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Version 3.1.1

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@martin-sicho martin-sicho released this 02 Jul 13:56
· 42 commits to main since this release
v3.1.1
3834213

Change Log

From v3.0.2 to v3.1.1

Fixes

  • Fixed a bug in QSPRDataset where property transformations were not applied.
  • Fixed a bug where an attached standardizer would be refit when calling
    QSPRModel.predictMols with use_applicability_domain=True.
  • Fixed random seed not set in FoldsFromDataSplit.iterFolds for ClusterSplit.

Changes

  • renamed PandasDataTable.transform to PandasDataTable.transformProperties
  • moved imputeProperties, dropEmptyProperties and hasProperty from MoleculeTable
    to PandasDataTable.
  • removed getProperties, addProperty, removeProperty, now use PandasDataTable
    methods directly.
  • Since the way descriptors are saved has changed, this release is incompatible with
    previous data sets and models. However, these can be easily converted to the new
    format by adding
    a prefix with descriptor set name to the old descriptor tables. Feel free to contact
    us if you require assistance with this.
  • Due to some changes in rdkit-2023.9.6, the add_rdkit
    option for molecule tables temporarily might not work.
    This also affects the current ChemProp integration, which was not adapted to 2.0.0 yet.
    In order to prevent these issues, QSPRpred now forces rdkit version rdkit-2023.9.5,
    but we will be working on resolving these.

New Features

  • Descriptors are now saved with prefixes to indicate the descriptor sets. This reduces
    the chance of name collisions when using multiple descriptor sets.
  • Added new methods to MoleculeTable and QSARDataset for more fine-grained control
    of clearing, dropping and restoring of descriptor sets calculated for the dataset.
    • dropDescriptorSets will drop descriptors associated with the given descriptor
      sets.
    • dropDescriptors will drop individual descriptors associated with the given
      descriptor sets and properties.
    • All drop actions are restorable with restoreDescriptorSets unless explicitly
      cleared from the data set with the clear parameter of dropDescriptorSets.
  • Added a proper API for parallelization backend selection and configuration (see
    documentation of ParallelGenerator and JITParallelGenerator for more information).
  • Clusters can now be added to a MoleculeTable with addClusters and retrieved with
    getClusters, similar to scaffolds.

Removed Features

  • removed support for PyBoost since the project was abandoned by the original developers and is no longer maintained
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