[Cdk-devel] pharmacophore update - pull request

[Rajarshi G. <rg...@in...>]

Hi, I've shifted to Git and have been updating the pharmcophore code a  
bit. The primary change is to create a subclass of QueryAtomContainer  
called PharmacophoreQuery that will allow us ot consider things such  
as excluded volumes. The previous form of the code did not allow us to  
do this.

While it does add a new class, code that uses the pharmacophore  
classes only needs to be updated by changing QueryAtomContainer (or  
IQueryAtomContainer) to PharmacophoreQuery. Everything else should  
stay the same.

Other changes also include updating to JDK 1.5 idioms and addition of  
tests and annotations.

This branch is based of the SF master, so I request a review and  
subsequent merge into master. You can pull these updates from me by  
doing

git pull git://rguha.ath.cx/cdk pcore

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Rajarshi Guha  <rg...@in...>
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