A toy molecular modeling pipeline written in common lisp, designed as a learning project.
I really wish to better understand modern computational biophysics tools and make progress in common lisp.
The goal is to write a complete toy suite in common lisp to perform molecular modeling, including
- a
.pdbparser - a preprocessor for generating topologies
- a simple force field
- a 3d viewer
- a geometry optimizer
- a docking engine
- a classical molecular dynamics engine
The task is huge, but at the same time, I want to keep each step simple. My main core idea is to rely on simple interactions. It will not be sufficiently physical to reproduce industry-standard results, but keeping a simple expression - let's say forcefield - throughout the project will make the transition from step to step smoother.
At the time I am writing this README file, I do not plan to overoptimize the pipeline but still, common sense is included. I will still try to be picky over the physics I provide and write a good amount of documentation.
I am currently entering the last year of my master's degree in computational physics. I wish I could pursue a PhD program at the end of the year, but as fundings are never acquired until they are, I eventually plan to join the pharma industry, as an engineer or run my own company. So, the project will not be written in few days but I do not plan to let it run for years as well. I will try to be consistent and provide new commits monthly. Grades first.
MIT License (see License File).
If you use or refer to this project, please cite:
Erwan Le Doeuff (weld). lispmol : a toy molecular modeling pipeline in common lisp. Published on GitHub, 2025. https://github.com/weld-lab/lispmol