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, ParmEd, rdkit, ase, HTMD, biopython, cctbx, pyrosetta, schrodinger’s Structure

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

Ask question about usage? Please post here

membrane

Installation
Example
Showcase from users
Usage
Contributing
Command line
API doc
Interface classes
Changelog
FAQ
Website
Acknowledgment
Cite
License

Installation

Released version

Available on conda-forge channel
```
conda install nglview -c conda-forge
```
Available on PyPI

   pip install nglview

Jupyterlab: nglview works best with jupyterlab >= 3.0 and no further steps needed. Known to work versions

nglview	lab	notebook	ipywidgets	Known issue(s)	VSCode
3.1.0	4.0.10	7.0.6	8.1.1	HTML embed doesn’t work	No
3.0.8	4.0.10	7.0.6	8.1.1	show_pdbid doesn’t work	Yes

Notes

If you are using notebook v5.0, you need to increase the iopub_data_rate_limit to visualize big structure (e.g: solvated system)

jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000

Development version

Requirement: ipywidgets >= 7.0, notebook >= 4.2

The development version can be installed directly from github:

notebook user

    git clone https://github.com/arose/nglview
    cd nglview
    python setup.py install

    # if you edit files in ./js folder, make sure to rebuild the code
    cd js
    npm install

    # probably need to activate widgetsnbextension
    # python -m ipykernel install --sys-prefix
    # jupyter nbextension enable --py --sys-prefix widgetsnbextension
    # jupyter nbextension enable --py --sys-prefix nglview

    # tested with ipywidgets 5.2.2, notebook 4.2.1

Example

Notebooks: please see our Jupyter notebook examples
Simple demo for trajectory (take time to load): biomembrane

Showcase from users

Please check user examples. Feel free to contribute.
Also check a series of excelent tutorials about/using nglview from volkamerlab

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, rdkit, HTMD, biopython.

Function	Description
`show_file(path)`	Shows any NGL supported file formats (pdb, gro, mol2, sdf, dx, ..) 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`
`show_rdkit(mol)`	Shows `rdkit` rdkit.Chem.rdchem.Mol
`show_ase(atoms)`	Shows `ase` Atoms
`show_asetraj(traj)`	Shows `ase` trajectory `traj`
`show_pymatgen(struct)`	Shows `pymatgen` Structure
`show_htmd(mol)`	Shows `HTMD` Molecules
`show_biopython(mol)`	Shows `Biopython` structural entities
`show_iotbx(mol)`	Shows `cctbx's iotbx` structure
`show_rosetta(pose)`	Shows `pyrosetta's Pose`
`show_iodata(obj)`	Shows `iodata's IOData`
`show_psi4(obj)`	Shows `psi4's Molecule`
`show_qcelemental`	Shows `QCelementary's Molecule`
`show_openbabel`	Shows `openbabel's OMol`
`show_prody`	Shows `prody's Ensemble or AtomGroup`

API

Representations

view.add_representation('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()

# update parameters for ALL cartoons of component 0 (default)
view.update_cartoon(opacity=0.4, component=0)

# remove ALL cartoons of component 0 (default)
view.remove_cartoon(opacity=0.4, component=0)

# Not using default representation
view = nv.show_file('your.pdb', default=False)
view.center()
view.add_rope()

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.stage.set_parameters(**{
    # "percentages, "dist" is distance to 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 trajectory
view.add_trajectory(traj)
# traj could be a `pytraj.Trajectory`, `mdtraj.Trajectory`, `MDAnalysis.Universe`,
# `parmed.Structure`, `htmd.Molecule` or derived class of `nglview.Trajectory`

# change representation
view[0].add_cartoon(...) # equal to view.add_cartoon(component=0)
view[1].add_licorice(...) # equal to view.add_licorice(component=1)

Add extra component

# Density volumes (MRC/MAP/CCP4, DX/DXBIN, CUBE)
# Or adding derived class of `nglview.Structure`
view.add_component('my.ccp4')

# add component from url
view.add_component('rcsb://1tsu.pdb')
# NOTE: Trajectory is a special case of component.

Mouse

# coot mouse style (https://en.wikipedia.org/wiki/Coot_(software))
view.stage.set_parameters(mouse_preset='coot')

Interaction controls

Movie making

Require: moviepy (pip install moviepy)

from nglview.contrib.movie import MovieMaker
movie = MovieMaker(view, output='my.gif', in_memory=True)
movie.make()

embed

API doc

Command line


# open a notebook and import nglview
nglview

# Require installing pytraj (PR for other backends is welcome)
# open notebook, load `my.pdb` to pytraj's trajectory then display `view`
nglview my.pdb

# load density data
nglview my.ccp4

# 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`
nglview myscript.py

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

# demo (don't need pytraj)
nglview demo

# specify web browser
nglview my.pdb --browser=google-chrome

FAQ

Q&A

Website

Talks

Talks about NGL and nglview

Contributing

Join us here

Projects integrating NGLView

(Feel free to make a PR to add/remove your project here. Thanks.)

AMBER - A package of programs for molecular dynamics simulations of proteins and nucleic acids
mbuild - A hierarchical, component based molecule builder
deepchem - Deep-learning models for Drug Discovery and Quantum Chemistry
htmd - High throughput molecular dynamics simulations
Moleidoscope - Molecular kaleidoscope
ssbio - Tools for enabling structural systems biology
hublib - hublib is a Python library for the HUBzero science gateway platform.
molPX: ipython API to visualize MD-trajectories along projected trajectories
nanoribbon
ase: Atomic Simulation Environment
pida: Software for analyzing multiple protein-protein interaction docking solutions,
pytim
MobleyLab/drug-computing Educational materials for, and related to, UC Irvine’s Drug Discovery Computing Techniques course.
pyiron: an integrated development environment for implementing, testing, and running simulations in computational materials science.
BioSimSpace: An interoperable framework for biomolecular simulation
pyrod: PyRod - Tracing water molecules in molecular dynamics simulations
kugupu: kugupu - a molecular network generator to study charge transport pathways in amorphous materials
pnab: proto-Nucleic Acid Builder
opencadd: A Python library for structural cheminformatics
teachopencadd: TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
query.libretexts.org: query.libretexts.org
datamol: A python library to work with molecules.
dynophores: Dynamic pharmacophore modeling of molecular interactions
pychemcurv: Discrete and local curvature applied to chemistry and chemical reactivity
AutoSolvate: Automated workflow for generating quantum chemistry calculation of explicitly solvated molecules
plipify: PLIPify: Protein-Ligand Interaction Frequencies across Multiple Structures
Melodia: Differential Geometry of Proteins Backbones
pyrosetta_viewer3d: Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab
py4vasp: Python interface for VASP
eminus: A plane wave density functional theory code.
MolSysMT: Molecular Systems Multi-Tool

Acknowledgment

Funding: Hai Nguyen is supported by NIH Grant GM103297, “The Center for HIV RNA Studies” (2015 to 02-2017).
Many thanks to nglview contributors

Cite

If you would like to acknowledge our work, feel free to cite:

Hai Nguyen, David A Case, Alexander S Rose; NGLview - Interactive molecular graphics for Jupyter notebooks, Bioinformatics, , btx789, https://doi.org/10.1093/bioinformatics/btx789

License

Generally MIT, see the LICENSE file for details.

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