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Kekulization Failure #120

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Olabisi-Aishat-Bello opened this issue Sep 4, 2024 · 3 comments
Open

Kekulization Failure #120

Olabisi-Aishat-Bello opened this issue Sep 4, 2024 · 3 comments
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@Olabisi-Aishat-Bello
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When trying to run this line of code:

sf.encoder('Cc1ccc(NC(=O)c2ccc(-c3[c]n(Br)ccs[nH]3)c(C(F)(F)F)c2)cc1Nc1nccc(-c2cccnc2)n1')

I get this error even though RDKit smiles parser is able to produce a Mol object from the same smiles string

EncoderError: kekulization failed
SMILES: Cc1ccc(NC(=O)c2ccc(-c3[c]n(Br)ccs[nH]3)c(C(F)(F)F)c2)cc1Nc1nccc(-c2cccnc2)n1

@MarioKrenn6240 MarioKrenn6240 self-assigned this Sep 6, 2024
@MarioKrenn6240 MarioKrenn6240 added question Further information is requested bug Something isn't working labels Sep 6, 2024
@MarioKrenn6240
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Thank you, i can reproduce the behaviour, and we are looking into this right now. Will come back to you soon!

@MarioKrenn6240
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Indeed, Robert Pollice identifies the problem, it makes a mistake in accounting for the valences for radicals. It should be easy to fix. We will do so hopefully soon and publish the fix as SELFIES2.1.3. Thanks for reporting this!

@Olabisi-Aishat-Bello
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Awesome! Thank you!

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