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nglview

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

From PyPI:

pip install nglview

Note: The above will try to install jupyter, traitlets and ipywidgets as dependencies. If that fails install it manually pip install jupyter.

From Conda

conda install -c omnia nglview

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_cartoon("protein", color="residueindex")
view.add_surface("protein", opacity=0.3)

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
    "theme": "dark",
}

Multiple widgets

You can have multiple widgets per notebook cell:

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

License

Generally MIT, see the LICENSE file for details.