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

[Peter]

2010/12/13 Eric Talevich <eric.talevich at gmail.com>:
> Hey folks,
>
> 1. For stand-alone functions that don't seem to fit anywhere else, I suggest
> creating a file called _utils.py (rather than Utils.py or Misc.py) -- this
> means it's protected, i.e. users know they're not supposed to access it
> directly -- then import it to the top level in __init__.py:
>
> from Bio.PDB._utils import renumber_residues, center_of_mass, ...
>
> Then you're allowed to move the functions in that module somewhere else
> later without going through the usual deprecation process.

On the down side, you'd be adding even more top level functions to
Bio.PDB.

Shouldn't some of these be methods instead (either returning modified
objects or acting in situ as appropriate)?

Peter