Remove stereochemistry from currency molecules.
Limit the size of eUtils queries to prevent an error 414.
Log the whole stacktrace when unable to connect to eUtils.
Only close streams that have been opened.
Create BKMException to collect the variety of possible exceptions in BKMDB initialisation.
Improve exception handling in main class.
Create interface to allow clearing of cache database.
Change logger to standard Java logger.
Don't quote organism names in PubMed query.
Ignore currency molecules when identifying pathways.
If a document can't be retrieved from PubMed, simply go to next document instead of ending the program.
Improving readability.
Fix breakpoints to ensure a reaction is counted at most once.
Always get the PDF link.