Atom indices issue

[kyleabeauchamp]

kyleb@kb-intel:~/dat/kinase/hmsm$ hmsm means-ghmm --filename hmms.jsonlines --lag-time 1 --n-states 3  --dir Trajectories/ --top system.subset.pdb --ext h5 -d AtomPairs.dat -o out.csv
None
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 174, in start
    instance = klass(args)
  File "/home/kyleb/opt/lib/python2.7/site-packages/mixtape-0.1-py2.7-linux-x86_64.egg/mixtape/commands/sample.py", line 112, in __init__
    self.atom_indices = np.loadtxt(args.atom_indices, dtype=int, ndmin=1)
  File "/home/kyleb/opt/lib/python2.7/site-packages/numpy/lib/npyio.py", line 719, in loadtxt
    raise ValueError('fname must be a string, file handle, or generator')
ValueError: fname must be a string, file handle, or generator

It seems that args.atom_indices is actually None here, presumably because I'm using pairwise distances instead.

[kyleabeauchamp]

Oh I figured it out. It's not implemented, but the NotImplemented exception isn't being raised until a few lines too late.

[rmcgibbo]

This is fixed by the featurizer framework. (Right?)

[kyleabeauchamp]

Yes