BROOD 5.0.0

Major Bug Fixes

• vBROOD now respects the user defined color atoms and color constraints in the generated Brood Query.

Minor Bug Fixes

• The -quickLook option in BROOD now properly enforces a valid range, reducing the possibility of getting an empty hit list as output.

• An issue has been fixed where occasional high memory usage of BROOD occurred while running the application in the ET mode.

Related Toolkit Information

Bioisostere TK 5.0.0

New Features

• The following new classes have been added as preliminary API:

  • OEBroodBuildResult

  • OEBroodCluster

  • OEBroodClusterBuilder

  • OEBroodComboBuilder

  • OEHitlistBuilderOptions

  • OEHitlistBase

  • OEScoreHitlist

  • OEBroodHitlist

  • OEMolCTBuilder

  • OESimilarity

• The following new methods have been added to OEBroodQuery:

  • GetQueryID

  • SetQueryID

• A new constructor overload has been added to OEHitlistBuilder that takes a OEHitlistBuilderOptions as an argument.

• A new overload of Setup has been added to OEBroodDBFilter that takes a molecule as argument.

• The following new methods have been added to OEBroodQuery:

  • GetBuildRes

  • GetScores

• The following new methods have been added to OEBroodScore:

  • Add

  • GetQueryIDs

• The following new functions have been added:

  • OECreateFlipperOptions

  • OECreateFragFilter

  • OEIsFragment

• The following methods have been removed from the OEHitlistBuilder, as they are no longer relevant:

  • GetTrimmedCount

  • TrimHitlist

  • An overload of GetHits that took a vector of OEBroodHit as an argument.

  • GetRemovedHits

Minor Bug Fixes

• The OECreateBroodQuery method now keeps any incoming color atoms associated with the query selection, when available, and does not add any additional color atoms to the query. The behavior is unchanged when no color atoms are present with the incoming selection.

• A bug in fragment property filtering has been resolved. Now by setting the SetUseProperty option in OEBroodScoreOptions to true, you can activate the fragment filtering based on the properties defined by OEExtrinsicPropOptions and OEIntrinsicPropOptions. Previously, the filter was not being applied correctly, which could lead to unexpected fragments being included in the results.

• An issue has been fixed related to proper usage of SetRangeSize and SetRangeOffset so that fragment retrieval from the database during the overlay step now properly respects the specified range boundaries.

• A bug has been fixed where the color score reported by GetColorScore could exceed its valid range in ROCS mode, causing the combined score to exceed its range as well. The color Tanimoto is now computed consistently from the scored conformer.