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
2020年2月22日(土) 20:36 丁邵珍 <164362...@qq.com>:
> 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 index in red circle(compd_A)? And then,
> I can exclude them, and use the code like:
> Compd_A.GetAtomWithIdx(index).SetProp('_protected','1') to protect the
> other atoms before transforming.
>
> SMILES: (1)compd_a:NC1=C2C=CC(=CC2=NC=C1);(2)compd_b:
> CCN(CC)CCCC(C)NC1=C2C=CC(=CC2=NC=C1)Cl
>
> Best wishes,
> Shaozhen
>
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