tinyfep

tinyfep aims to be a simplified and abstracted version of the FEP+ method for molecular simulations from scratch. Some algorithms are simplifications or approximations of the original ones, yet they provide a glimpse into the core functionality. For now, it's primary purpose is educational, catering to those eager to gain an intuition about how these simulations work. Also, tinyfep will always stay under 400 lines of core code. DISCLAIMER: I'm not a chemist so take everything with a grain of salt.

Features:

• SMILES String Parsing: Convert basic SMILES strings into recognizable molecular structures. TODO: not every Element is currently supported
• Mock Molecular Dynamics: Simulate molecular behavior using abstracted energy calculations.
• Energy Functions: Simplified calculations for Lennard-Jones, hydrogen bonds, and ionic interactions.
• Advanced Sampling Techniques: Get a taste of methods like Replica Exchange and Metadynamics.

Usage:

git clone https://github.com/juvi21/tinyrep
cd tinyfep
python3 tinyfep.py --smiles <SMILES> <SMILES>
./run_tests.sh 

⚠Limitations:

• The SMILES parser is elementary, focusing mainly on elements found in proteins.
• Molecular dynamics simulations are more "mock" than "dynamics".
• The energy calculations, though enlightening, are a far cry from real-world complexities.
• The advanced sampling techniques are more illustrative than functional.

Future Plans:

• Integration with Real MD Engines: Incorporating tools like GROMACS or OPENMM.
• Support for More Complex SMILES: Handling aromaticity, ring closures, and branched structures.
• Enhanced Error Estimations: Adopting more sophisticated techniques for error calculations.
• CSV Parsing: 'Cause sometimes you just want your molecular data in neat rows and columns.

Contributing:

You are always welcomed to make 'tinyrep' better or point out mistakes :)

License:

This project is licensed under the MIT License.