True, but this will get screwed up on writing anyway as all the
atoms need to have distinct ids in the written pdb. Or am I
misunderstanding your scenario?
yes - I was thinking of writing only mol2, by giving the Particle
that represents mol2 ( regardless to mol1) - so the ids should be ok.
I guess I would propose having a "source_pdb_index" attribute (or
something similar) in atoms, but that it always gets ignored on
writing (since either it is already correct, in which case you
might as well ignore it, or it is incorrect, in which case you have
to ignore it).
would be useful for the scenario above I think