Convert SMILES to an SDF file

A list into one file

Many programs want structures as an SDF file rather than a list of SMILES. Athanor draws each SMILES in 2D, writes it as a MOL record, puts the name you gave on the record’s first line, and closes each with $$. The coordinates are 2D; tools that need 3D will generate their own conformers.

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.