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.
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
Open a notebook
jupyter notebook
and issue
import nglview
view = nglview.show_pdbid("3pqr") # load "3pqr" from RCSB PDB and display viewer widget
viewA 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 |
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# 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",
}You can have multiple widgets per notebook cell:
from ipywidgets.widgets import Box
w1 = NGLWidget(...)
w2 = NGLWidget(...)
Box(children=(w1,w2))Generally MIT, see the LICENSE file for details.
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent