nglview 0.5.2a0

IPython widget to interactively view molecular structures and trajectories.

[](http://mybinder.org/repo/hainm/nglview-notebooks)
[](https://zenodo.org/badge/latestdoi/11846/arose/nglview)
[](https://travis-ci.org/arose/nglview)
[](http://bioconda.github.io)

An [IPython/Jupyter](http://jupyter.org/) widget to interactively view molecular structures and trajectories. Utilizes the embeddable [NGL Viewer](https://github.com/arose/ngl) for rendering. Support for showing data from the file-system, [RCSB PDB](http:www.rcsb.org), [simpletraj](https://github.com/arose/simpletraj) and from objects of analysis libraries [mdtraj](http://mdtraj.org/), [pytraj](http://amber-md.github.io/pytraj/latest/index.html), [mdanalysis](http://www.mdanalysis.org/).

Should work with Python 2 and 3. If you experience problems, please file an [issue](https://github.com/arose/nglview/issues).



Table of contents
=================

* [Installation](#installation)
* [Example](#example)
* [Usage](#usage)
* [Command line](#command-line)
* [Interface classes](doc/interface_classes.md)
* [Changelog](CHANGELOG.md)
* [FAQ](#faq)
* [License](#license)


Installation
============

Released version
----------------

- Available on `bioconda` channel

`conda install nglview -c bioconda`

- Available on [PyPI](https://pypi.python.org/pypi/nglview/)

`pip install nglview`

Development version
-------------------

The development version can be installed directly from github:

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

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](./examples/README.md)

Usage
=====

Open a notebook

jupyter notebook

and issue

```Python
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](http:www.rcsb.org), [simpletraj](https://github.com/arose/simpletraj) and from objects of analysis libraries [mdtraj](http://mdtraj.org/), [pytraj](http://amber-md.github.io/pytraj/latest/index.html), [mdanalysis](http://www.mdanalysis.org/), [ParmEd](http://parmed.github.io/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
---------------

```python
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](http://arose.github.io/ngl/doc/#User_manual/Usage/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](http://arose.github.io/ngl/doc).

```Python
view.representations = [
{"type": "cartoon", "params": {
"sele": "protein", "color": "residueindex"
}},
{"type": "ball+stick", "params": {
"sele": "hetero"
}}
]
```

The widget constructor also accepts a `representation` argument:

```Python
initial_repr = [
{"type": "cartoon", "params": {
"sele": "protein", "color": "sstruc"
}}
]

view = nglview.NGLWidget(struc, representation=initial_repr)
view
```


Properties
----------

```Python
# set the frame number
view.frame = 100
```

```Python
# 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")
```

```python
# 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)
```

```python
# update camera type
view.camera = 'orthographic'
```

```python
# change background color
view.background = 'black'
```
Trajectory
----------

```python
# 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
-------------------

```python
# Density volumes (MRC/MAP/CCP4, DX/DXBIN, CUBE)
view.add_component('my.ccp4')

# NOTE: Trajectory is a special case of component.
```
Multiple widgets
----------------

You can have multiple widgets per notebook cell:

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

API doc
-------
[Please check here](http://arose.github.io/nglview/latest/api.html)

Command line
============

```bash
# highly experimental code and very buggy, require installing pytraj.

# open notebook, load `my.pdb` to pytraj's trajectory then display `view`
nglview my.pdb

# 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` then execute it
nglview myscript.py

# open notebook and execute 1st cell
nglview mynotebook.ipynb

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

FAQ
===

[Q&A](https://github.com/arose/nglview/wiki/Q&A)

License
=======

Generally MIT, see the LICENSE file for details.