[cctbxbb] Left to dry by iotbx_pdb_ext.input.construct_hierarchy()

[James Stroud]

Hello all,

This seems like it should qualify as a bug. If I have an instance of iotbx_pdb_ext.input and I create a hierarchy with construct_hierarchy(), then I must retain the reference to that hierarchy or apparently I can never get it back:

>>> hierarchy = my_pdb.construct_hierarchy()
>>> def some_local_scope_function(a_pdb):
      local_hierarchy = a_pdb.construct_hierarchy()
>>> some_local_scope_function(my_pdb)
[…]
RuntimeError: atom has another parent atom_group already.

Wouldn't better behavior just return the previously constructed hierarchy given that multiple hierarchies can't be made? If each atom apparently remembers to which atom_group it belongs (and presumably on up), then shouldn't it make sense that an iotbx_pdb_ext.input be able to remember it's own hierarchy and produce it upon demand?

Looking at a iotbx_pdb_hierarchy_ext.root, I don't find a reference to the iotbx_pdb_ext.input from which it was created. So, although passing around a hierarchy might be the obvious work-around, the end-user still needs to do some accounting if said user wants to track which roots belong to which inputs, and vice versa.

James

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20130325/05050436/attachment.htm>