SMILES encodes a molecular structure as text. SDF stores structure records with associated fields. A .db download is a SQLite catalogue file: it is a data container, not a standalone chemistry search engine. Keep identifiers linked to structures and check chemical representation when exchanging files.
Use SMILES for a concrete structure query
SMILES strings describe atoms, bonds, ring closures and, where encoded, charge and stereochemistry. Different strings can describe the same structure. A text comparison is therefore not a substitute for parsing and comparing molecules.
Preserve the distinction between aromatic and aliphatic notation, salts or other disconnected components, and specified or unspecified stereochemistry. A valid-looking string should still be inspected after import. If a query behaves unexpectedly, check the rendered structure before interpreting the result.
Sources: RDKit Book: molecular representations and stereochemistry
Understand what an SDF record contains
An SDF file can combine connection-table structures with named data fields. It is useful when transferring a chemical catalogue to a compatible chemistry application. Field names and meanings are catalogue-specific, so check the supplied schema and keep the source identifiers intact.
A structure record does not establish that material is physically held, that it has a particular purity, or that it has been tested in an assay. Treat these as separate data questions. The distinction is especially important when a catalogue combines physical stock and virtual structures.
Sources: RDKit: reading structure files and working with molecules
Use the HTS customer database downloads
The Downloads page offers customer databases for the current stock and virtual libraries. The .db files can be opened with a SQLite-compatible database browser or imported into your own workflow. The schema and field definitions on the Downloads page explain the contents.
SQLite stores the data but does not provide chemical graph matching by itself. For structural comparison in an offline workflow, use a suitable chemistry toolkit and make its handling of stereochemistry, charge and aromaticity explicit. The HTS website provides the online structure search directly.
Sources: SQLite: application file format
Prepare a bulk search without changing identities
The HTS bulk tool accepts up to 100,000 identifier queries per batch and up to 1,000 SMILES queries. Large searches run progressively in the browser; keep the tab open or pause and resume in the same tab. Use the download and export options to retain the data you need.
- Keep one complete HTS ID, supplier ID or CAS query per row for identifier searching.
- Choose the identifier or SMILES search mode that matches your file contents.
- Keep leading zeroes in IDs and do not let a spreadsheet reinterpret them as numbers.
- Check import totals and duplicate handling before starting a large batch.
- Inspect the resulting structures and availability labels before adding hits to an enquiry.
Common questions
Can I draw structures just by opening a .db file?
Not with SQLite alone. A database browser displays stored fields; a chemistry application or toolkit is needed to interpret and depict molecular structures.
Are the virtual database entries available stock?
No. Virtual entries require a synthesis enquiry. Keep catalogue source and availability information linked to each structure in your workflow.
Sources & further reading
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Catalogue information is distinct from experimental activity data. Counts refer to entries; categories can overlap. Availability, documentation and synthesis feasibility are confirmed individually. Questions or corrections? Email the team.