There is a (minimally tested) atom::clone method as was mentioned in the "This week in IMP" email last week.

On Thu, Mar 12, 2009 at 2:36 PM, Keren Lasker <kerenl@salilab.org> wrote:
I would like to implement a function copy_molecule ( which requires  creating new particles with the appropriate attributes).
More generally, I would like to have a functionality of taking a root of some hierarchy and copying all attributes values into a new root.
did someone do something similar already ?

thanks,
Keren.
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