OEDOCKING 4.0.0.2

March 2021

  • The default value of the -targetMask parameter in ReceptorInDU has been changed to targetComplexNoSolvent to reflect best practices for receptor generation.
  • The -targetMask parameter in ReceptorInDU now provides added flexibility to create user defined masks.
  • Protein constraints, custom constraints, and extra molecules are now properly transferred and serialized when converting OEB format receptors to OEDU format receptors using OEB2DUReceptor.
  • POSIT now properly handles .lst files containing empty lines as input to -receptor parameters.
  • Component names are now consistent when converting between OEChem::OEMolBase and OEBio::OEDesignUnit receptors.
  • Documentation regarding Receptors has been updated.

OEDOCKING 4.0.0.0

Fall 2020

New features

  • A new utility, ReceptorInDU, has been added that makes a receptor inside a design unit OEDU file.
  • A new utility, OEB2DUReceptor, has been added that converts a receptor OEB or OEB.GZ file into a OEDU receptor file.
  • The GUI application MakeReceptor now outputs OEDU receptor files with receptors created inside a design unit.
  • The following programs in the OEDocking applications suite now expect OEDU files (with receptors inside a Design Unit), for receptors. These programs no longer support receptor input from OEB or OEB.GZ files.
  • POSIT now produces OEDU files as output containing design units consisting of pose ligand structures and protein active site structures.
  • A new parameter, -nostructs, has been added to FRED and HYBRID. When this flag is set to true, both the docked and undocked structure files will be suppressed.
  • A new utility, DU2OEBReceptor, has been added that converts an OEDU receptor file into a receptor OEB or OEB.GZ file.
  • The utility DU2Receptor has been removed from the OEDocking application suite. The receptors are now created inside a design unit, and can be created using the ReceptorInDU utility application.

Documentation changes

  • The Tutorials section has been updated.

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 OEReceptor.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.