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dekhn
3 days ago
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Parsing Chemistry
I wrote a very simple SMILES parser using pyparsing
https://github.com/dakoner/smilesparser/tree/master
I wouldn't say it's intended for production work, but it has been useful in situations where I didn't want to pull in rdkit.
dalke
3 days ago
[–]
I see you include the dot disconnect "." as part of the Bond definition.
You also define Chain as:
Chain <<= pp.Group(pp.Optional(Bond) + pp.Or([Atom, RingClosure]))
I believe this means your grammar allows the invalid SMILES C=.N
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