Implemented option exclude. Added logging of the total time stat
Improved the benchmark out info: added total processing time per molecule, nAtoms and nBonds
Implemented option inputfilter
Implemented 2 new options
Merged upstream to fork. Solved lots of conflicts. Now FileWriter is used and more try {} blocks are added.
Changed the default values for options: -l and -r
Fixed a bug: missing break in the inchi case which caused -x option to be activated when -i option is active
Merge pull request #6 from ntk73/master

Added new options.