code: public void writePocketsToPMesh(String outPutFileName) {
  
          try {
              for (int i = 0; i < pockets.size(); i++) {// go through every
                  // pocket
                  BufferedWriter writer = new BufferedWriter(new FileWriter(outPutFileName + "-" + i + ".pmesh"));
                  List<Point3d> pocket = pockets.get(i);
                  writer.write(pocket.size() + "\n");
                  for (int j = 0; j < pocket.size(); j++) {// go through every
                      // grid point of the
                      // actual pocket
                      Point3d actualGridPoint = (Point3d) pocket.get(j);
                      Point3d coords = gridGenerator.getCoordinatesFromGridPoint(actualGridPoint);
                      writer.write(coords.x + "\t" + coords.y + "\t" + coords.z + "\n");
                  }
                  writer.close();
              }
          } catch (IOException e) {
              logger.debug(e);
          }
      }
docs: Method writes the pockets to pmesh format.