MolDraw › Chemistry tools › SDF to SMILES Converter
SDF to SMILES Converter (batch)
In short: Paste an SD file or open one with hundreds of records. Get one canonical SMILES per line with the record name or any SD field, then download a .smi or CSV file. It is free, runs in your web browser and needs no download.
Reads V2000 and V3000 records, 2D or 3D. Nothing is uploaded: the structures are read on your device.
SMILES then the name. Aspirin gives CC(Oc(cccc1)c1C(O)=O)=O and caffeine C[n]1c(C(N(C)C(N2C)=O)=O)c2nc1, in the same canonical form as the batch converter.Ready.
SMILES (one per line, tab, name)
How to convert SDF to SMILES
- Paste the SDF text or press Open .sdf file.
- In Name for each SMILES, keep the title line or choose an SD data field such as an ID.
- Keep Keep stereochemistry ticked for isomeric SMILES, or untick it for plain SMILES.
- Press Convert to SMILES. Failed records are shown in red with the reason.
- Press Download .smi, Download CSV or Copy.
SDF and SMILES
An SDF (structure-data file) holds many molecules. Each record has a title line, a MOL block with atoms, coordinates and bonds, optional data fields such as > <ID>, and ends with $$$$. SMILES writes the same structure as one line of text, without coordinates. It is the usual format for compound lists, spreadsheets and machine learning.
The converter reads V2000 and V3000 records, charges, isotopes and explicit hydrogens. Hydrogens are written implicitly in the SMILES. Rows also get a Hill formula and the molecular weight.
| Molecule | Canonical SMILES from this tool |
|---|---|
| Aspirin | CC(Oc(cccc1)c1C(O)=O)=O |
| Caffeine | C[n]1c(C(N(C)C(N2C)=O)=O)c2nc1 |
| Ethanol | CCO |
Limitations
- Canonical SMILES differ between programs. Compare SMILES made by the same program, or use InChIKeys to match structures across programs.
- For long conjugated chains with several E/Z double bonds (for example retinol), the / and \ marks are written in a style that some programs read as conflicting; check such structures.
- Query features (R groups, atom lists, any-bonds) and polymers (Sgroups) are not converted.
- 2D records without wedge bonds have no stereo, so their SMILES has none.
Want to see a structure? Paste any SMILES into MolDraw, a free online chemical structure editor, to draw and edit it.
Open MolDraw editorFrequently asked questions
How do I convert an SDF file to SMILES?
Open the .sdf file or paste its text and press Convert to SMILES. Each record gives one line: the SMILES, a tab and the name. Press Download .smi for a SMILES file or Download CSV for a table with name, SMILES, formula and molecular weight.
Can it convert hundreds of structures at once?
Yes. Records are converted in your browser in small batches, so a file with a few hundred molecules takes a second or two. The limit is 20,000 records per file. Failed records are listed with the reason and do not stop the others.
Is the SMILES canonical?
Yes. The same structure always gives the same SMILES, whatever the atom order in the file. The SMILES uses the canonical form of the OpenChemLib engine, the same one as the MolDraw batch converter. Other programs, such as RDKit or Open Babel, write a different but equivalent canonical SMILES.
How is stereochemistry read?
From wedge and hash bonds in 2D records and from the coordinates in 3D records. Each stereocentre is written as drawn (absolute), as most programs do; the V2000 chiral flag is not used. Untick Keep stereochemistry to get SMILES without @ and / marks.
Which name is used for each SMILES?
By default the title line, the first line of each record. You can pick any SD data field instead, for example a compound ID or PUBCHEM_IUPAC_NAME, from the list.
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