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

[Rodrigo Faccioli]

Hello,

I saw this post about some features that we have already implemented.  One
example is split the pdb into chains. You can see [1] my own example.

Does Joao want to talk to us some details about it? Unfortunately, I had
talked to Eric about our idea to contribute for BioPython project. Although,
I don't have time, in this moment, because I have to finish some issues for
my PhD, I believe that Joao and us can work together in some issues.

[1]
https://github.com/rodrigofaccioli/ContributeToBioPython/blob/master/scripts/split_pdb_chains.py

Thanks in advance,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Mon, Dec 13, 2010 at 7:28 PM, Eric Talevich <eric.talevich at gmail.com>wrote:

> 2010/12/13 Peter <biopython at maubp.freeserve.co.uk>
>
> > 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)?
> >
>
> Agreed, wherever that's possible. I'm just recommending keeping a
> "utils/misc" module as protected in absence of any more informative name
> for
> its contents. If renumber_residues stays as a method on Structure or
> Entity,
> then we don't need a _utils.py yet.
>
> I think the top level is a good place for functions that don't operate on
> any particular one of the objects defined in that sub-package -- to use
> João's example, joining several PDB files together.
>
> -E
>
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