Chandrajit Bajaj

Dynamic Packing Grids (DPG)


DPG can efficiently maintain the molecular surface using only linear space and supports quasi-constant time insertion, deletion and movement (i.e., updates) of atoms or groups of atoms. DPG also supports constant time neighborhood queries from arbitrary points. The supported functionalities can be summarized as

  • Core functions
    • Add, Remove and Move an atom of a molecule
    • Intersection and arbitrary range queries
  • Extensions
    • Molecular Surface Maintenance
      • Identifying all exposed atoms of the molecule
      • Produce a patch complex representation of the surface
    • Energetics
      • Given the pdb and integration points sampled on the surface, compute the Born radii
      • Cmpute the polarization energy
    • Multi-resolution (in progress)
      • Range and intersection queries at residue, secondary structure, or chain level
      • Clustering of atoms and mutiresolution molecular surface maintenance


C. Bajaj, R. Chowdhury, and M. Rasheed
A dynamic data structure for flexible molecular maintenance and informatics
In SIAM/ACM Joint Conference on Geometric and Physical Modeling 2009, pages 259 to 270, 2009. (pdf)

  • Library in TexMol containing core functions

Software Usage Installation, usage and programming guidelines for the packages.

Example Results