code: public void sitefinder() {
          //logger.debug("SITEFINDER");
          try {
              assignProteinToGrid();
          } catch (Exception ex1) {
              logger.error("Problems with assignProteinToGrid due to:" + ex1.toString());
          }
          // 3. Step scan allong x,y,z axis and the diagonals, if PSP event add +1
          // to grid cell
          int[] dim = gridGenerator.getDim();
          //		logger.debug("	SITEFINDER-SCAN - dim:" + dim[0] + " grid:"
          //				+ this.grid[0].length + " grid point sum:" + this.grid.length
          //				* this.grid[0].length * this.grid[0][0].length);
          axisScanX(dim[2], dim[1], dim[0]);// x-Axis
          axisScanY(dim[2], dim[0], dim[1]);// y-Axis
          axisScanZ(dim[0], dim[1], dim[2]);// z-Axis
  
          diagonalAxisScanXZY(dim[0], dim[2], dim[1]);// diagonal1-Axis
          diagonalAxisScanYZX(dim[1], dim[2], dim[0]);// diagonal2-Axis
          diagonalAxisScanYXZ(dim[1], dim[0], dim[2]);// diagonal3-Axis
          diagonalAxisScanXYZ(dim[0], dim[1], dim[2]);// diagonal4-Axis
  
          //debuggCheckPSPEvent();
  
          findPockets();
  
          sortPockets();
      }
docs: Main method which calls the methods: assignProteinToGrid,
  GridScan, and FindPockets.