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

[Amr AL-HOSSARY]

OK. I'll try to comply to it..
However, I expect a (nice) amount of difficulties. :)

Amr

BTW 
Is anybody willing to aid?

-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org
[mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of Spencer Bliven
Sent: Tuesday, December 10, 2013 7:05 AM
To: Amr AL-HOSSARY
Cc: biojava-dev
Subject: Re: [Biojava-dev] Biojava Structure and its derivatives are PDB
centered

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
>
>
>
>
>
>
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>
_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev