qaa 1.0.0rc1

Quasi-Anharmonic Analysis

Features

qaa analyzes molecular dynamics (MD) trajectories by using joint diagonalization (JADE) to separate the information. The JADE [1] and QAA [2] code are based on the original code written in Matlab.

[1]

Cardoso, J. F.; Souloumiac, A. “Blind Beamforming for Non-Gaussian Signals.” IEE Proc F Radar Signal Process 1993, 140 (6), 362.

[2]

Ramanathan, A.; Savol, A. J.; Langmead, C. J.; Agarwal, P. K.; Chennubhotla, C. S. “Discovering Conformational Sub-States Relevant to Protein Function.” Plos One 2011, 6 (1), e15827.

Requirements

• Python 3.8+

• click 7.0+

• numpy 1.20+

• scipy 1.6+

• matplotlib 3.3+

• scikit-learn 0.24+

• mdtraj 1.9+

• nptyping 1.4+

• holoviews 1.14+

Installation

You can install Quasi-Anharmonic Analysis via pip from PyPI:

$ pip install qaa

If you want to visualize the tutorial notebooks, you can install the extra dependencies via pip from PyPI:

$ pip install qaa[jupyter]

Usage

Please see the Command-line Reference for details.

Contributing

Contributions are very welcome. To learn more, see the Contributor Guide.

License

Distributed under the terms of the BSD 3 Clause license, Quasi-Anharmonic Analysis is free and open source software.

Issues

If you encounter any problems, please file an issue along with a detailed description.

Credits

This project was generated from @cjolowicz’s Hypermodern Python Cookiecutter template.