Chemical File Converter
Convert chemical structures between SDF, MOL and SMILES. Preview molecules, check errors and download the converted files.
How can I convert chemical structure files and check parsing errors?
Upload a UTF-8 SDF, MOL or SMILES file, or paste molecular text. Choose the output representation, MOL version, coordinate handling and explicit-hydrogen option. The isolated RDKit service sanitizes each record and reports failures individually. Export the valid records, or require the whole batch to succeed. Download converted structures, a CSV/JSON report, rejected source records and a 2D PNG preview as one ZIP.
Your result
A little clarity, right here.
Start with your own content or load the example. Your result will appear here.
Three simple steps
How to use Chemical File Converter
Choose one structure file or paste SMILES, MOL or SDF text. A chosen file takes precedence over pasted text.
Choose your output and handling options, then inspect the per-record validation report and 2D preview.
Download the ZIP and keep its report with the converted files. Correct rejected records before rerunning when needed.
Common questions
Good to know
Understand the result.
Keep the original.
Is this tool free, and are my files uploaded?
This tool is free with no account required. When you run the tool, your input goes to a separate processing service. Temporary files are deleted when the job ends. You can download the result to your device.
What are the limits and details?
One upload up to 8 MiB or 500,000 pasted characters; up to 200 records, 64,000 characters per record, 500 explicit atoms and 1,000 bonds per molecule, with 10,000 converted atoms per batch. SMILES expressions support 16,000 characters and optional names; blank lines and lines starting with # are ignored. SDF records must end with $$$$; 50 unique text data fields per record, names up to 80 characters and values up to 4,000 characters. MOL/SMILES omit SDF fields, which remain in the report. Ordinary specified stereochemistry, isotopes, atom maps and formal charges follow RDKit’s representation; canonical SMILES can reorder atoms. Query/wildcard, polymer/substance, enhanced stereo and CXSMILES extensions are unsupported. Coordinates are preserved within format precision or generated as 2D depictions, without energy minimization. SMILES has no coordinates. No identity validation, salt/tautomer normalization or property prediction is performed. The preview shows up to 12 exported molecules. ZIP output is capped at 6 MiB and the JSON report at 8 MB. Processing stops after two minutes.