The default value of the
-targetMaskparameter in ReceptorInDU has been changed to
targetComplexNoSolventto reflect best practices for receptor generation.
-targetMaskparameter 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
.lstfiles containing empty lines as input to
Component names are now consistent when converting between
Documentation regarding Receptors has been updated.
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 reads OEDU files and 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.
DU2Receptorhas 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.
The Tutorials section has been updated.
OEDocking TK 188.8.131.52¶
Default value of
Target Maskhas been changed to
OEDesignUnitComponents::TargetComplexNoSolvent, to reflect best practices for receptor generation.
OEMakeReceptorOptionsnow provides added flexibility to create user defined mask.
An issue causing
OEPositto occasionally ignore the
Posit Methodshas been fixed.
Constraints (both protein constraints and custom constraints) are now properly serialized in the
OEReceptorin a .OEDU file.
All of the protein constraints, custom constraints, and extra molecules are now properly transferred in the
OEDesignUnit, when OEB format receptors are used.
OEDocking TK 4.0.0¶
A new class,
OEMakeReceptorOptions, has been added that provides choices for making an
OEMakeReceptorfunction now takes an
OEMakeReceptorOptions, and adds an
A new class,
OEDockOptions, has been introduced that provides choices for
OEDockclass constructor now has an overload that takes an
The following methods now have an overload that accepts as an argument an
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
OEPoseOptimizerclass constructor now has an overload that takes an
OEPoseOptimizer.Optimizemethod now takes an
Flexible POSIT with
OEPosit.Docknow uses the
OEFF14SBParsleyfor pose optimization.
A new method,
OEPosit.RankDesignUnits, has been added that ranks an
OEReceptorfor posing with multiple receptors.
With the introduction of the new
OEReceptorclass 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:
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:
OEHybridclass documentation has been modified to clarify that it is derived from
OEDocking::OEScoreBasehas been removed.
All the OEDocking TK examples have been reorganized to reflect the modified API behavior.