An IPython widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering.

Very much work in progress. Please contact me if you want to take part. Should work with Python 2 and 3. If you experience problems, please file an issue.

Table of contents

• Installation
• Usage
• [Interface classes](#Interface classes)
• Changelog
• License

Installation

From PyPI:

pip install nglview

Usage

Open a notebook

ipython notebook

and issue

import nglview
struc = nglview.PdbIdStructure( "3pqr" )  # load file from RCSB PDB
w = nglview.NGLWidget( struc )            # create widget
w                                         # display widget

Trajectories

To enable trajectory access pass a second Trajectory argument to the widget constructor or supply a combined Structure/Trajectory object as the first argument.

Seperate Structure and Trajectory objects using FileStructure and SimpletrajStructure (requires the simpletraj package):

import nglview
struc = nglview.FileStructure( "mystruc.pdb" )
traj = nglview.SimpletrajStructure( "mytraj.xtc" )
nglview.NGLWidget( struc, traj )

Combined Structure/Trajectory object utilizing MDTrajTrajectory which wraps a trajectory loaded with MDTraj:

import nglview
import mdtraj
t = mdtraj.load( "mytraj.xtc", top="mystruc.gro" )
strucTraj = nglview.MDTrajTrajectory( t )
nglview.NGLWidget( strucTraj )

Representations

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

w.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"
    } }
]
nglview.NGLWidget( struc, representation=initial_repr )

Adaptors

A number of adaptor classes are available to make structures and trajectories available to the widget. They can support either the Structure (S) or the Trajectory (T) interface as well as both combined.

Class	Description	Interface
FileStructure( path )	Loads path from filesystem	S
PdbIdStructure( pdbid )	Fetches pdbid from RCSB PDB	S
SimpletrajTrajectory( path )	Uses simpletraj to access trajectory at path	T
MDTrajTrajectory( t )	Wraps MDTraj trajectory t	S and T

Interface classes

You can create your own adaptors simply by following the interfaces for Structure and Trajectory, which can also be combined into a single class.

Structure

class MyStructure(nglview.Structure):
    ext = "pdb"  # or gro, cif, mol2, sdf
    def get_structure_string( self ):
        return "structure in the self.ext format"

Trajectory

class MyTrajectory(nglview.Trajectory):
    def get_coordinates_list( self, index ):
        # return list of coordinates for frame at given index
        return [ x1, y1, z1, x2, y2, z2 ]

Combined

class MyStructureTrajectory(nglview.Structure, nglview.Trajectory):
    ext = "pdb"  # or gro, cif, mol2, sdf
    def get_structure_string( self ):
        return "structure in the self.ext format"
    def get_coordinates_list( self, index ):
        # return list of coordinates for frame at given index
        return [ x1, y1, z1, x2, y2, z2 ]

Changelog

Version 0.2

• MIGRATION: changed get_string to get_structure_string
• MIGRATION: changed get_coordinates to get_coordinates_list
• DOC: usage, interface classes
• ADD: MDTrajTrajectory adaptor
• CODE: added interface classes
• CODE: suggested packages; mdtraj, simpletraj

Version 0.1

• initial version, no release

License

Generally MIT, see the LICENSE file for details.