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
Here at NM, various tricks are sometimes used to store the identity
for these sorts of things; e.g. setting the isotope number, adding
atom classes or atom data. We could make an API addition to return the
identity of the new atoms after calling .Add functions if you pass in
a suitable vector.
-
since atoms seem to get repurposed on copy constructor/+= etc, I think a
better tracking system would be very useful.
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