[Rdkit-discuss] atom indexing

[Ling C. <lin...@gm...>]

Dear colleagues,

I got some questions about atom indexing. Just wonder if you could help me?

   1. In m3=Chem.CombineMols(m1,m2) , is it guaranteed that the atom
   indices in m3 is equivalent to the indices in m1 followed by the indices in
   m2?
   2. If I construct an editable mol from m1, is it that the atomic indices
   in the editable mol is equivalent to that in m1? And when I convert the
   editable mol back, suppose the atom indexing is also preserved?
   3. Same as #2, but for an RWMol instead of an editable mol.
   4. If I delete an "F" atom from an editable mol, is there a way to mark
   the atom in the new mol that was originally bonded to the "F"? I mean, if I
   get its atomic index before the deletion, suppose it won't be preserved.
   5. Similar to #4, but for DeleteSubstructs.

Alternatively, if there is a way to mark atoms, I don't need the atom
indices anyway.

Thank you!

Ling