Python Jupyter Notebook Shell
Latest commit 2e03fa9 Nov 17, 2017 @avirshup avirshup Merge pull request #186 from Autodesk/simplify-build
Simplify and speed up build
Permalink
Failed to load latest commit information.
.github Run tests from repo root (fixes weird coverage issues) Jun 14, 2017
DockerMakefiles A couple tweaks, trigger full test suite Nov 17, 2017
deployment build tweaks and fixes Nov 17, 2017
docs Use installed tests Nov 9, 2017
moldesign build tweaks and fixes Nov 17, 2017
.coveragerc Get coverage working Nov 9, 2017
.coveralls.yml Add coverage tests May 23, 2017
.dockerignore Add "full-stack" docker image, get notebook image working again Oct 5, 2017
.gitattributes Switch to versioneer versioning May 18, 2016
.gitignore Fix pull-cache, split tokens Nov 16, 2017
CONTRIBUTING.md Fix Method subclass's call signatures; fix toy models for test suite Oct 4, 2016
DEVELOPMENT.md Get first tutorial running Jun 13, 2017
LICENSE Add copyright notice to all files May 14, 2016
MANIFEST.in Run tests from repo root (fixes weird coverage issues) Jun 14, 2017
NOTICES Vendor python-3 shutil.which for py2 compatibility Aug 15, 2017
README.md Create README.md Jun 15, 2017
codeship-services.yml Fix pull-cache, split tokens Nov 16, 2017
codeship-steps.yml A couple tweaks, trigger full test suite Nov 17, 2017
environment.yml Gets pyscf building again May 30, 2017
nb-output-filter.sh Clean up project root and MDT image layers May 22, 2017
pytest.ini Mark subset of tests for faster screening Jun 28, 2017
requirements.txt Add "full-stack" docker image, get notebook image working again Oct 5, 2017
setup.cfg Switch to versioneer versioning May 18, 2016
setup.py Platform-independent home directories Aug 22, 2017
versioneer.py Upgrade versioneer Nov 2, 2016

README.md

PyPI version github release tag Python versions License Codeship Status for Autodesk/molecular-design-toolkit Coverage Status

Try it now: Binder

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')
protease.draw()

Create a small molecule and relax its geometry:

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

Contributing

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

License

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

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.