Szybki TK 1.9.2¶

New features¶

Two new classes, OEFreeFormConf and OEFreeFormConfAdvanced, have been added to provide conformer free energy functionality. The methods in OEFreeFormConf provide high-level functionality; those in OEFreeFormConfAdvanced provide finer control of the functionality.

In general, the new conformer free energy functionality provides 2 new capabilities: (1) methods to estimate restriction free energy and (2) methods to find conformers similar to the one specified from a pool of minimum energy conformers.
The OEFreeFormConfOptions API methods have been modified and enhanced with OEOmegaOptions and various OESzybkiOptions sub-options. The enhanced API allows greater control over the details of free energy calculation.

The OESzybkiOptions class has been simplified and now consists of various sub-options: OESzybkiGeneralOptions, OESzybkiOptOptions, OESzybkiSolventOptions, and OESzybkiProteinOptions. The specific methods to set or get option values are now provided through these sub-option classes.

The following table shows the older, deprecated option functions and their new sub-option replacements:

Deprecated Option Method	New Sub-option Method
`OESz::OESzybki::SetIEFFCluster`	`OESzybkiGeneralOptions::SetIEFFCluster`
`OESz::OESzybkiOptions::SetIEFFCluster`	`OESzybkiGeneralOptions::SetIEFFCluster`
`OESz::OESzybki::GetIEFFCluster`	`OESzybkiGeneralOptions::GetIEFFCluster`
`OESz::OESzybkiOptions::GetIEFFCluster`	`OESzybkiGeneralOptions::GetIEFFCluster`
`OESz::OESzybki::SetRemoveCoulombTerms`	`OESzybkiGeneralOptions::SetRemoveCoulombTerms`
`OESz::OESzybkiOptions::SetRemoveCoulombTerms`	`OESzybkiGeneralOptions::SetRemoveCoulombTerms`
`OESz::OESzybki::GetRemoveCoulombTerms`	`OESzybkiGeneralOptions::GetRemoveCoulombTerms`
`OESz::OESzybkiOptions::GetRemoveCoulombTerms`	`OESzybkiGeneralOptions::GetRemoveCoulombTerms`
`OESz::OESzybki::SetRemoveAttractiveVdWForces`	`OESzybkiGeneralOptions::SetRemoveAttractiveVdWForces`
`OESz::OESzybkiOptions::SetRemoveAttractiveVdWForces`	`OESzybkiGeneralOptions::SetRemoveAttractiveVdWForces`
`OESz::OESzybki::GetRemoveAttractiveVdWForces`	`OESzybkiGeneralOptions::GetRemoveAttractiveVdWForces`
`OESz::OESzybkiOptions::GetRemoveAttractiveVdWForces`	`OESzybkiGeneralOptions::GetRemoveAttractiveVdWForces`
`OESz::OESzybki::SetLigandRMSDHeavy`	`OESzybkiGeneralOptions::SetLigandRMSDHeavy`
`OESz::OESzybkiOptions::SetLigandRMSDHeavy`	`OESzybkiGeneralOptions::SetLigandRMSDHeavy`
`OESz::OESzybki::GetLigandRMSDHeavy`	`OESzybkiGeneralOptions::GetLigandRMSDHeavy`
`OESz::OESzybkiOptions::GetLigandRMSDHeavy`	`OESzybkiGeneralOptions::GetLigandRMSDHeavy`
`OESz::OESzybki::SetCalculateGradients`	`OESzybkiGeneralOptions::SetCalculateGradients`
`OESz::OESzybkiOptions::SetCalculateGradients`	`OESzybkiGeneralOptions::SetCalculateGradients`
