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Table 1 Overview of indexing and searching errors

From: Sachem: a chemical cartridge for high-performance substructure search

Cartridge Indexing failures Rejected queries
1M 10M 94M n reason
Bingo 105 1024 9754 0  
OrChem 2 4 – 12 Unsupported aromatic bond in SMILES
pgchem 30 255 2527 146 Fragmented SMILES, queries with [*]
RDKit 72 707 6911 4 Chemical structure considered invalid
Sachem 0 0 0 0  
  1. Measurements are slightly influenced by errors that some cartridges exhibited during benchmarking, due to both indexing and searching errors. Indexing errors are primarily reported as unacceptable data in the SDF files from PubChem, most frequently as invalid atom valences or stereochemistry. Note that Bingo beta version can lower the number of indexing errors by using algorithms that work with ‘incorrect’ structures (this feature is disabled by default)
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