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John, thanks for your valuable advice.
It is mostly like that CircularFingerprinter could not be "reversed" to corresponding molecule structure as I wanted.
Signatures could satisfy my requests. But how to convert atom index into vertexIndex in the job of calling this method signatureStringForVertex(vertexIndex, height) , I could not figure out a way for this conversion from CDK JavaDoc.
Signatures usually gets rid of aromaticity/chirality infomation when "cutting" a fragment from a full molecule. Is there a
straightforward strategy to recover all the lost info from signatures? All info play key role in AI modelling.
key properties such as aromaticity, charge,stereotypical type etc. as well as height/sphere stored in a substructure based on CircularFP are highly preferred.
🐛 Bug
by getSpheres(paras ) to get all atoms according with specified sphere,but only return sphere=1 atoms without more ones.
To Reproduce
Steps to reproduce the behavior:
Environment
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