`OESz::OESzybki::GetCalculateGradients`	`OESzybkiGeneralOptions::GetCalculateGradients`
`OESz::OESzybkiOptions::GetCalculateGradients`	`OESzybkiGeneralOptions::GetCalculateGradients`
`OESz::OESzybki::SetVerbose`	`OESzybkiGeneralOptions::SetVerbose`
`OESz::OESzybkiOptions::SetVerbose`	`OESzybkiGeneralOptions::SetVerbose`
`OESz::OESzybki::GetVerbose`	`OESzybkiGeneralOptions::GetVerbose`
`OESz::OESzybkiOptions::GetVerbose`	`OESzybkiGeneralOptions::GetVerbose`
`OESz::OESzybki::SetIntramolecularVdWCutoff`	`OESzybkiGeneralOptions::SetIntramolecularVdWCutoff`
`OESz::OESzybkiOptions::SetIntramolecularVdWCutoff`	`OESzybkiGeneralOptions::SetIntramolecularVdWCutoff`
`OESz::OESzybki::GetIntramolecularVdWCutoff`	`OESzybkiGeneralOptions::GetIntramolecularVdWCutoff`
`OESz::OESzybkiOptions::GetIntramolecularVdWCutoff`	`OESzybkiGeneralOptions::GetIntramolecularVdWCutoff`
`OESz::OESzybki::SetTemperature`	`OESzybkiGeneralOptions::SetTemperature`
`OESz::OESzybkiOptions::SetTemperature`	`OESzybkiGeneralOptions::SetTemperature`
`OESz::OESzybki::GetTemperature`	`OESzybkiGeneralOptions::GetTemperature`
`OESz::OESzybkiOptions::GetTemperature`	`OESzybkiGeneralOptions::GetTemperature`
`OESz::OESzybki::SetSoluteDielectric`	`OESzybkiGeneralOptions::SetSoluteDielectric`
`OESz::OESzybkiOptions::SetSoluteDielectric`	`OESzybkiGeneralOptions::SetSoluteDielectric`
`OESz::OESzybki::GetSoluteDielectric`	`OESzybkiGeneralOptions::GetSoluteDielectric`
`OESz::OESzybkiOptions::GetSoluteDielectric`	`OESzybkiGeneralOptions::GetSoluteDielectric`
`OESz::OESzybki::SetForceFieldType`	`OESzybkiGeneralOptions::SetForceFieldType`
`OESz::OESzybkiOptions::SetForceFieldType`	`OESzybkiGeneralOptions::SetForceFieldType`
`OESz::OESzybki::GetForceFieldType`	`OESzybkiGeneralOptions::GetForceFieldType`
`OESz::OESzybkiOptions::GetForceFieldType`	`OESzybkiGeneralOptions::GetForceFieldType`
`OESz::OESzybki::SetCalculateFrozenTerms`	`OESzybkiOptOptions::SetCalculateFrozenTerms`
`OESz::OESzybkiOptions::SetCalculateFrozenTerms`	`OESzybkiOptOptions::SetCalculateFrozenTerms`
`OESz::OESzybki::GetCalculateFrozenTerms`	`OESzybkiOptOptions::GetCalculateFrozenTerms`
`OESz::OESzybkiOptions::GetCalculateFrozenTerms`	`OESzybkiOptOptions::GetCalculateFrozenTerms`
`OESz::OESzybki::SetGradTolerance`	`OESzybkiOptOptions::SetGradTolerance`
`OESz::OESzybkiOptions::SetGradTolerance`	`OESzybkiOptOptions::SetGradTolerance`
`OESz::OESzybki::GetGradTolerance`	`OESzybkiOptOptions::GetGradTolerance`
`OESz::OESzybkiOptions::GetGradTolerance`	`OESzybkiOptOptions::GetGradTolerance`
`OESz::OESzybki::SetOptimizerType`	`OESzybkiOptOptions::SetOptimizerType`
`OESz::OESzybkiOptions::SetOptimizerType`	`OESzybkiOptOptions::SetOptimizerType`
`OESz::OESzybki::GetOptimizerType`	`OESzybkiOptOptions::GetOptimizerType`
