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Python

Scientific Computing
Grid of complex molecular structures rendered from SELFIES and SMILES strings

Molecular String Renderer: Robust Visualization Infrastructure

A robust, type-safe Python library for converting chemical string representations (SMILES, SELFIES, InChI) into …...

Computational Chemistry

Recent Advances in the SELFIES Library (2023)

Major updates to the SELFIES library, improved performance, expanded chemistry support, and new customization features....

Computational Chemistry
SELFIES strings guarantee 100% valid molecules - even when generated randomly

Converting SELFIES Strings to 2D Molecular Images

Visualize SELFIES molecular representations and test their 100% robustness through random sampling experiments.

Computational Chemistry
Aspirin molecular structure generated from SMILES string

Converting SMILES Strings to 2D Molecular Images

Learn how to create 2D molecular images from SMILES strings using RDKit and PIL, with proper formatting and legends.

Scientific Computing
Comparison of exponential sampling methods showing histograms from both inverse transform and von Neumann methods overlaid with the theoretical exponential distribution

Exponential Random Number Generation: Two Classic Algorithms Compared

Compare inverse transform sampling and von Neumann's rejection method for exponential random numbers with Python …

Scientific Computing
Velocity Autocorrelation Function showing the signature negative region characteristic of liquid dynamics

Digital Restoration: Modernizing Rahman's 1964 Argon Simulation

How I used modern software engineering (caching, vectorization, and dependency locking) to reproduce a 60-year-old …...

Scientific Computing
Velocity Autocorrelation Function showing the signature negative region characteristic of liquid dynamics and the cage effect discovered by Rahman

Digital Restoration: Modernizing Rahman's 1964 Argon Simulation

A high-fidelity replication of foundational molecular dynamics using modern software engineering practices: caching, …...

Computational Chemistry
3D ball-and-stick model of butane molecule representing the structural isomer generation process

Synthetic Isomer Data Generation Pipeline

An end-to-end cheminformatics pipeline transforming 1D chemical formulas into 3D conformer datasets using graph …...

Computational Chemistry
Coulomb matrix heatmap visualization showing molecular structure encoding on logarithmic scale

Understanding Coulomb Matrices for Molecular Machine Learning

Learn how Coulomb matrices encode 3D molecular structure for machine learning from basic theory to Python implementation …

Computational Social Science
Top features for Economics and Public Finance policy classification across Congresses

How Does Congress Actually Work? Data from 15K Bills

What happens to bills in Congress? Analyzing 15K+ bills from the 117th Congress to understand legislative patterns, …

Scientific Computing
Molecular structure alignment showing protein conformations and RMSD calculation

Kabsch Algorithm: NumPy, PyTorch, TensorFlow, and JAX

Learn about the Kabsch algorithm for optimal point alignment with implementations in NumPy, PyTorch, TensorFlow, and JAX …

Scientific Computing
Energy conservation plot showing kinetic, potential, and total energy oscillations for a copper adatom diffusion simulation

Automated Adatom Diffusion Workflow

Python-wrapped reference implementation for surface diffusion simulations using LAMMPS and EAM potentials, with …...