molecules Documentation¶

Installation¶

Stable release¶

To install molecules, run this command in your terminal:

pip install molecules

This is the preferred method to install molecules, as it will always install the most recent stable release.

If you don’t have pip installed, this Python installation guide can guide you through the process.

From sources¶

The sources for molecules can be downloaded from the Github repo.

You can either clone the public repository:

git clone git://github.com/yngtodd/molecules

Or download the tarball:

curl  -OL https://github.com/yngtodd/molecules/tarball/master

Once you have a copy of the source, you can install it with:

python setup.py install

Usage¶

To use molecules in a project:

import molecules

Contributing¶

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions¶

Report Bugs¶

Report bugs at https://github.com/yngtodd/molecules/issues.

If you are reporting a bug, please include:

Your operating system name and version.
Any details about your local setup that might be helpful in troubleshooting.
Detailed steps to reproduce the bug.

Fix Bugs¶

Look through the GitHub issues for bugs. Anything tagged with “bug” is open to whoever wants to implement it.

Implement Features¶

Look through the GitHub issues for features. Anything tagged with “feature” is open to whoever wants to implement it.

Write Documentation¶

molecules could always use more documentation, whether as part of the official molecules docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback¶

The best way to send feedback is to file an issue at https://github.com/yngtodd/molecules/issues.

If you are proposing a feature:

Explain in detail how it would work.
Keep the scope as narrow as possible, to make it easier to implement.
Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!¶

Ready to contribute? Here’s how to set up molecules for local development.

Fork the molecules repo on GitHub.
Clone your fork locally:

git clone git@github.com:your_name_here/molecules.git

Create a branch for local development:

git checkout -b name-of-your-bugfix-or-feature

Now you can make your changes locally.

When you’re done making changes, check that your changes pass style and unit tests, including testing other Python versions with tox:

tox

To get tox, just pip install it.

Commit your changes and push your branch to GitHub:

git add .
git commit -m "Your detailed description of your changes."
git push origin name-of-your-bugfix-or-feature

Submit a pull request through the GitHub website.

Pull Request Guidelines¶

Before you submit a pull request, check that it meets these guidelines:

The pull request should include tests.
If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
The pull request should work for Python >= 3.6 and for PyPy. Check https://travis-ci.org/yngtodd/molecules under pull requests for active pull requests or run the tox command and make sure that the tests pass for all supported Python versions.

Tips¶

To run a subset of tests:

py.test test/test_molecules.py

Credits¶

Development Lead¶

Todd Young GitHub: yngtodd

Contributors¶

None yet. Why not be the first?

History¶

0.0.1 (2018-10-3)¶

First release on PyPI.

molecules¶

molecules package¶

Subpackages¶

molecules.data package¶

Subpackages¶

molecules.data.dataloaders package¶

Submodules¶

molecules.data.dataloaders.dataset module¶

class molecules.data.dataloaders.dataset.ContactMapDataset(path, name=None)[source]¶

Bases: object

Data handling for Numpy stored contact maps

load_data(shape=None)[source]¶

Load numpy array data.

Parameters:	shape (tuple, optional) – Shape of the data. Format: (H x W x C)
Returns:	X_train (np.ndarray) – Training set. X_test (np.ndarray) – Test set.

molecules.data.dataloaders.fspeptide module¶

molecules.data.dataloaders.onefme module¶

molecules.data.dataloaders.utils module¶

Module contents¶

molecules.ml package¶

Subpackages¶

molecules.ml.rl package¶

Subpackages¶

molecules.ml.rl.models package¶

Submodules¶

molecules.ml.rl.models.fc_policy module¶

Module contents¶

Submodules¶

molecules.ml.rl.reinforce module¶

Module contents¶

molecules.ml.supervised package¶

Module contents¶

molecules.ml.unsupervised package¶

Subpackages¶

molecules.ml.unsupervised.conv_vae package¶

Submodules¶

molecules.ml.unsupervised.conv_vae.decoder module¶

molecules.ml.unsupervised.conv_vae.encoder module¶

Module contents¶

molecules.ml.unsupervised.embeddings package¶

Module contents¶

molecules.ml.unsupervised.model_weights package¶

Module contents¶

Submodules¶

molecules.ml.unsupervised.callbacks module¶

molecules.ml.unsupervised.vae module¶

Module contents¶

molecules.sim package¶

Subpackages¶

molecules.sim.analysis package¶

Submodules¶

molecules.sim.analysis.contact_maps module¶

Module contents¶

molecules.sim.simulation package¶

Submodules¶

molecules.sim.simulation.openmm_simulation module¶

Module contents¶

Submodules¶

molecules.sim.contact_maps module¶

molecules.sim.openmm_reporter module¶

molecules.sim.openmm_simulation module¶

Module contents¶

molecules.utils package¶

Submodules¶

molecules.utils.matrix_op module¶

molecules.utils.read_file module¶

Module contents¶

Feedback¶

If you have any suggestions or questions about molecules feel free to email me at youngmt1@ornl.gov.

If you encounter any errors or problems with molecules, please let me know! Open an Issue at the GitHub http://github.com/yngtodd/molecules main repository.