Convert an SDF file to SMILES
Free, no sign-up. It runs in your browser on Athanor’s own engine, and your structures never leave your device.
SDF file
SMILES
The result appears here, with a picture of every structure.
How to do it
Open an .sdf file or paste its text.
Press Convert. Every record is read, up to 500 at a time.
Copy the SMILES list or download it as a .smi file, one structure and its name per line.
A whole file, a line per structure
An SDF file holds many MOL records, each closed by $$. Athanor reads each record, keeps the name on its first line, and writes one SMILES per line followed by that name, the usual layout of a .smi file. A record that cannot be read is listed with its line number and left out, rather than dropped silently.
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.
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