membrane

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.

nglview

Table of contents¶

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:

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

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')

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

License¶

Generally MIT, see the LICENSE file for details.