[Cdk-devel] Re: [Cdk-user] BioPolymers and CML I/O

[Egon W. <e.w...@sc...>]

On Wednesday 10 August 2005 11:59 am, Egon Willighagen wrote:
> > Are there any easy ways of resolving this
> > problem? Looking in the code for the CMLCoreModule class, I see that
> > there are no variables handling protein specific information. Can such
> > variables be added and methods such as the storeAtomData() be modified
> > to read them from the CML file?
>
> As you said, just using the atom information is actually enough to restore
> the CDK BioPolymer... so let's do that first... I'll reply in a different
> email on this to not flood the CML discussion list with implementation
> details.

What we need first is a trigger for CMLCoreModule that makes it aware of 
biopolymers... the startsWith("pdb:", atom/scalar/@dictRef) should do...

When this event is catched, the CMLCodeModule should throw a 
startStrand event, possibly prepended by a startBioPolymer event to the CDOPI.

It require some bookkeeping, like currentStrand = null, when no strand is 
active, and = "X" when a strand is identified. And the same for BioPolymer...

Ok, when that part is updated, we need to update the CDOPI implementation for 
CDK, to catch startBioPolymer and startStrand events, and construct the 
appropriate CDK classes.

I'm ready to do this, as soon as I can easily build protein structures in CDK.

Egon

PS. can we meet online?