OEMedChem TK 1.0.3

New features

• A new class, OEMCSFragDatabase, has been implemented that supports an MCS fragmentation approach for returning Tanimoto and Tversky MCS similarity scores from a query against an indexed set of input structures. This approach is similar to the OEMatchedPairAnalyzer and the API is functionally equivalent to the OEFPDatabase API for ease of use. Because the indexing phase of the input structures can be time-consuming, new functions to capture and reload the MCS fragmentation index are provided as OEReadMCSFragDatabase and OEWriteMCSFragDatabase.

• A new options class, OEMCSFragDatabaseOptions, has been added to control the indexing phase of OEMCSFragDatabase usage.

• A new constant, MCSFrags, has been added to support OEMCSFragDatabase serialization and may be returned by OEGetMatchedPairAnalyzerFileType.

• Two new functions, OEConfigureMCSFragDatabaseOptions and OESetupMCSFragDatabaseOptions, have been added to allow configuration of indexing parameters from the command line for OEMCSFragDatabaseOptions.

• A new function, OEMCSFragDatabaseCoreQuery, has been added to annotate MCS fragment SMILES cores returned from OEMCSFragDatabase.GetSortedScores and OEMCSMolSimScore with SMARTS qualifiers. This allows more restrictive and meaningful mapping highlights to be applied for depicting similarity hit results.

• The OEMCSFragDatabase class now supports user-customization of the similarity score returned by implementing a class derived from OEMCSSimFuncBase. Two concrete implementations of scoring functions, OEMCSTanimotoSim and OEMCSTverskySim, have been added.

• The indexing performance of OEMatchedPairAnalyzer has been significantly improved. While this is highly dependent on the input structures and the requested indexing parameters, the provided default indexing settings with a drug-like set of structures show an indexing improvement of ~25%.

• A new overloaded function, OEIsMatchedPairAnalyzerFileType, has been added to simplify the validation of matched pair index files. The now unnecessary OEIsReadableMatchedPairAnalyzer and OEIsWriteableMatchedPairAnalyzer functions have been deprecated.

Documentation changes

• New documentation has been added for the OEMCSFragDatabase API and the ancillary support functions, classes, and constants.