Jupyter notebook add-ons for the Molecular Design Toolkit. NBMolViz provides visualization and interactivity for 3D Molecular Structures in Jupyter notebooks.
After installing it, you'll never need to use the NBMolViz package directly. It's instead called through MDT to provide enhanced functionality in notebooks.
When you install
nbmolviz, you'll need to both install the python library and enable the notebook extensions.
- Install the python library:
$ pip install nbmolviz
- Activate notebook extensions: To enable for your user account:
$ python -m nbmolviz activate --user
To enable within your current virtual environment:
$ python -m nbmolviz activate --sys-prefix
To globally enable for all users (use with caution! This may require
$ python -m nbmolviz activate --global
Upgrading from older versions
Upgrade the library to the newest version $ pip install --upgrade nbmolviz
Remove old notebook extensions (you will be notified if it's necessary to run with
$ python -m nbmolviz uninstall
- Activate the notebook extension as above
Draw a small molecule:
import moldesign as mdt mol = mdt.from_name('ethylene') mol.draw()
Draw a protein:
import moldesign as mdt mol = mdt.from_pdb('3aid') mol.draw()
<img src="img/protein.png style="width: 600px;"/>
Interactively select atoms (the currently selected atoms will be available as
import moldesign as mdt mol = mdt.from_pdb('3aid') selector = mdt.widgets.ResidueSelector(mol) selector
$ git clone https://github.com/autodesk/notebook-molecular-visualization $ cd notebook-molecular-visualization # ./set_filters.sh # tells git to clean up notebooks before committing $ python setup.py jsdeps $ pip install -e . $ jupyter nbextension install --py --symlink --user nbmolviz $ jupyter nbextension enable --py --user nbmolviz $ cd tests/galileo && npm install
This will build your widgets into a folder at
python setup.py jsdeps and reload any notebook browser windows.
To run visual tests
cd tests/nb && ../galileo/bin/galileo --launchnb
Releasing a new version
Travis automatically releases commits that are tagged, so to trigger a new release, just do:
git tag <new tag version> git push origin --tags
If you want to see what will be included in a release, run
check-manifest. You could also manually build a release with
python setup.py sdist and manually release with
python setup.py sdist upload -r pypi.
This package started life as hackathon project for the CECAM 2015 Macromolecular Simulation Workshop. It's since undergone a complete source rewrite, and is being released by BioNano Research at Autodesk as part of our suite of Molecular Design Tools.
The visualizers offered by this library were built using:
- ipywidgets - UI library for interactivity in Jupyter notebooks
- 3Dmol.js - 3D molecular visualization library for web browsers
Copyright 2017 Autodesk Inc.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.