hmmm. Been a month. Oh well. Here is a picure of an 'isomer network': for the isomers of C6H12. I generated them using molgen , compared the structures all-v-all with the CDK , and visualized the connectivity graph with the help of JUNG . So hardly any work actually by me... Each vertex in the graph is a structure, and each edge is a tanimoto similarity between fingerprints of greater than 0.5 - fairly arbitrary, but I just wanted to see if it worked. The next step is to use predicted spectrum similarity instead of molecular-fingerprint similarity.
An Online Research Notebook