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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