This package was written to extract the principal axes and the rotational diffusion tensor of a molecule (typically a protein in solution) from Molecular Dynamics Simulations.
The method is based on the theoretical description of Brownian rotational dynamics of a rigid body developed by Favro (1960). The method has been implemented before (pydiffusion by Max Linke). My implementation adds the ability to compute what I call the "instantaneous" diffusion tensor and principal axis frame, as well as the ability to fit a semi-isotropic or isotropic model.
I am currently rewriting the code, mainly to include extensive documentation with sphinx and testing with pytest, aiming towards code that is more user-friendly, readable, and robust. Check-out rotationaldiffusion/mdaapi.py to get a flavour of the new code.
May or may not be implemented
- [X] use git for version control
- [X] align using MDAnalysis
- [ ] better testing (work in progress)
- [ ] continuous integration tests
- [ ] add proper logging, warnings, and errors
- [ ] make some functions private
- [ ] implement consistent variable naming
- [ ] command-line interface
- [ ] tutorial
- [ ] better documentation (work in progress)
- [X] automated documentation
- [ ] online documentation
- [ ] add doctests
- [ ] custom sphinx template
- [X] use codecov to check how much code is tested => Pycharm IDE uses coverage
- [ ] optimize project tree for publishing
- [ ] publish to PyPI
- [ ] publish to conda-forge (or similar)
- [̶ ]̶ ̶a̶d̶d̶ ̶p̶a̶r̶a̶l̶l̶e̶l̶i̶z̶a̶t̶i̶o̶n̶
- [ ] add acknowledgement / funding (RESOLV)
This package was written by Simon Holtbruegge. Feel free to contact me in case you experience any issues or need assistance with using the code ([simon.holtbruegge@rub.de](mailto:simon.holtbruegge@rub.de)).