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:
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