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Steinbeck-Lab / cheminformatics-microservice

This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.
https://docs.api.naturalproducts.net
MIT License
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CDKSDG CIF 2D rendering 500 error #219

Closed CS76 closed 1 year ago

CS76 commented 1 year ago

Endpoint:

https://dev.api.naturalproducts.net/v1/depict/2D?smiles=CC1%253DCC%28%253DC2C3%253DC%28CCC3%29C%28%253DO%29OC2%253DC1%29O%255BC%2540%2540H%255D4%255BC%2540%2540H%255D%28%255BC%2540H%255D%28%255BC%2540%2540H%255D%28%255BC%2540%2540H%255D%28CO%29O4%29O%29O%29O&generator=cdksdg&width=512&height=512&rotate=0&CIP=true&unicolor=true

Error Log:


 File "/code/app/modules/toolkits/cdk_wrapper.py", line 55, in getCDKSDG
    molecule = SmilesParser.parseSmiles(smiles)
org.openscience.cdk.exception.org.openscience.cdk.exception.InvalidSmilesException: org.openscience.cdk.exception.InvalidSmilesException: could not parse 'CC1%3DCC(%3DC2C3%3DC(CCC3)C(%3DO)OC2%3DC1)O%5BC%40%40H%5D4%5BC%40%40H%5D(%5BC%40H%5D(%5BC%40%40H%5D(%5BC%40%40H%5D(CO)O4)O)O)O', Endpoints of ringbond are the same - loops are not allowed
CC1%3DCC(%3DC2C3%3DC(CCC3)C(%3DO)OC2%3DC1)O%5BC%40%40H%5D4%5BC%40%40H%5D(%5BC%40H%5D(%5BC%40%40H%5D(%5BC%40%40H%5D(CO)O4)O)O)O
CS76 commented 1 year ago

The old image cache might be causing this issue. System prune resolved it. Closing this now