In this project the student will extend Jmol with the ability to view pharmacophores. The pharmacophore is a concept of ligand binding where a set of three or more spheres (other versions have been defined too, but this is the starting point) define what a molecule should look like to fit well into the protein cavity. The spheres indicate areas where proton donors/acceptors or other features should be, and the pharmacophore defines the intersphere distances.
- add ability to contain pharmacophores in the data model
- add a scripting command to define such spheres
- add ability to draw (transparent) spheres at arbitrary place with arbitrary radius