De Novo Chem Blog
Deep dives into cheminformatics, AI/ML for molecular design, and the open-source tools we're building for researchers.
Packaging a Publication-Quality Drawing Toolkit: acacia-chem
Packaging the RDKit drawing helpers from the first four posts into a single installable Python package, with consistent styles, reaction composition, grid layouts, and reproducible exports.
A Reusable Drawing Toolkit
Packaging the RDKit drawing helpers from the first three posts into a single installable Python package, with descriptive styles, grid layouts, and bulk exports.
Getting Indole Orientation Right: A Technical Note on 2D Molecular Layout
A deep dive into the fused-ring layout problem in RDKit and CoordGen, and the Indigo + RDKit hybrid solution that gave us publication-ready indole orientations.
Drawing Reactions: Highlighting and Annotating Molecules in RDKit
A step-by-step guide to emphasizing key features of a molecule with RDKit by condensing common fragments into compact abbreviation labels, highlighting specific atoms and bonds, and adding atom-mapping numbers, legends, and annotations to publication-ready structure drawings.
Drawing Reactions: Highlighting and Mapping Reactions with RDKit
A step-by-step guide to drawing publication-ready reaction schemes with RDKit by applying per-side abbreviations to reactant and product panels, highlighting the atoms and bonds involved in a reaction center, and adding manual atom-map numbers to visually connect reactants to products.
Drawing Reactions: Taming Catalysts, Reagents, and Crowded Rows with RDKit
A step-by-step guide to composing publication-ready reaction schemes with RDKit by separating reactants, products, catalysts, and conditions, aligning products to reactants via their maximum common substructure, and rendering crisp PNG or SVG figures.
Drawing a Single Molecule: From RDKit Default to Publication-Ready
A step-by-step guide to turning RDKit's default molecule drawings into crisp, publication-ready figures using fixed bond lengths, line widths, fonts, palettes, and flexicanvas.
What do chemists call their chemicals?
An analysis of chemical naming conventions in patents and academic literature.
Why we're building De Novo Chem
We're building De Novo Chem to make chemistry more accessible for everyone.