moldesign 0.7.2

The Molecular Design Toolkit: Dead-simple chemical simulation, visualization, and cloud computing in a notebook

# Molecular Design Toolkit [](https://badge.fury.io/py/moldesign)

Molecular modeling without the pain - a Python 2.7 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 On the command line, run: `shell pip install moldesign python -m moldesign intro `

See [the documentation](docs/install.rst) for development instructions and other use cases.

## Code Example

You’ll almost always import the package and its units module: `python import moldesign as mdt from moldesign import units as u `

Download a protein from the PDB and visualize it in 3D (in a notebook): `python protease = mdt.from_pdb('3AID') protease.draw() `

Create a small molecule and relax its geometry: `python mol = mdt.from_name('bipyridine') mol.set_energy_model(mdt.models.RHF(basis='STO-3G')) min_trajectory = mol.minimize(nsteps=20) min_trajectory.draw_orbitals() `

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

## Get help

• [API Documentation](https://autodesk.github.io/molecular-design-toolkit)

• [Forums](https://forum.bionano.autodesk.com/c/Molecular-Design-Toolkit)

• [Email us](mailto:[e-mail])

## Contributing

See [CONTRIBUTING.md](CONTRIBUTING.md) for details. Note that the [Notebook Molecular Visualization](https://github.com/autodesk/notebook-molecular-design) library and [PyCloudComputeCannon](https://github.com/autodesk/py-cloud-compute-cannon) are also developed under this project’s umbrella.

## License

See [NOTICES](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

http://www.apache.org/licenses/LICENSE-2.0

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.