Updated the virtual screen software
Updated the virtual screen software

Brand new revision of the virtual screening code. It's more readable and works
with more freedom. You no longer have to specify the reaction template,
substructures, ligands, etc. Instead, structures are arbitrarily added on to
each other in order.

Still, this is a work in progress. Right now, it has only been tested on a few
structures and only creates one combination. I still have to set it up to create
many combinations and produce many output structures.

ericchansen/q2mm,Q2MM/q2mm,ericchansen/q2mm,arosale4/q2mm,Q2MM/q2mm,arosale4/q2mm