Merge pull request #35 from locsmith/speed

Speed
Merge pull request #36 from locsmith/speed

latest updates to mak calculations fast
Merge pull request #38 from locsmith/speed

Speed
Merge pull request #37 from locsmith/clean_up

Clean up
remove dead commented out code
Merge remote-tracking branch 'xcamshift/master'
move Index_translator to be a local class where its is used
remove redundant method _get_target_atom_list_name
remove redundant method _get_distance_list_name