Blog
Notes from rebuilding the cheminformatics stack from the ground up.
Reactions and retrosynthesis — from 1985 to today
How reactions get written down and walked backward through. From MDL's RXN file and Reaction SMILES through RInChI to the open retrosynthesis tools.
Spectroscopy file formats — from 1988 to today
How NMR, mass-spec, IR, and Raman data are stored on disk. Carriers, references, and the formats that bridge structure and spectroscopy.
Cheminformatics file formats — from 1971 to today
How molecules are stored on disk. From PDB through MDL Mol/SDF to CIF and CDXML: single-molecule formats, dataset bundles, and crystal-structure formats. Reaction files live in the reactions article.
Chemistry line notations — from 1949 to today
How chemists write a molecule down in a single string. Notations, identifiers, patterns, and reactions — what each one adds and how they coexist.