still in need of a solution.
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Indeed, however, you lose the index of the atom in the original molecule you
want to create a bond to, due to the index/id reordering that happens upon
the fragment::Separate.
I am doing two fragment::separate calls. The first is to remove the
sidechain from the protein to create a protein /w
since atoms seem to get repurposed on copy constructor/+= etc, I think a
better tracking system would be very useful.
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