OEMedChem TK 0.9.6

Beta-API changes

• New functions have been added to support matched pair index serialization (see OEGetMatchedPairAnalyzerFileType, OEIsReadableMatchedPairAnalyzer, OEIsWriteableMatchedPairAnalyzer, OEReadMatchedPairAnalyzer, OEWriteMatchedPairAnalyzer).

• A new option to remove unnecessary index node information during the index export activity is now available (see OEMatchedPairOptions.ExportCompression).

• New methods have been added to the analyzer and option classes to allow altering options that do not invalidate an active index (see OEMatchedPairOptions.ValidAlterOpts, OEMatchedPairOptions.ValidIndexOpts, OEMatchedPairAnalyzer.ModifyOptions, OEMatchedPairAnalyzerOptions.ModifyOptions).

• A new method has been added to the analyzer options class to support command-line specification of options (see OEMatchedPairAnalyzerOptions.SetProcessorType).

• A new argument has been added to the functions that apply matched pair transformations that limits application of transformations only to those that meet or exceed the specified number of matched pairs (see OEApplyChEMBL18SolubilityTransforms and OEMatchedPairApplyTransforms).

New features

• The matched pair analyzer now supports the ability to be saved and restored to disk or stream. This allows checkpoint backups during a long analysis run or a long analysis run to be restored from disk for subsequent use without the need to re-run the analysis (see OEReadMatchedPairAnalyzer and OEWriteMatchedPairAnalyzer).

• The ChEMBL18 solubility data has been re-indexed with the latest version of the matched pair analyzer to include hydrogen-member transformations. The result is a larger number of transformations and potentially a larger number of transformed and annotated structures returned from OEApplyChEMBL18SolubilityTransforms. For a 10K test set of structures, using OEMatchedPairContext.Bond0 resulted in an average of three times more output structures and OEMatchedPairContext.Bond2 produced an average of 4.5 times the number of output structures as the previous release when applying all transformations by overriding the default value of minMMPThreshold parameter with 0. Using the default value (5) for the minMMPThreshold parameter, the number of annotated structures from the 10K test set compared to the previous version is approximately the same for the OEMatchedPairContext.Bond0 context and approximately 25% less structures for the OEMatchedPairContext.Bond2 context. The number of structures produced is input dataset-dependent, so tuning of the minMMPThreshold parameter is highly encouraged.

• New functions to configure matched pair indexing options and to set indexing options from the command line have been added (see OEConfigureMatchedPairIndexOptions and OESetupMatchedPairIndexOptions). Example scripts have been updated to demonstrate the use of these new functions.

• A new method has been added to return a count of the number of active index nodes (see OEMatchedPairAnalyzer.NumIndexNodes).

Minor bug fixes

• Structures returned from the application of matched pair transformations will now have their coordinates cleared. Previously, newly added atoms were simply placed at the origin, possibly affecting stereochemistry and generating odd depiction output.

Documentation fixes

• Documentation of the new serialization support is now available for OEGetMatchedPairAnalyzerFileType, OEIsReadableMatchedPairAnalyzer, OEIsWriteableMatchedPairAnalyzer, OEReadMatchedPairAnalyzer, OEWriteMatchedPairAnalyzer, OEMatchedPairAnalyzer.ModifyOptions, OEMatchedPairOptions.ExportCompression, OEMatchedPairAnalyzerFileType, OEMatchedPairOptions.ValidAlterOpts and OEMatchedPairOptions.ValidIndexOpts.

• Documentation of the new command-line configuration support is now available for OEConfigureMatchedPairIndexOptions and OESetupMatchedPairIndexOptions.