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. |
- 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+
You can install Quasi-Anharmonic Analysis via pip from PyPI:
$ pip install qaaIf you want to visualize the tutorial notebooks, you can install the extra dependencies via pip from PyPI:
$ pip install qaa[jupyter]Please see the Command-line Reference for details.
Contributions are very welcome. To learn more, see the Contributor Guide.
Distributed under the terms of the BSD 3 Clause license, Quasi-Anharmonic Analysis is free and open source software.
If you encounter any problems, please file an issue along with a detailed description.
This project was generated from @cjolowicz's Hypermodern Python Cookiecutter template.