The executable file is "match" in the bin directory. To run:

match <mol density file 1> <mol density file 2> <min density val> <max density val> <mol potential file 1> <mol potential file 2>

The density and potential files are in .rawiv format, which can be converted from .dx file using dx2rawiv in the bin directory. 
The output is the similarity score between the two molecules. 

When the program executes, it writes out two temporary files for each molecule: .ctr file for the contour tree and .dct file for the dual contour tree. Those files are used for future fast comparison of the molecule. The .ctr file is for the entire volume and should not change unless you update the data for the molecule. The .dct file is range specific. If you want to try the match with a different range, you should delete the .dct files.

To compile the program, type 

make
make install