OEMedChem TK 1.0.7

New features

• The performance of appending segments of matched pair indices together has been significantly improved over previous versions. This activity is a common use-case with parallel index creation approaches.

• A new OEMatchedPairAnalyzer.GetMaxMolIdx method has been added to make identifying the largest molecule index registered to a matched pair index more convenient.

• A new OEMatchedPairAnalyzer.GetMolecule method has been added to make retrieving a molecule from the MMP index more convenient and to eliminate the need to maintain a separate OEMolDatabase for this activity.

• A new OEApplyChEMBL24SolubilityTransforms function has been added to return modified structures using ChEMBL24 solubility data. The existing OEApplyChEMBL18SolubilityTransforms API will be deprecated in future versions.

• A new indexing option, OEMatchedPairOptions.IndexHSingleCuts, has been added to limit the H-member matched pair index information to single-cut transformations only. The current OEMatchedPairOptions.IndexHSites option will continue to provide H-member index information for all of single-, double-, or triple-cut transformations. OEMatchedPairOptions.IndexHSingleCuts takes precedence over OEMatchedPairOptions.IndexHSites if both options are provided.

New features (Preliminary API)

• The following preliminary APIs have been added to provide fast multithreaded generation of matched pair indices:

  • OECreateMMPIndexFile function

  • OECreateMMPIndexOptions option class

  • OECreateMMPIndexStatus class

• New OEReadMMPIndexMolecules and OEWriteMMPIndexMolecules functions have been implemented as preliminary APIs to support multithreaded and parallel matched pair index creation activities.

• New function overloads to OEMatchedPairGetTransforms have been added to allow extracting transforms and related matched molecular pairs using 1 or more identified site(s) of substitution on a probe structure.

• New free functions and overloads, OEGetMatchedMolecularPairs, have been added to allow extracting related matched molecular pairs using either a molecule ID or a probe structure with one or more identified site(s) of substitution.

API changes

• A public class, OEMatchedPairTransform, has been altered to remove unnecessary implementation details. Several of the methods exposed were previously inaccessible or unnecessary for wrapped language use. The simplified API retains the common methods for interrogating the transforms and matched pairs returned from OEMatchedPairGetTransforms. This is potentially a breaking API change. For custom code using the removed methods, please contact support@eyesopen.com for details on migration activity that might be required.

• The OEMedChem::OEIsMCSFragDatabaseFiletype function has been renamed OEIsMCSFragDatabaseFileType to follow OpenEye Toolkit’s naming scheme.

• The OEMCSFragDatabase.CoreToMolecules, OEMCSFragDatabase.CoreToMoleculeCount, OEMCSFragDatabase.GetMaxCoreMolecule, OEMCSFragDatabase.GetMaxCoreMoleculeCount, and OEMCSFragDatabase.MoleculeToCores methods and the OEMoleculeToCores function have graduated from preliminary API to stable API status for the 2018.Oct release.

Minor bug fixes

• The OEGetBemisMurcko function has been corrected so that chain bonds between rings are no longer returned in the OERegionType.Ring role sets.

• OEMatchedPairGetTransforms has been fixed and no longer returns unusual matched pair transforms related to group bond-insertion changes.

• A bug that seemed to allow reactions to be added to a matched pair index has been fixed so that reaction input is now explicitly rejected. Attempting to add a reaction to the index will now return a status of OEMatchedPairIndexStatus.NoStructure.

• New options were added to OEMatchedPairIndexStatus to return additional indexing failure conditions.

• OEMatchedPairIndexStatus.NoFragmentationBonds may now be returned from OEMatchedPairAnalyzer.AddMol when the input structure has no fragmentation bonds, depending on the H-member indexing option in use.

Python-specific changes

• A new match pair index example has been added to demonstrate the creation of an MMP index via parallel processing using the Python multiprocessing module.

Documentation changes

• The MCS fragment database examples and match pair index examples have been modified to separate the index creation step from database query activities. See the list of currently available examples in the OEMedChem TK Examples section.