Dear Shaozhen,
RDKit can render molecule with atom index,
So you can check the indexes and identify which atoms should be protected.
An example to visualize molecule with atom index is below.
https://gist.github.com/iwatobipen/7001d81080756fea46968d1966c36f59
I hope it helps you.
Thanks,
Taka
Dear developers:
As shown bellow, compd_A could be converted to compd_B within serveral reaction
transformations.
Atoms in red circle(compd_A) are identify as activated atoms, and the other
atoms should be protected when precessing transformations. Is there some way I
could identify the atom
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