Means bug

[kyleabeauchamp]

kyleb@kb-intel:~/dat/kinase/hmsm$ hmsm  means-ghmm --filename hmms.jsonlines --lag-time 1 --n-states 3 -o out.csv --dir Trajectories --top system.subset.pdb --ext h5 -a AtomIndices.dat 
Traceback (most recent call last):
  File "/home/kyleb/opt/bin/hmsm", line 5, in <module>
    pkg_resources.run_script('mixtape==0.1', 'hmsm')
  File "/home/kyleb/opt/lib/python2.7/site-packages/pkg_resources.py", line 505, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/kyleb/opt/lib/python2.7/site-packages/pkg_resources.py", line 1245, in run_script
    execfile(script_filename, namespace, namespace)
  File "/home/kyleb/opt/lib/python2.7/site-packages/mixtape-0.1-py2.7-linux-x86_64.egg/EGG-INFO/scripts/hmsm", line 8, in <module>
    app.start()
  File "/home/kyleb/opt/lib/python2.7/site-packages/mixtape-0.1-py2.7-linux-x86_64.egg/mixtape/cmdline.py", line 175, in start
    instance.start()
  File "/home/kyleb/opt/lib/python2.7/site-packages/mixtape-0.1-py2.7-linux-x86_64.egg/mixtape/commands/pullmeans.py", line 62, in start
    logprob = log_multivariate_normal_density(xx, self.model['means'],
NameError: global name 'log_multivariate_normal_density' is not defined
``

[rmcgibbo]

PR coming.

[rmcgibbo]

$ hmsm means-ghmm --filename hmms.jsonlines --n-state 2 --lag-time 1 --out f --dir ~/local/msmbuilder/Tutorial/XTC/RUN00/ --ext xtc -a AtomIndices.dat --top ~/local/msmbuilder/Tutorial/native.pdb
Saving the indices of the sampled states in CSV format to f