plot_free_energy_2d.py fails with "ValueError: a and p must have same size"

[mabianchet]

plot_free_energy_2d.py fails with "ValueError: a and p must have same size"

[msultan]

How are you calling the function? My guess is that your data array is not the same size as your probability pi.

[msultan]

The pi vector has to be the same size as the data.

[mabianchet]

Hi msultant
hanks for your answer

The error appears running the example file of the distribution
% python plot_free_energy_2d.py

[msultan]

Is this from the examples page?

[msultan]

@cxhernandez Is there some disconnectivity issue with the FS-peptide dataset?

[msultan]

I am not getting this error on my mac mini

python plot_free_energy_2d.py 
fs_peptide already is cached
/Users/muneeb/anaconda/lib/python3.5/site-packages/mdtraj-1.9.0.dev0-py3.5-macosx-10.6-x86_64.egg/mdtraj/formats/pdb/pdbfile.py:196: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors.
  warnings.warn('Unlikely unit cell vectors detected in PDB file likely '
loading trajectory-1.xtc...
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/Users/muneeb/anaconda/lib/python3.5/site-packages/sklearn/cluster/k_means_.py:1279: DeprecationWarning: This function is deprecated. Please call randint(0, 279999 + 1) instead
  0, n_samples - 1, init_size)
MSM contains 1 strongly connected component above weight=0.50. Component 0 selected, with population 100.000000%
/Users/muneeb/anaconda/lib/python3.5/site-packages/numpy/ma/core.py:6385: MaskedArrayFutureWarning: In the future the default for ma.maximum.reduce will be axis=0, not the current None, to match np.maximum.reduce. Explicitly pass 0 or None to silence this warning.
  return self.reduce(a)
/Users/muneeb/anaconda/lib/python3.5/site-packages/numpy/ma/core.py:6385: MaskedArrayFutureWarning: In the future the default for ma.minimum.reduce will be axis=0, not the current None, to match np.minimum.reduce. Explicitly pass 0 or None to silence this warning.
  return self.reduce(a)

[mabianchet]

Dear msultant,

Shame on me, i introduced a typo in the example script that coincidentally reproduce the error in my script. A fresh copy of the script works well.

The problem was with my use of msmbuilder, changing the clustering methods fix it.

I apologize again.

[cxhernandez]

Glad to hear you figured out the issue!