This is my personal code base (Thomas Evangelidis), written throughout my academic and professional work since ~2010.
It contains command-line tutorials, Bash utilities, and Python scripts covering:
- Cheminformatics
- Computer-Aided Drug Design (CADD)
- Computational Biophysics (e.g., GROMACS/PLUMED workflows)
- NMR spectrum analysis (e.g., Sparky, TopSpin)
- Various related tooling and methodology notes
- The material is provided AS IS, without any warranty of any kind.
- Use at your own risk. Verify commands before running them and back up your data.
- Many scripts and tutorials are old and may be obsolete or non-functional with current software versions and operating systems.
- Even when outdated, these notes can still serve as a useful introduction to the way of executing specific programs and the methodology behind the operations.
The original folder/subfolder structure has been preserved.
Where applicable, tutorial text files have Markdown (.md) versions for better rendering on GitHub.
Merge requests (pull requests) are welcome.
I’m especially interested in contributions that:
- Modernize commands and environments,
- Replace deprecated tools/flags with current best practices,
- Fix broken links and paths,
- Improve clarity and correctness.
Please open an Issue to discuss larger refactors before submitting a PR.