case, a bridgehead atom is also a fused-ring atom. Maybe
> these looped compounds have too complex topology for this type of analysis.
>
> I don't see a straight way forward to identify just the bridgehead atoms.
>
> Best wishes,
> Andreas
>
> On Sat, Dec 3, 2022 at 12:53 PM Wim Dehaen <wim...@gm...> wrote:
>
>> Hi Andreas,
>> I don't have a good SMARTS pattern available for this but here is a
>> function that should return bridgehead idx and not include non bridgehead
>> fused ring atoms:
>>
>> ```
>> def return_bridgeheads_idx(mol):
>>     bh_list=[]
>>     intersections=[]
>>     sssr_idx = [set(x) for x in list(Chem.GetSymmSSSR(mol))]
>>     for i,ring1 in enumerate(sssr_idx):
>>         for j,ring2 in enumerate(sssr_idx):
>>             if i>j:
>>                 intersections+=[ring1.intersection(ring2)]
>>     for iidx in intersections:
>>         if len(iidx)>2: #condition for bridgehead
>>             for idx in iidx:
>>                 neighbors = [a.GetIdx() for a in
>> mol.GetAtomWithIdx(idx).GetNeighbors()]
>>                 bh_list+=[idx for nidx in neighbors if nidx not in iidx]
>>     return tuple(set(bh_list))
>> ```
>>
>> Here are 6 test molecules:
>>
>> ```
>> mol1 = Chem.MolFromSmiles("C1CC2CCC1C2")
>> mol2 = Chem.MolFromSmiles("C1CC2C1C1CCC2C1")
>> mol3 = Chem.MolFromSmiles("N1(CC2)CCC2CC1")
>> mol4 = Chem.MolFromSmiles("C1CCC12CCCCC2")
>> mol5 = Chem.MolFromSmiles("C1CC2C1CCCCC2")
>> mol6 = Chem.MolFromSmiles("C1CCC(C(CCC3)C23)C12")
>> for mol in [mol1,mol2,mol3,mol4,mol5,mol6]:
>>     print(return_bridgeheads_idx(mol))
>> ```
>>
>> giving the expected answer:
>>
>> (2, 5)
>> (4, 7)
>> (0, 5)
>> ()
>> ()
>> ()
>>
>> hope this is helpful!
>>
>> best wishes
>> wim
>>
>> On Sat, Dec 3, 2022 at 8:34 AM Andreas Luttens <and...@gm...>
>> wrote:
>>
>>> Dear users,
>>>
>>> I am trying to identify bridgehead atoms in multi-looped ring systems.
>>> The issue I have is that it can be sometimes difficult to distinguish these
>>> atoms from ring-fusion atoms. The pattern I used (see below) looks for
>>> atoms that are part of three rings but cannot be bonded to an atom that
>>> also fits this description, in order to avoid ring-fusion atoms. The code
>>> works, except for cases where bridgehead atoms are bonded to a ring-fusion
>>> atom.
>>>
>>> *PASS:*
>>> pattern = Chem.MolFromSmarts("[$([x3]);!$([x3][x3])]")
>>> rdkit_mol = Chem.MolFromSmiles("C1CC2CCC1C2")
>>> print(rdkit_mol.GetSubstructMatches(pattern))
>>> >>>((2,),(5,))
>>>
>>> *FAIL:*
>>> pattern = Chem.MolFromSmarts("[$([x3]);!$([x3][x3])]")
>>> rdkit_mol = Chem.MolFromSmiles("C1CC2C1C1CCC2C1")
>>> print(rdkit_mol.GetSubstructMatches(pattern))
>>> >>>()
>>>
>>> Any hint on what alternative pattern I could use to isolate true
>>> bridgeheads would be greatly appreciated. Maybe other strategies are more
>>> suitable to find these atoms?
>>>
>>> Thanks in advance!
>>>
>>> Best regards,
>>> Andreas
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdk...@li...
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
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