import py3Dmol
import random
import matplotlib.pyplot as plot
view = py3Dmol.view(query='pdb:1hvr')
view.setStyle({'cartoon':{'color':'red'}})
!pip install biopandas
Collecting biopandas Downloading biopandas-0.2.2-py3-none-any.whl Requirement already satisfied: numpy in /Users/noriakioshita/.pyenv/versions/anaconda3-4.0.0/lib/python3.5/site-packages (from biopandas) Requirement already satisfied: pandas in /Users/noriakioshita/.pyenv/versions/anaconda3-4.0.0/lib/python3.5/site-packages (from biopandas) Requirement already satisfied: pytz>=2011k in /Users/noriakioshita/.pyenv/versions/anaconda3-4.0.0/lib/python3.5/site-packages (from pandas->biopandas) Requirement already satisfied: python-dateutil>=2 in /Users/noriakioshita/.pyenv/versions/anaconda3-4.0.0/lib/python3.5/site-packages (from pandas->biopandas) Requirement already satisfied: six>=1.5 in /Users/noriakioshita/.pyenv/versions/anaconda3-4.0.0/lib/python3.5/site-packages (from python-dateutil>=2->pandas->biopandas) Installing collected packages: biopandas Successfully installed biopandas-0.2.2
import MDAnalysis as mda
u = mda.Universe('output.pdb')
/Users/noriakioshita/.pyenv/versions/anaconda3-4.0.0/lib/python3.5/site-packages/MDAnalysis/topology/guessers.py:56: UserWarning: Failed to guess the mass for the following atom types: Cl "".format(', '.join(misses)))
from py3dmol import vizinterfaces as p3d
--------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-39-502703adfacc> in <module>() ----> 1 from py3dmol import vizinterfaces as p3d ImportError: No module named 'py3dmol'
viz = p3d.MdaViz(u)
viz.make_animation()
--------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-40-cf8441c80c3c> in <module>() ----> 1 viz = p3d.MdaViz(u) 2 viz.make_animation() NameError: name 'p3d' is not defined