OECreateMMPIndexStatus OECreateMMPIndexFile(const std::string& mmpdbfname,
                                            const std::string& molfname,
                                            const OECreateMMPIndexOptions& opts);

This function reads the input structures from the provided molfname filename and generates an OEMatchedPairAnalyzer index from those structures which is saved to the provided mmpdbfname output file. Options for indexing are provided in the OECreateMMPIndexOptions argument.

In general, the provided input structures should have been thoroughly normalized, deduplicated or have data merged onto unique input structures for duplicate structures. There are no options for structure normalization or cleanup activities as part of this automatic indexing.