SZYBKI

New Features

• The following two new options have been added to both OptLigandInDU and OptimizeDU:

  • -receptorMask enables the use of proteinMask from the design unit receptor.

  • -ignoreAroBent enables the ability to ignore failure due to excess deviation from planarity for aromatic rings.

• The default for -optimize for both OptLigandInDU and OptimizeDU has been changed to poseCartesian to perform constrained Cartesian optimization, ensuring holding of the ligand pose.

Minor Bug Fixes

• OptimizeDU no longer crashes when a nonexistent .lst or .list file is passed as an argument to -in.

Related Toolkit Information

Szybki TK 2.9.0

New Features

• A new class, OEOELigandChargeOptions, has been added that provides options related to ligand charge assignment. The following classes now derive from OEOELigandChargeOptions, enabling greater flexibility in ligand charge assignment:

  • OEProteinLigandOptOptions

  • OETorsionScanOptions

  • OEBoundEntropyOptions

  • OELigandEntropyOptions

• The default optimization type has been changed to PoseCartesian in both OEFixedProteinLigandOptimizer and OEFlexProteinLigandOptimizer.

• The following two new constants have been added to the OESzybkiReturnCode namespace:

  • AromaticRingDev: refers to failure due to excessive aromatic distortion.

  • OptimizerFailed: refers to the optimizer failing to find a solution.

• The following class methods now take an optional predicate describing residues that should be considered as part of the protein target during optimization:

  • SetProtein in OEFixedProteinLigandOptimizer

  • Optimize in OEFlexProteinLigandOptimizer

  • Energy in OEFlexProteinLigandOptimizer

• The following new preliminary API classes have been added, enabling optimization of a ligand with torsion constraints:

  • OELigandEnergy

  • OELigandOptOptions

  • OELigandOptResults

  • OETorConstraintOptimizer

  • OETorConstraintOptOptions

Major Bug Fixes

• OEFixedProteinLigandOptimizer and OEFlexProteinLigandOptimizer no longer fail to optimize with the ExcessiveOverlap error code prematurely.

Minor Bug Fixes

• OEFreeFormConfOptions now sets the latest Sage force field as the default.

• An issue has been fixed in OETorsionScan where scanning using the option SetUseInternalCoord set to true would occasionally produce large unphysical energies at certain angles.