Table 1 Parameters of the chemical structure query executed via the SPARQL procedure call
Parameter name | Description and values |
|---|---|
Common parameters | |
sachem:query | Query molecule structure, formatted as SMILES or MDL |
sachem:topn | Maximum number of results to return |
Substructure search parameters | |
sachem:searchMode | Chooses between exact structure and substructure search, values: |
sachem:substructureSearch | |
sachem:exactSearch | |
sachem:tautomerMode | Tautomer handling, accepted values: |
sachem:ignoreTautomers (do not consider tautomerism) | |
sachem:inchiTautomers (use InChI-based algorithm [17] for tautomer matching) | |
sachem:chargeMode | Selects coalescing of unspecified charge values in query: |
sachem:defaultChargeAsAny (unspecified charge is wildcard) | |
sachem:defaultChargeAsZero (unspecified charge matches only uncharged atoms) | |
sachem:ignoreCharges (ignores all charge annotations) | |
sachem:isotopeMode | Selects coalescing of unspecified isotope values in query: |
sachem:defaultIsotopeAsStandard (unspecified isotope matches only the standard isotope) | |
sachem:defaultIsotopeAsAny (unspecified isotope is wildcard) | |
sachem:ignoreIsotopes (ignore all isotope annotations) | |
sachem:stereoMode | Handling of stereochemistry: |
sachem:strictStereo (remove results with conflicting stereochemistry information) | |
sachem:ignoreStereo (ignore all stereochemistry annotations) | |
Similarity search parameters | |
sachem:cutoff | Minimum similarity score of returned results in range 0–1, defaults to 0.8 |