SDF to SMILES Converter
Flatten an SDF / SD compound library into one SMILES per molecule. Paste a multi-record file or upload it — the order is preserved.
SDF to SMILES converter
SDF (Structure-Data File, also called SD file) is the most common format for compound libraries. Each record stores one molecule with its 2D or 3D coordinates plus attached properties. Converting to SMILES gives you a compact, one-line representation for each molecule that is easy to store in a CSV or pass to another tool.
Multi-record files are supported
Paste a whole SDF with many records (separated by $$$$) and you get one SMILES
per line, in the same order. This is the usual way to flatten a screening library.
Frequently asked questions
Are properties lost?
Yes — SMILES only stores the structure. Any SDF data fields are dropped. If you need to keep them, convert to a format that preserves annotations, or join the SMILES back to your source table by record order.
Which SMILES flavour is produced?
A standard OpenBabel SMILES. Enable Canonicalize if you need the canonical form for deduplication.