[Biojava-l] Class PdbToXML converter

[Simon Brocklehurst]

Vera Fleischer wrote:

> Hi,
>
> I'm interested in using the PdbtoXML converter and I'm wondering what
> the XML structure of the resulting files will look like. The class
> description mentions that the resulting XML "will validate against the
> biojava:MacromolecularStructure DTD." Is there any way I can get some
> details on this DTD?

Hi

To look at the XML, try to get the eventbasedparsing.Pdb2XML application
running.  The XML is quite simple, you should be able to get the idea by
inspection of the XML.  The parsing system is not complete, however, so
I'm a bit reluctant to start putting out DTD's and Schemas right now.

The current state of the system is certainly good enough for populating
reasonably rich objects that can be used for both analysis and
visualisation of three-dimensional structure. I think it's at the stage
where I hope we won't need to break code written on top of this XML - the
use case is that we have good(ish) structure analysis and 3-D
visualisation systems built on this parser running internally at CAT, but
it's likely that there will be a need to add to the XML in a backwards
compatible way.

Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com