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 and stores it in
m_iaBondList
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.
Here we go through the ReferenceQueue and remove garbage
collected SoftValue objects from the HashMap by looking them
up using the SoftValue.key data member.
Publishes the current JMV state to the specified file
It writes the filename, representation, colorscheme, gradient,
and the matrix coordinates of the molecule
transformation.