Hola RDkitters,
I have a number of analogue molecules (how lucky) - from which I can
extract a scaffold using Dalke's MCS code (great piece of work, btw).
I would like to identify each R group from each molecule. My current idea
which I wanted to bounce with you was, for every molecule that I have:
0. Substructure search for the MCS scaffold, this will give ma a set of
atom ids.
1. For every atom id above find if it is connected to something else (so
get neighbours and check for indices which are not in the MCS scaffold set)
2. If there is a connection to an R group break that bond
3. Somehow (how?) retrieve the fragment part and label it Rn (I need to
have distinct sets; R1 R2 R3 etc.)
Is there a better way to do this? Am I missing something?
Many Thanks,
-
Jean-Paul Ebejer
Early Stage Researcher
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