Program:TutorialOur PDB TutorialConnolly functionAtomic Density functionPDB
The Atomic Density (AD) function, fa : M → R, improves the Connolly function by taking a sequence of, say k, neighborhood balls around a point x with increasing radii, computing (roughly) the Connolly function with respect to each radius, and obtaining the final function value at x based on these k Connolly function values.
Since we cannot efficiently work with the function defined as above, we approximate. This is done by determining which atoms (using Van der Waalls representation) intersect the atom at our chosen point. We then interpolate between the centers and find the best fit cubic polynomial. Taking logarithims we make the work approximately linear to get a solution. This solution is our value for the atomic density.
