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CIS/TRANS for consecutive double bonds #50

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fgrunewald opened this issue Nov 22, 2024 · 1 comment
Open

CIS/TRANS for consecutive double bonds #50

fgrunewald opened this issue Nov 22, 2024 · 1 comment

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@fgrunewald
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A curious problem arises for cis trans definition of consecutive double bonds. Should the smiles be C1=CC=C(C=C1)/C=C/C=C//C2=CC=CC=C2 or C1=CC=C(C=C1)/C=C/C=C/C2=CC=CC=C2. I think commonly one symbol is used. In either case our annotation fails since the middle atom only get's assigned one classification based on the first bond

@pckroon
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pckroon commented Nov 22, 2024

If I carefully read the opensmiles syntax definition C1=CC=C(C=C1)/C=C//C=C/C2=CC=CC=C2 is invalid. / (and \) is a 'bond' token, and it's not allowed to have 2 bonds directly following eachother.

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