Notebook-integrated tools for molecular simulation and visualization
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Molecular Design Toolkit

Molecular modeling without the pain - a Python library offering integrated simulation, visualization, analysis, and cloud computing.

The toolkit aims to lower the barriers between you and your science by integrating mature, open source simulation packages with a readable abstract API, Jupyter notebook visualization, and native cloud computing.

Get started

MDT requires Docker and Python 2.7. (Python 3.5+ is supported in the development version, and will be available in the stable 0.8 release.)

On the command line, run:

pip install moldesign
python -m moldesign intro

Note: depending on how python is installed on your system, some users may need to install the package as root: sudo pip install moldesign.

The best way to get started is to play with the examples that python -m moldesign intro will pull up. See the documentation for complete API docs, development instructions and other installation scenarios.

Code Example

You'll almost always import the package and its units module:

import moldesign as mdt
from moldesign import units as u

Download a protein from the PDB and visualize it in 3D (in a notebook):

protease = mdt.from_pdb('3AID')

Create a small molecule and relax its geometry:

mol = mdt.from_name('bipyridine')
min_trajectory = mol.minimize(nsteps=20)

For in-depth examples, see the built-in example notebooks (run python -m moldesign intro to launch).

Get help


See for details. Note that the Notebook Molecular Visualization library and PyCloudComputeCannon are also developed under this project's umbrella.


See NOTICES for details about incorporated code.

Copyright 2016 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.