[Biopython-dev] upcoming Bio.PDB enhancements - RNA

Kristian Rother krother at rubor.de
Tue Jun 1 09:59:31 UTC 2010


Got some comments & questions.

> 2. PDB headers seem to have become better structured in recent years, in
> ... parse_pdb_header needs some attention as well.

I haven't looked into this code for years .. I think it might be a little

> 3. Kristian asked on this list awhile ago about the proper location for
> his new code that works with RNA structures. While RCSB's PDB contains
> some RNA structures, the RNA world doesn't revolve around it. Similarly,
> João needs a place to put code for structure prediction/validation
> servers, command-line wrappers, secondary structures, etc.
> I propose a new sub-package called Bio.Struct for these enhancements:
> from Bio.Struct import RNA
> # Would this work for you, Kristian?

Yes, it would be more descriptive than the originally proposed Bio.RNA . I
am just concerned whether I could keep the 2D structure-related modules in
the same package.

> Alternatively, we could do all of this within the PDB module -- so picture
> the above examples with "PDB" in place of "Struct". This raises the chance
> of naming collisions, though, and doesn't solve issue #3 above.

I like Bio.PDB.RNA less for the same reasons plus the 2D structure issue.

> We'll leave the existing PDB module layout alone, in general. I think it
> will be necessary to add a few more attributes to the
> Bio.PDB.Structure.Structure class, but we can do this without breaking
> compatibility.
> Comments?

What about the modules for constructing coordinates & Loop Closure
(currently available on my Github branch)? I placed them in Bio.PDB
because they are not limited to RNA and are conceptually similar to the
operations performed by Bio.PDB.NeighborSearch and Bio.PDB.SVDSuperimposer
- or would it be better to gather such things in some other package within


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