OEDocking TK 4.0.0.2

March 2021

• Default value of Target Mask has been changed to OEDesignUnitComponents.TargetComplexNoSolvent, to reflect best practices for receptor generation.

• Target Mask in OEMakeReceptorOptions now provides added flexibility to create user defined mask.

• An issue causing OEPosit to occasionally ignore the Posit Methods has been fixed.

• Constraints (both protein constraints and custom constraints) are now properly serialized in the OEReceptor in a .OEDU file.

• All of the protein constraints, custom constraints, and extra molecules are now properly transferred in the OEReceptor and the OEDesignUnit, when OEB format receptors are used.

OEDocking TK 4.0.0

Fall 2020

New features

• A new class, OEMakeReceptorOptions, has been added that provides choices for making an OEReceptor inside an OEDesignUnit.

• The OEMakeReceptor function now takes an OEDesignUnit and an OEMakeReceptorOptions, and adds an OEReceptor inside the OEDesignUnit object.

• A new class, OEDockOptions, has been introduced that provides choices for OEDockMethod and OESearchResolution in the OEDock class.

• The OEDock class constructor now has an overload that takes an OEDockOptions argument.

• The following methods now have an overload that accepts as an argument an OEDesignUnit containing an OEReceptor:

  • OEDock.Initialize

  • OEDock.CacheScoringSetup

  • OEScore.Initialize

  • OEScore.CacheScoringSetup

  • OEPosit.AddReceptor

• A new method, OESinglePoseResult.GetDesignUnit, has been added added that returns the resulting design unit containing the pose ligand and the target.

• A new class, OEPoseOptimizerOptions, has been added that provides choices for force fields and flexibility in performing pose optimization with OEPoseOptimizer.

• The OEPoseOptimizer class constructor now has an overload that takes an OEPoseOptimizerOptions.

• The OEPoseOptimizer.Optimize method now takes an OEDesignUnit to optimize.

• Flexible POSIT with OEPosit.Dock now uses the OEFF14SBParsley for pose optimization.

• A new method, OEPosit.RankDesignUnits, has been added that ranks an OEDesignUnit containing an OEReceptor for posing with multiple receptors.

• With the introduction of the new OEReceptor class and the corresponding behavior of the OEDocking TK, several previously existing APIs have been deprecated. The following table shows the deprecated APIs and their replacements:

  Deprecated API	New API
  OEDocking::OEBoxBase	OEBox
  OEDocking::OEBox
  OEDocking::OECustomConstraints	OEReceptorCustomConstraints
  OEDocking::OEFeature	OEReceptorConstraintFeature
  OEDocking::OEProteinConstraint	OEReceptorProteinConstraint
  OEDocking::OESphereBase	OESphere
  OEDocking::OEAlignReceptors	OEStructuralSuperposition
  OEDocking::OEIsReceptor	OEDesignUnit.HasReceptor
  OEDocking::OEReceptorClear	OEReceptor.Clear
  OEDocking::OEReceptorClearCustomConstraints	OEReceptor.ClearCustomConstraints
  OEDocking::OEReceptorClearProteinConstraints	OEReceptor.ClearProteinConstraints
  OEDocking::OEReceptorGetBoundLigand	OEDesignUnit.GetLigand
  OEDocking::OEReceptorGetCustomConstraints	GetCustomConstraints
  OEDocking::OEReceptorGetInnerContourLevel	OEReceptor.GetInnerContourLevel
  OEDocking::OEReceptorGetOuterContourLevel	OEReceptor.GetOuterContourLevel
  OEDocking::OEReceptorHasBoundLigand	OEDesignUnit.HasLigand
  OEDocking::OEReceptorHasCustomConstraints	OEReceptor.HasCustomConstraints
  OEDocking::OEReceptorHasInnerContourLevel	OEReceptor.HasInnerContourLevel
  OEDocking::OEReceptorHasNegativeImageGrid	OEReceptor.HasNegativeImageGrid
  OEDocking::OEReceptorHasOuterContourLevel	OEReceptor.HasOuterContourLevel
  OEDocking::OEReceptorHasProteinConstraints	OEReceptor.HasProteinConstraints
  OEDocking::OEReceptorSetCustomConstraints	OEReceptor.SetCustomConstraints
  OEDocking::OEReceptorSetInnerContourLevel	OEReceptor.SetInnerContourLevel
  OEDocking::OEReceptorSetOuterContourLevel	OEReceptor.SetOuterContourLevel
  OEDocking::OEReceptorAddCachedScore	OEDock.CacheScoringSetup
  OEDocking::OEReceptorSetCachedScore	OEScore.CacheScoringSetup
  OEDocking::OEReadReceptorFile	OEReadDesignUnit
  OEDocking::OEReadReceptorToBytes
  OEDocking::OEWriteReceptorFile	OEWriteDesignUnit
  OEDocking::OEWriteReceptorToBytes
  OEDocking::OEBoxArea	OEBoxArea
  OEDocking::OEBoxExtend	OEBoxExtend
  OEDocking::OEBoxTranslate	OEBoxTranslate
  OEDocking::OEBoxVolume	OEBoxVolume
  OEDocking::OEBoxXDim	OEBoxXDim
  OEDocking::OEBoxYDim	OEBoxYDim
  OEDocking::OEBoxZDim	OEBoxZDim
  OEDocking::OEBoxXMid	OEBoxXMid
  OEDocking::OEBoxYMid	OEBoxYMid
  OEDocking::OEBoxZMid	OEBoxZMid
  OEDocking::OEInBox	OEInBox
  OEDocking::OESetupBox	OESetupBox
  OEDocking::OESetupBoxCenterAndExtents
  OEDocking::OEInSphere	OEInSphere
  OEDocking::OESphereArea	OESphereArea
  OEDocking::OESphereVolume	OESphereVolume

• With the introduction of the new APIs, several obsolete functionalities have been deprecated without any suitable replacements. These functionalities were added in the early development days of OEDocking TK and are no longer deemed useful:

  • OEDocking::OEAlignReceptorFunction

  • OEDocking::OEReceptorAddExtraMols

  • OEDocking::OEReceptorClearBoundLigand

  • OEDocking::OEReceptorClearExtraMols

  • OEDocking::OEReceptorHasExtraMols

Documentation changes

• The OEHybrid class documentation has been modified to clarify that it is derived from OEDock.

• Documentation for OEDocking::OEDockBase and OEDocking::OEScoreBase has been removed.

• All the OEDocking TK examples have been reorganized to reflect the modified API behavior.