Of Zero-Order Bonds and Bonding Systems
In search of a backward-compatible upgrade path to multi-atom bonding.
An Introduction to the ChemDraw CDXML Format
Filling in some blanks for one of the most important standards in chemistry.
Running InChI Anywhere with WebAssembly
A solution to an immediate problem, and a peek into a possible future for computational chemistry and cheminformatics.
Parsing InChI: It's Complicated
SMILES and InChI may look like two solutions to the same problem, but looks can be deceiving.
Purr: A SMILES Toolkit for Rust
Pulling back the covers on a new way to work with SMILES.
Fast Hydrogen Counting in SMILES
What gets removed must be added back. The question is how?
Benchmarking Iteration from a Rust Trait
Quantitating the relative performance of slices and boxed Iterators in graphs.
Matched Molecular Pairs
Stepping outside the black box to answer the question of what to test next.
SMILES Formal Grammar Revisited
Encapsulating the full OpenSMILES syntax using a set of streamlined production rules.
Abstract Syntax Trees for SMILES
Designing a suite of power tools for SMILES manipulation in Rust.
A Workbench for Machine Learning in Chemistry
Kick the tires on a short, hackable aqueous solubility predictor built from a DeepChem graph convolutional network.
SMILES Reading Performance: RDKit vs ChemCore
Rust and C++/Python cheminformatics toolkits face off on a core task.
Start Seeing Valence and Core Electrons
Inexpensive molecular validation through simple integer arithmetic.
Running a SMILES Validation Benchmark
Cleaner cheminformatics datasets begin with standards.
Edmonds' Blossom Algorithm Part 1: Cast of Characters
Understanding a classic algorithm in graph theory that remains relevant today.
Interactive Rust in a REPL and Jupyter Notebook with EVCXR
Explore Rust and its libraries with immediate feedback.
Getting Started with DeepChem
Build a workbench for exploring machine learning primitives in chemistry.
Saying No to Browser UI Frameworks
Why the winning move in the JavaScript UI framework game may be not to play.
A Smallest Set of Smallest Rings
Understanding a useful but limited tool for chemical structure analysis.
Getting Started with RDKit and Jupyter
Quickly set up an environment for cheminformatics and machine learning experimentation.
Python Extensions in Pure Rust with PyO3
Avoid a lot of manual labor when creating Python wrappers.
Wrapping Rust Types as Python Classes
A step-by-step guide to rolling your own pythonic Rust wrappers.
A Guide to Molecular Standardization
Toward practical rules for improved data quality in cheminformatics.