Greetings!!
I hope this email finds you well.
I need a SMARTS pattern that matches this molecule fragment
[image: image.png]
The first pattern I used was:
[*;R2]~1~[*;R2]~[*;R2]~[*;R2]~[*;R2]~[*;R2]~1
However, it also matches this fragment. This is not the expected behavior
but it agrees with the pattern, so I tried adding the ring size constrain.
[image: image.png]
Now the pattern I am using is this:
[*;R2r6]~1~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~1
It worked quite well but now it fail to find matches in this molecule
[image: image.png]
Does anyone know what I am doing wrong??
Code:
-------
m1 = Chem.MolFromSmiles(
"c1ccc2cc3c(ccc4c5ccccc5c5cc6c7cc8c(cc7c6cc5c34)c3cccnc38)cc2c1")
m2 = Chem.MolFromSmiles(
"b1cccc2c1c1c(c3ccc4ccc4c3c3c4c5cc[nH]c5c4c13)c1ncc3ccccc3c21")
m3 = Chem.MolFromSmiles(
"b1ccbc2c1c1ccoc1c1c2c2ccsc2c2[nH]c3ncc4c(c3c21)=c1ncccc1=4")
p = Chem.MolFromSmarts("[*;R2]~1~[*;R2]~[*;R2]~[*;R2]~[*;R2]~[*;R2]~1")
for m, expected_value in zip([m1,m2,m3],[1,2,2]):
print(len(m.GetSubstructMatches(p)) == expected_value)
p = Chem.MolFromSmarts(
"[*;R2r6]~1~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~1")
for m, expected_value in zip([m1,m2,m3],[1,2,2]):
print(len(m.GetSubstructMatches(p)) == expected_value)
All the best,
Eduardo
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