An IPython/Jupyter widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering. Support for showing data from the file-system, RCSB PDB, simpletraj and from objects of analysis libraries mdtraj, pytraj, mdanalysis.

Should work with Python 2 and 3. If you experience problems, please file an issue.

Table of contents

• Installation
• Example
• Usage
• Command line
• Interface classes
• Changelog
• FAQ
• License

Installation

Released version

• Available on bioconda channel

  conda install nglview -c bioconda

• Available on PyPI

  pip install nglview

Development version

The development version can be installed directly from github:

git clone https://github.com/arose/nglview
cd nglview
python -m pip install .

If for any reasons that the widget is not shown, try reinstall below packages

conda install traitlets=4.2.1 ipywidgets==4.1.1 notebook=4.1.0

Example

Please see our Jupyter notebook examples

Usage

Open a notebook

jupyter notebook

and issue

import nglview
view = nglview.show_pdbid("3pqr")  # load "3pqr" from RCSB PDB and display viewer widget
view

A number of convenience functions are available to quickly display data from the file-system, RCSB PDB, simpletraj and from objects of analysis libraries mdtraj, pytraj, mdanalysis, ParmEd.

Function	Description
show_structure_file(path)	Shows structure (pdb, gro, mol2, sdf) in path
show_pdbid(pdbid)	Shows pdbid fetched from RCSB PDB
show_simpletraj(struc_path, traj_path)	Shows structure & trajectory loaded with simpletraj
show_mdtraj(traj)	Shows MDTraj trajectory traj
show_pytraj(traj)	Shows PyTraj trajectory traj
show_parmed(structure)	Shows ParmEd structure
show_mdanalysis(univ)	Shows MDAnalysis Universe or AtomGroup univ

API

Representations

view.add_representation(repr_type='cartoon', selection='protein')

# or shorter
view.add_cartoon(selection="protein")
view.add_surface(selection="protein", opacity=0.3)

# specify color
view.add_cartoon(selection="protein", color='blue')

# specify residue
view.add_licorice('ALA, GLU')

# clear representations
view.clear_representations()
...

And many more, please check Selection language

Representations can also be changed by overwriting the representations property of the widget instance view. The available type and params are described in the NGL Viewer documentation.

view.representations = [
    {"type": "cartoon", "params": {
        "sele": "protein", "color": "residueindex"
    }},
    {"type": "ball+stick", "params": {
        "sele": "hetero"
    }}
]

The widget constructor also accepts a representation argument:

initial_repr = [
    {"type": "cartoon", "params": {
        "sele": "protein", "color": "sstruc"
    }}
]

view = nglview.NGLWidget(struc, representation=initial_repr)
view

Properties

# set the frame number
view.frame = 100

# parameters for the NGL stage object
view.parameters = {
    # "percentages, "dist" is distance too camera in Angstrom
    "clipNear": 0, "clipFar": 100, "clipDist": 10,
    # percentages, start of fog and where on full effect
    "fogNear": 0, "fogFar": 100,
    # background color
    "backgroundColor": "black",
}

# note: NGLView accepts both origin camel NGL keywords (e.g. "clipNear")
# and snake keywords (e.g "clip_near")

# parameters to control the `delay` between snapshots
# change `step` to play forward (positive value) or backward (negative value)
# note: experimental code
view.player.parameters = dict(delay=0.04, step=-1)

# update camera type
view.camera = 'orthographic'

# change background color
view.background = 'black'

Trajectory

# adding new one
view.add_trajectory(traj)

# traj could be `pytraj.Trajectory`, `mdtraj.Trajectory`, `MDAnalysis.Universe`, `parmed.Structure`
# change representation
view.trajectory_0.add_cartoon(...)
view.trajectory_1.add_licorice(...)

Add extra component

# Density volumes (MRC/MAP/CCP4, DX/DXBIN, CUBE)
view.add_component('my.ccp4')

# NOTE: Trajectory is a special case of component.

Multiple widgets

You can have multiple widgets per notebook cell:

from ipywidgets.widgets import Box
w1 = NGLWidget(...)
w2 = NGLWidget(...)
Box(children=(w1,w2))

API doc

Please check here

Command line

# highly experimental code and very buggy, require installing pytraj.

# open notebook, load `my.pdb` to pytraj's trajectory then display `view`
nglview my.pdb

# open notebook, create trajectory with given topology `my.parm7` and trajecotry file `traj.nc`,
# then display `view`
nglview my.parm7 -c traj.nc

# load all trajectories with filename ending with 'nc'
# make sure to use quote " "
nglview my.parm7 -c "*.nc"

# open notebook, copy content from `myscript.py` then execute it
nglview myscript.py

# open notebook and execute 1st cell
nglview mynotebook.ipynb

# create a remote notebook
# just follow its instruction
nglview my.pdb --remote
nglview my.parm7 -c traj.nc --remote
nglview mynotebook.ipynb --remote

FAQ

Q&A

License

Generally MIT, see the LICENSE file for details.