[Biopython-dev] Features of the GSOC branch ready to be merged

[Kristian Rother]

Hi Joao,

I got two things to add to Erics comments:

- When renumbering a chain, the id's of some residues are changed. Have
you tested whether the keys in Chain.child_dict are changed as well?

- Could you refactor a method Chain.change_residue_numbers(old_ids,
new_ids) that does the changing of the calculated identifiers? I think
this would have a some advantages (shorter code is more testable, easier
to deal with the point above, I could use this for some custom numbering
schemes).

- Currently, Chain.renumber_residues in the lines
      last_num = residue.id[1]+displace
      residue.id = (residue.id[0], residue.id[1]+displace, residue.id[2])
  are repating 3 times.

Best regards,
    Kristian