msmbuilder

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**ds = dataset("traj-0000.h5", fmt='hdf5', mode='r')** Both my data and Jupyter Notebook are in the same folder, however I get an error which is as follows: **NoSuchNodeError: group ``/`` does not...

aasthajhunjhunwala

Issue with module import from scikit-learn

1

When importing msmbuilder (3.7.0), I came across an import error regarding scikit-learn (0.21.2). msmbuilder was unable to execute the command `from sklearn.grid_search import ParameterGrid` within `msmbuilder/utils/param_sweep.py`. `sklearn.grid_search` has been deprecated...

jacknicoludis

how to create "meta.pandas.pickl" file

1

Hi, I need to extract the pairwise distances of carbon alpha atom in a trajectory. For this I have a small script. Here is the part of the script about...

qasimpars

Hi, I find that the function `sample_states()` in `io.sampling` is useful for sampling conformations from each of _N_ microstates in my MSM. Using the following code: `import mdtraj as md`...

rsatijaUT

anuginu

Hi, I installed python 3.6.8 (Anaconda) and MSMBuilder on my Windows laptop (Windows10, 64-bit). When I went through the tutorial, I got stuck running featurize.py. I kept getting the following...

proteinevolver

cxhernandez

cxhernandez

Hello everyone! I have a question about PCA in MSMbuilder (sklearn). It's there any way to find the contribution of each feature (residues, dihedral angles, and others ) to the...

ortizdiego166

I have the following error when I try hmm_model = VonMisesHMM(n_states = 2).fit(train) : msmbuilder/hmm/vonmises.pyx in msmbuilder.hmm.vonmises.VonMisesHMM.fit() msmbuilder/hmm/vonmises.pyx in msmbuilder.hmm.vonmises.VonMisesHMM._validate_sequences() NameError: name 'check_iter_of_sequences' is not defined

kritikamehta15