Implement CDK IChemObjectReaderErrorHandler to get more detailled error descriptions when reading MOL/SD files

FelixBaensch / MORTAR

MOlecule fRagmenTAtion fRamework

MIT License

18 stars 3 forks source link

Implement CDK IChemObjectReaderErrorHandler to get more detailled error descriptions when reading MOL/SD files #131

Open JonasSchaub opened 3 days ago

JonasSchaub commented 3 days ago

See the comment by Egon here: https://github.com/cdk/cdk/pull/1106#issuecomment-2351561851

johnmay commented 3 days ago

I think it is implemented... https://github.com/cdk/cdk/blob/a59dc85decd67bc1c0e61546a5d20602725b1761/base/core/src/main/java/org/openscience/cdk/io/DefaultChemObjectReader.java#L73

johnmay commented 3 days ago

Sorry the point is more what controls the exception... but yes leave this open. We should perhaps at least log the warning.

JonasSchaub commented 3 days ago

If I understand Egon's comment correctly, an application that uses CDK, like our "Molecule fragmentation framework" (MORTAR) here, should implement this interface and set it as error handler in the readers to define where to send the error messages (like in Bioclipse).

johnmay commented 3 days ago

Yes sorry I thought this was on the CDK issues :-). Carry on