Skip to main content

Table 1 Parameters of the chemical structure query executed via the SPARQL procedure call

From: Interoperable chemical structure search service

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: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