move HackyMatrix to it's own file
add a test for HackyMatrix
Rename HackyMatrix to MatrixAdapter
Merge pull request #89 from js850/matrix

MatrixAdapter
Merge remote-tracking branch 'origin/master' into refactor
reformat the optimize folder using pycharm
reformat potentials using pycharm
reformat systems using pycharm
reformat accept_tests using pycharm
reformat amber module using pycharm
reformat landscape module using pycharm
reformat transition_states module using pycharm
reformat utils module using pycharm