[Biojava-dev] Biojava Structure and its derivatives are PDB centered

[Spencer Bliven]

Amr-

Yes, the Structure>Chain>Group>Atom data structure defined by BioJava
contains concepts used in the PDB format, but that doesn't mean that a new
implementation is needed to write a MOL2 parser. For instance, each
MOLECULE could be used to create a model in the biojava Structure
containing a single chain and group for the ligand. (I'm not sure whether
there are conventions for protein-sized structures in MOL2, all the
examples I've seen are for small ligands.) The intent of separating Atom
from AtomImpl was primarily to provide a pure interface for the API, not
necessarily to allow different concepts of how to organize 3D points into a
meaningful system. Any new file parsers should use the existing data
structures.

-Spencer


On Mon, Dec 9, 2013 at 2:33 AM, Amr AL-HOSSARY <amr_alhossary at hotmail.com>wrote:

> Dear Biojava Development team,
>
>
>
> I noticed that we don't implement a reader/writer for MOL2 file format and
> I
> thought of implementing one.
>
> But I noticed that the Structure interface (and almost all
> structure-related
> classes are PDB centered).
>
>
>
> For example, AtomImpl is an implementation of the interface Atom.. sounds
> nice.
>
> AtomImpl is mentioned to be an implementation of an Atom of A PDB file, and
> so it implements Atom, Serializable, and PdbRecord .. hum that sounds
> logic,
> although it should have been called AtomPdBImpl, but no problem.
>
> Now Atom itself extends Serializable and PDBRecord !!!!!!!
>
> In PDBRecord there are two overloaded forms of toPDB(). That is logic, but
> what is not logic is letting Atom (as an abstract definition of Atom)
> implements PDBRecord and passing toPDB() to all implementing classes.
>
>
>
> IMHO, the solution to this mess is to introduce an interface called
> Parsable
> or Persistable, including methods read() and write(), and implementing
> objects would implement it in different ways.
>
> Or simply to create a helper class that takes the Atom object and write the
> appropriate format.
>
>
>
> A similar problem is present for Structure and StructureImpl in a less
> severity form.
>
>
>
>
>
> Another solution is to rewrite the structure package in the
> org.biojava3.structure with the new PDB-free mind orientation.
>
>
>
>
>
> Regards
>
>
>
> Amr
>
>
>
>
>
> Best Regards,
> Amr AL-HOSSARY
>
>
>
>
>
>
> Amr Ali AL-HOSSARY |   Ph.D. Student | International PhD program in
> Computational Biology and Bioinformatics | School of Computer Engineering |
> Nanyang Technological University | Singapore (GMT+8) |  Email:
> <mailto:aalhossary at pmail.ntu.edu.sg> aalhossary at pmail.ntu.edu.sg |
>  Mobile:
> +65-94572816
>
>
>
>
>
>
>
>
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