OEMedChem TK 0.9.6¶
New functions have been added to support matched pair index serialization (see
A new option to remove unnecessary index node information during the index export activity is now available (see
New methods have been added to the analyzer and option classes to allow altering options that do not invalidate an active index (see
A new method has been added to the analyzer options class to support command-line specification of options (see
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
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
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.Bond0resulted in an average of three times more output structures and
OEMatchedPairContext.Bond2produced 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
0. Using the default value (5) for the
minMMPThresholdparameter, the number of annotated structures from the 10K test set compared to the previous version is approximately the same for the
OEMatchedPairContext.Bond0context and approximately 25% less structures for the
OEMatchedPairContext.Bond2context. The number of structures produced is input dataset-dependent, so tuning of the
minMMPThresholdparameter is highly encouraged.
New functions to configure matched pair indexing options and to set indexing options from the command line have been added (see
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
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 of the new serialization support is now available for