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unmtransinfo / CFChemApps

Web application for visualizing chemical structures
http://3.145.25.193/depict/
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Bug: SMILES like `cccccc` do not work and return 500 server error #12

Closed Priyansh-Kedia closed 7 months ago

Priyansh-Kedia commented 11 months ago

This issue is mostly because we are not using sanitize=False while creating mol object from SMILEs Please read this discussion here for more understanding

However, expected behaviour should be consistent by specifying explicit ways of sanitizing SMILES

jeremyjyang commented 11 months ago

Note that some SMILES are illegal, such as "cccccc". There can be no aromatic non-ring molecule. However, we want an error message from RDKit indicating SMILES parsing error, or whatever the RDKit exception is, not a 500 server error.

Priyansh-Kedia commented 11 months ago

Note that some SMILES are illegal, such as "cccccc". There can be no aromatic non-ring molecule. However, we want an error message from RDKit indicating SMILES parsing error, or whatever the RDKit exception is, not a 500 server error.

Correct, however the DEPICT portal developed using ChemAxon does not sanitize SMILES and presents results for SMILES like cccc. Should we handle it the same way or show error about illegal SMILES?

Jack-42 commented 7 months ago

This issue was resolved by #17