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

[João Rodrigues]

Hello everyone,

My suggestion with this _utils.py file was only to provide a temporary
storage solution for these functions. This would be temporary until
Struct.py is mature enough. I'd say these would fit perfectly under it since
they are pretty general functions (i.e. not restricted to DNA, Protein,
etc). The downside is indeed as Peter noted, that the Bio.PDB grows larger.
Indeed, as you suggested, renumber_residues is a method of Structure. I
could change it to Entity to allow its usage on chains but I think that
would be adding an unnecessary (and perhaps confusing) method for
Residue.py.

Some of what we've been discussing has been implement by Rodrigo in his git
branch and would indeed be a good addition. I'd like to see these routine
actions "translated" from Bio.PDB classes to an easy interface callable from
the command line. For me at least, this would be extremely valuable (and
allow me to drop those weird FORTRAN files :). Now, how this should be
structured, I guess the best place would be inside an _utils.py file under
Bio.Struct. However, since this is not yet in the main trunk, I'd say we can
(for now) create a similar file under Bio.PDB and then just move it to
Bio.Struct when the time comes.

Regarding an immediate solution, adding the keyword arguments seems perfect
IMO. I'd also add start_id and last_id to allow renumbering of specific
parts.

Best

João