Mutual Information

Imports¶

In [1]:

%matplotlib inline

import numpy as np

from sklearn.pipeline import Pipeline
from msmbuilder.example_datasets import FsPeptide
from msmbuilder.featurizer import DihedralFeaturizer
from msmbuilder.preprocessing import RobustScaler
from msmbuilder.decomposition import tICA
from msmbuilder.cluster import KMeans
from msmbuilder.msm import MarkovStateModel
from msmbuilder.tpt import net_fluxes, paths

import mdtraj as md

from matplotlib.colors import rgb2hex
from nglview import MDTrajTrajectory, NGLWidget
import msmexplorer as msme

from mdentropy.metrics import DihedralMutualInformation

rs = np.random.RandomState(42)

/home/travis/miniconda3/envs/docenv/lib/python3.6/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
/home/travis/miniconda3/envs/docenv/lib/python3.6/site-packages/sklearn/grid_search.py:42: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. This module will be removed in 0.20.
  DeprecationWarning)
/home/travis/miniconda3/envs/docenv/lib/python3.6/site-packages/statsmodels/compat/pandas.py:56: FutureWarning: The pandas.core.datetools module is deprecated and will be removed in a future version. Please use the pandas.tseries module instead.
  from pandas.core import datetools
/home/travis/miniconda3/envs/docenv/lib/python3.6/site-packages/seaborn/apionly.py:6: UserWarning: As seaborn no longer sets a default style on import, the seaborn.apionly module is deprecated. It will be removed in a future version.
  warnings.warn(msg, UserWarning)

Load Trajectories¶

In [2]:

trajectories = FsPeptide(verbose=False).get().trajectories

/home/travis/miniconda3/envs/docenv/lib/python3.6/site-packages/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 '

Build Markov Model¶

In [3]:

pipeline = Pipeline([
        ('dihedrals', DihedralFeaturizer()),
        ('scaler', RobustScaler()),
        ('tica', tICA(n_components=2, lag_time=10)),
        ('kmeans', KMeans(n_clusters=12, random_state=rs)),
        ('msm', MarkovStateModel(lag_time=1))             
        ])

msm_assignments = pipeline.fit_transform(trajectories)
msm = pipeline.get_params()['msm']

MSM contains 1 strongly connected component above weight=1.00. Component 0 selected, with population 100.000000%

Identify Top Folding Pathway¶

In [4]:

sources, sinks = [msm.populations_.argmin()], [msm.populations_.argmax()]
net_flux = net_fluxes(sources, sinks, msm)
paths, _ = paths(sources, sinks, net_flux, num_paths=0)

samples = msm.draw_samples(msm_assignments, n_samples=1000, random_state=rs)

xyz = []
for state in paths[0]:
    for traj_id, frame in samples[state]:
        xyz.append(trajectories[traj_id][frame].xyz)
pathway = md.Trajectory(np.concatenate(xyz, axis=0), trajectories[0].topology)
pathway.superpose(pathway[0])

Out[4]:

<mdtraj.Trajectory with 4000 frames, 264 atoms, 23 residues, without unitcells at 0x2ab067182ac8>

Calculate Mutual information¶

In [5]:

dmutinf = DihedralMutualInformation(n_bins=3, method='knn', normed=True)
M = dmutinf.partial_transform(pathway)
M -= M.diagonal() * np.eye(*M.shape) 

labels = [str(res.index) for res in trajectories[0].topology.residues
          if res.name not in ['ACE', 'NME']]
ax = msme.plot_chord(M, threshold=.5, labels=labels,)

/home/travis/miniconda3/envs/docenv/lib/python3.6/site-packages/mdentropy-0.3.0-py3.6.egg/mdentropy/metrics/base.py:59: RuntimeWarning: invalid value encountered in true_divide
  return floor_threshold(result - np.nan_to_num(correction / shuffle))

In [6]:

from nglview import MDTrajTrajectory, NGLWidget

t = MDTrajTrajectory(pathway)
view = NGLWidget(t)
view

Widget Javascript not detected.  It may not be installed properly. Did you enable the widgetsnbextension? If not, then run "jupyter nbextension enable --py --sys-prefix widgetsnbextension"

In [7]:

scores = np.real(np.linalg.eig(M)[1][0])
scores -= scores.min()
scores /= scores.max()

cmap = msme.utils.make_colormap(['rawdenim', 'lightgrey', 'pomegranate'])
reslist = [str(res.index) for res in pathway.topology.residues][1:-1]

view.clear()
view.clear_representations()
view.add_cartoon('protein', color='white')
for i, color in enumerate(cmap(scores)):
    view.add_representation('ball+stick', reslist[i], color=rgb2hex(color))
view.camera = 'orthographic'

(mutual-information.ipynb; mutual-information.eval.ipynb; mutual-information.py)