Posts tagged cheminformatics

Apr 27, 2026

Cheminformatics file formats from 1971 to today

How molecules are stored on disk, from the PDB format and MDL molfiles to CIF, CML, CDXML and CXSMILES, with ethanol as the running example.

aspirin.molV2000

 13 13  0  0  0  0  0  0  0  0999 V2000    2.2500    3.2476    0.0000 C   0  0  0      1.5000    1.9486    0.0000 C   0  0  0      0.0000    1.9486    0.0000 O   0  0  0      2.2500    0.6495    0.0000 O   0  0  0      3.7500    0.6495    0.0000 C   0  0  0      4.5000    1.9486    0.0000 C   0  0  0      6.0000    1.9486    0.0000 C   0  0  0      6.7500    0.6495    0.0000 C   0  0  0

Apr 25, 2026

Chemistry line notations from 1949 to today

How chemists write a molecule as one line of text, from WLN and SMILES to InChI and the notations made for machine learning, with caffeine as the running example.

notations smiles inchi cheminformatics