Re: [Cdk-devel] JmolAdapter, Biopolymers and PDBreader updates

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

On Monday 07 February 2005 09:58 am, Egon Willighagen wrote:
> On Thursday 03 February 2005 04:12 pm, Ola Spjuth wrote:
> > Also we were hoping for the extended Biopolymer-related classes (by
> > Martin Eklund) to be added to CDK.
>
> As said, I've applied this to CVS. But I'm having second thoughts...

Martin, 

I've reverted the patch; not that I don't like it at it, but it adds too many 
problems at this moment. What we can do is make it an official patch
meanwhile (so that people can apply it using a build.xml option.

For this, I need the output of 'cvs diff -u cdk-unpatched cdk-with-patch', 
where the cdk-unpatched directory basically is HEAD, and cdk-with-patch is 
HEAD + your modifications.

To summarize the current problems:
- no junit testing (required for data module)
- PDB file reading for small molecules (?)
- the patchs breaks some PDB reading tests
- Polymer != Protein, while Strand might be an extension of Polymer
  (see start of discusion on that in another email)
- there are a lot of Amino Acid structures in PDBReader which needs
  to go in the cdk.template.AminoAcid.java (or something like that)

Nothing we can't work out...

Egon