Creates the neighbor list, listing the neighbors of each
atom for drawing bonds
It creates a 2D array, where each element contains an array of integers
that correspond to the indeces of its neighbors
Creates GridSearchPairs to determine closeness of atoms for bond search
Here's how it works:
gridSearch() divides the space that the molecule occupies into a 3-d grid of cubes,
or gridboxes.
Publishes the current JMV state to the specified file
It writes the filename, representation, colorscheme, gradient,
and the matrix coordinates of the molecule
transformation.