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.