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rdkit / mmpdb

A package to identify matched molecular pairs and use them to predict property changes.
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Which "cut-smarts" patterns (i.e. fragmentation parameters) are used by default for Transform function? #44

Closed chengthefang closed 2 years ago

chengthefang commented 2 years ago

Hi All,

I am wondering which "cut-smarts" patterns are used by default in Transform function. That is, how does the program fragment a given molecule when applying a built MMPDB to do the transform? I couldn't find the parameter that controls the fragmentation methods in "transform" function.

Ideally, the transform function will fragment a molecule in the same way as how the MMPDB was built. But I am not sure if it is the case.

Thank you! Cheng

KramerChristian commented 2 years ago

Hi Cheng,

mmpdb transform uses the same fragmentation pattern that was used to generate the DB. The pattern is stored in the DB and is automatically retreived from there.

Bests, Christian