Convert SMILES to a MOL file

From a line of text to coordinates

A SMILES string says which atoms are bonded to which, but not where they sit. A MOL file needs coordinates, so Athanor lays the structure out in 2D, the way a chemist would draw it, and writes the atoms, bonds, charges and stereo flags. The file is the V3000 form of the format, which modern programs read; see the MOL format for the difference from V2000.

What a conversion keeps

Athanor’s engine was checked on 1,222 structures from its own library, each sent from SMILES to a MOL file and back, and compared by RDKit with stereochemistry included: 1,212 came back as exactly the same molecule, with every R/S and E/Z label. The ten that did not show the three gaps the engine still has: a radical (as in nitric oxide or TEMPO) is not yet written into MOL files; the E/Z of a double bond inside a very large ring can be lost; and a metal sandwich compound such as ferrocene is written with multi-center bonds, which some programs read differently. The converter reads every MOL file it writes back again and marks any structure that does not come back the same.