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