Moved Docs/notes to docs/notes
Removed msmbuilder_extras and utils.ACF
Merge pull request #136 from SimTk/utils-cleanup

Removed msmbuilder_extras and utils.ACF
minor tweak to BACE
some little changes to docs
Minor changes to tutorial
Merge branch 'master' of github.com:SimTk/msmbuilder
Added fix to Cluster.py that removes the assignments, generators, and distances options and adds the output_dir option. The Assignments, etc. are therefore named in a regular manner but to the output_dir. Additionally, I removed the output for Ward's method (output_zmatrix). It behaves in the same way as the assignments. It ends up saved to output_dir.
Fixed typo in Cluster.py.
I hadn't removed the zmatrix output argument from Cluster.py yet. I just removed it now.
Cluster.py now only has the output filenames hardcoded once. I removed the check_paths function, and essentially put it in the main function. In order to get the zmatrix_fn to the cluster function, I created an empty dictionary in main (extra_kwargs) that can house any additional data necessary for the clustering step. This is then passed as kwargs to cluster. This addresses issue #127. How's this @rmcgibbo?
Changing the parser arguments broke the Cluster.py tests. This commit fixes them so that the correct options are passed to the script. Also changed the Assignments.h5.distances name from Assignments.h5.dist.
Added fix to Cluster.py that removes the assignments, generators, and distances options and adds the output_dir option. The Assignments, etc. are therefore named in a regular manner but to the output_dir. Additionally, I removed the output for Ward's method (output_zmatrix). It behaves in the same way as the assignments. It ends up saved to output_dir.
Cluster.py now only has the output filenames hardcoded once. I removed the check_paths function, and essentially put it in the main function. In order to get the zmatrix_fn to the cluster function, I created an empty dictionary in main (extra_kwargs) that can house any additional data necessary for the clustering step. This is then passed as kwargs to cluster. This addresses issue #127. How's this @rmcgibbo?
Added fix to Cluster.py that removes the assignments, generators, and distances options and adds the output_dir option. The Assignments, etc. are therefore named in a regular manner but to the output_dir. Additionally, I removed the output for Ward's method (output_zmatrix). It behaves in the same way as the assignments. It ends up saved to output_dir.
Cluster.py now only has the output filenames hardcoded once. I removed the check_paths function, and essentially put it in the main function. In order to get the zmatrix_fn to the cluster function, I created an empty dictionary in main (extra_kwargs) that can house any additional data necessary for the clustering step. This is then passed as kwargs to cluster. This addresses issue #127. How's this @rmcgibbo?
Changing the parser arguments broke the Cluster.py tests. This commit fixes them so that the correct options are passed to the script. Also changed the Assignments.h5.distances name from Assignments.h5.dist.
Typo in Cluster.py -o argument, where I had written Assignments.h5.dist rather than Assignments.h5.distances.
Merge branch 'cluster_args' of github.com:SimTk/msmbuilder into cluster_args