OEMedChem TK 1.0.7¶
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.
OEMatchedPairAnalyzer.GetMaxMolIdxmethod has been added to make identifying the largest molecule index registered to a matched pair index more convenient.
OEMatchedPairAnalyzer.GetMoleculemethod has been added to make retrieving a molecule from the MMP index more convenient and to eliminate the need to maintain a separate
OEMolDatabasefor this activity.
OEApplyChEMBL24SolubilityTransformsfunction has been added to return modified structures using ChEMBL24 solubility data. The existing
OEApplyChEMBL18SolubilityTransformsAPI 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_IndexHSitesoption will continue to provide H-member index information for all of single-, double-, or triple-cut transformations.
OEMatchedPairOptions_IndexHSingleCutstakes precedence over
OEMatchedPairOptions_IndexHSitesif both options are provided.
New features (Preliminary API)¶
The following preliminary APIs have been added to provide fast multithreaded generation of matched pair indices:
New function overloads to
OEMatchedPairGetTransformshave 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.
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 email@example.com for details on migration activity that might be required.
OEMedChem::OEIsMCSFragDatabaseFiletypefunction has been renamed
OEIsMCSFragDatabaseFileTypeto follow OpenEye Toolkit’s naming scheme.
OEMCSFragDatabase.MoleculeToCoresmethods and the
OEMoleculeToCoresfunction have graduated from preliminary API to stable API status for the 2018.Oct release.
Minor bug fixes¶
OEMatchedPairGetTransformshas 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
New options were added to
OEMatchedPairIndexStatusto return additional indexing failure conditions.
OEMatchedPairIndexStatus_NoFragmentationBondsmay now be returned from
OEMatchedPairAnalyzer.AddMolwhen the input structure has no fragmentation bonds, depending on the H-member indexing option in use.
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.