Hi,
One thing I think could be improved in CDK is the handling/description of
post-processing after reading in chemical structures from different formats.
One way would be to device what steps need to be taken in CDK depending on
choice of input format, but an even better way would be to have a method
standardize(IAtomContainer) that would, regardless of previous file
reading/formats, result in the same chemical representation with atom types and
aromaticity detected etc. (possibly there is a need for multiple
standardize(..) methods for different use cases). As it is now I sometimes find
myself in situations when the result I get depend on the order I invoke the cdk
functionality, which is not always apparent or easy to debug.
Cheers,
/Ola
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