Dynamic Packing Grids


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
Bioinformatics (2011) 27 (1): 55-62. DOI: 10.1093/bioinformatics/btq627

Download DPG

  • Library also contained in TexMol

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

Example Results