In [1]:

    

import numpy as np
import numpy.random as npr
import matplotlib.pyplot as plt
%matplotlib inline


    

In [2]:

    

from msmbuilder.example_datasets import FsPeptide, MetEnkephalin
from msmbuilder.featurizer import DihedralFeaturizer

fs = FsPeptide().get().trajectories
n_atoms = fs[0].n_atoms
dih_model = DihedralFeaturizer(['phi', 'psi', 'omega', 'chi1', 'chi2', 'chi3', 'chi4'])
fs_dih_feat = dih_model.transform(fs)


    

    




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In [3]:

    

import pyemma
tica = pyemma.coordinates.tica(fs_dih_feat,lag=100,dim=10)


    

    




/Users/joshuafass/anaconda/envs/py27/lib/python2.7/site-packages/pyEMMA-2.0.1-py2.7-macosx-10.5-x86_64.egg/pyemma/coordinates/util/stat.py:31: DeprecationWarning: Call to deprecated function hist. Called from pyemma.coordinates.util.stat line 31. Please use pyemma.coordinates.histogram()
  def hist(transform, dimensions, nbins):

In [4]:

    

np.max(tica.feature_TIC_correlation[:,0]),np.argmax(tica.feature_TIC_correlation[:,0])


    

    
Out[4]:





(0.61325799955361537, 78)

In [5]:

    

Y = np.vstack(tica.transform(fs_dih_feat))
Y.shape


    

    
Out[5]:





(280000, 10)

In [6]:

    

plt.plot(sorted(Y[:,0]))


    

    
Out[6]:





[<matplotlib.lines.Line2D at 0x12eab46d0>]






    

In [7]:

    

plt.plot(sorted(Y[:,0])[::1000])


    

    
Out[7]:





[<matplotlib.lines.Line2D at 0x12f3083d0>]






    

In [8]:

    

ind = sorted(range(len(Y)),key=lambda i:Y[i,0])


    

In [9]:

    

plt.plot(Y[ind,0][::100])
plt.figure()
plt.plot(Y[ind,1][::100])


    

    
Out[9]:





[<matplotlib.lines.Line2D at 0x145e60c10>]






    













    

In [10]:

    

import mdtraj


    

In [11]:

    

traj = fs[0]


    

In [12]:

    

for f in fs[1:]:
    traj = traj+f


    

In [13]:

    

frames = traj[ind[::1000]]
frames = frames.superpose(frames,0)


    

In [14]:

    

frames.save_pdb('fs_tic1_movie.pdb')