greetings all,
i have thought about the problem some more, and in the end came to the
conclusion that looping through all rings really is necessary. In the gist
below you can see the adjusted code, making use of Pat Walters' method
<https://sourceforge.net/p/rdkit/mailman/message/30387811/> for finding all
rings. Apologies for the code being messy.
https://gist.github.com/dehaenw/41eb8e4c39c1158e88b36c6dfc2606d8
fortunately, this one manages to also detect these difficult cases, see
below:
i did not check how fast it is, but i guess it will be a fair bit slower.
best wishes,
wim
On Fri, Aug 25, 2023 at 8:28 PM Wim Dehaen <wimdeh...@gmail.com> wrote:
> Dear Andreas,
> that's a good find. i agree the breaking case can be considered bridgehead
> structure, as it's essentially bicyclo-[3.2.1]-octane plus an extra bond. I
> need to think about this some more, but it might be related to getting the
> ringinfo as SSSR instead of exhaustively. The best solution may therefore
> be to just prune non ring atoms from the graph, enumerate all rings and
> check it really exhaustively.
> FWIW: rdMolDescriptors.CalcNumBridgeheadAtoms(mol) returns 0 for mol =
> Chem.MolFromSmiles("C1CC2C3C2C1C3") too, so this may be an rdkit bug on
> this end.
> best wishes
> wim
>
> On Fri, Aug 25, 2023 at 5:20 PM Andreas Luttens <andreas.lutt...@gmail.com>
> 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 <wimdeh...@gmail.com> 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 <
>>> andreas.lutt...@gmail.com> 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
>>>> Rdkit-discuss@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>
>>>
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