>>> >> 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 SVN now contains a version which does this (AtomDecorator::get_input_index()). Not really tested (other than it compiles and the tests pass).