[Cdk-devel] Implementing MDMoleculeConvention

[Ola S. <ola...@fa...>]

Hi Egon,

I am not that experienced with parsing XML and since there is  
absolutely no javadoc describing the methods netither in  
CMLCoreModule nor ICMLModule, PDBConvention, QSARConvention I need  
some help.

1) When are the methods in ICMLModule called?

2) What should each method do? Javadoc please!

3) How can I debug my Convention? Can I write a JUnit test and run it  
from within Eclipse?

4) As an MDMolecule has an <atomArray> for residues and one for  
chargegroups, how can I reuse the existing atomArray parser?

5) Do I need to handle id and title separately or is it handled in  
the superclass? If not, where/how do I handle it?

6) I don't understand how I know the parent of an element and how sub  
elements should be stored. Will need assistance with code for this.

7) How/where do I return my resulting MDMolecule?


I think what I need is an explanation of the data flow and javadoc  
for each method explaining how it should be used.

I have committed the MDMoleculeConvention but it is just a stub...  
Please have a look at it when you have time.

Cheers,

    .../Ola