Addtest the two similar molecule files, now does an extensive search for both subgraph and areMoleculesEqual

Implemented basic logic for subgraph serach: works for small unit test, has not been tested on entire db

Molecule class now implements Serializable, bug: atomArrayList compare; comment out for now, extra prints for each stage of compares in areMoleculesEqual()

Added the atom class, which contains a hashmap(adj list) of connected atoms along with degrees and atom names. Started storing fields from the text into the molecule