`OESz::OESzybkiOptions::GetOptimizerType`	`OESzybkiOptOptions::GetOptimizerType`
`OESz::OESzybki::SetMaxIter`	`OESzybkiOptOptions::SetMaxIter`
`OESz::OESzybkiOptions::SetMaxIter`	`OESzybkiOptOptions::SetMaxIter`
`OESz::OESzybki::GetMaxIter`	`OESzybkiOptOptions::GetMaxIter`
`OESz::OESzybkiOptions::GetMaxIter`	`OESzybkiOptOptions::GetMaxIter`
`OESz::OESzybki::SetSolventDielectric`	`OESzybkiSolventOptions::SetSolventDielectric`
`OESz::OESzybkiOptions::SetSolventDielectric`	`OESzybkiSolventOptions::SetSolventDielectric`
`OESz::OESzybki::GetSolventDielectric`	`OESzybkiSolventOptions::GetSolventDielectric`
`OESz::OESzybkiOptions::GetSolventDielectric`	`OESzybkiSolventOptions::GetSolventDielectric`
`OESz::OESzybki::SetSaltConcentration`	`OESzybkiSolventOptions::SetSaltConcentration`
`OESz::OESzybkiOptions::SetSaltConcentration`	`OESzybkiSolventOptions::SetSaltConcentration`
`OESz::OESzybki::GetSaltConcentration`	`OESzybkiSolventOptions::GetSaltConcentration`
`OESz::OESzybkiOptions::GetSaltConcentration`	`OESzybkiSolventOptions::GetSaltConcentration`
`OESz::OESzybki::SetCavitySolventParameter`	`OESzybkiSolventOptions::SetCavitySolventParameter`
`OESz::OESzybkiOptions::SetCavitySolventParameter`	`OESzybkiSolventOptions::SetCavitySolventParameter`
`OESz::OESzybki::GetCavitySolventParameter`	`OESzybkiSolventOptions::GetCavitySolventParameter`
`OESz::OESzybkiOptions::GetCavitySolventParameter`	`OESzybkiSolventOptions::GetCavitySolventParameter`
`OESz::OESzybki::SetSolventModel`	`OESzybkiSolventOptions::SetSolventModel`
`OESz::OESzybkiOptions::SetSolventModel`	`OESzybkiSolventOptions::SetSolventModel`
`OESz::OESzybki::GetSolventModel`	`OESzybkiSolventOptions::GetSolventModel`
`OESz::OESzybkiOptions::GetSolventModel`	`OESzybkiSolventOptions::GetSolventModel`
`OESz::OESzybki::SetAtomicRadii`	`OESzybkiSolventOptions::SetAtomicRadiiType`
`OESz::OESzybkiOptions::SetAtomicRadii`	`OESzybkiSolventOptions::SetAtomicRadiiType`
`OESz::OESzybki::GetAtomicRadiiType`	`OESzybkiSolventOptions::GetAtomicRadiiType`
`OESz::OESzybkiOptions::GetAtomicRadiiType`	`OESzybkiSolventOptions::GetAtomicRadiiType`
`OESz::OESzybki::SetUseCurrentCharges`	`OESzybkiSolventOptions::SetChargeEngine`
`OESz::OESzybkiOptions::SetUseCurrentCharges`	`OESzybkiSolventOptions::SetChargeEngine`
`OESz::OESzybki::GetUseCurrentCharges`	`OESzybkiSolventOptions::SetChargeEngine`
`OESz::OESzybkiOptions::GetUseCurrentCharges`	`OESzybkiSolventOptions::SetChargeEngine`
`OESz::OESzybki::SetEveryConfAM1BCCCharges`	`OESzybkiSolventOptions::SetChargeEngine`
`OESz::OESzybkiOptions::SetEveryConfAM1BCCCharges`	`OESzybkiSolventOptions::SetChargeEngine`
`OESz::OESzybki::GetEveryConfAM1BCCCharges`	`OESzybkiSolventOptions::SetChargeEngine`
`OESz::OESzybkiOptions::GetEveryConfAM1BCCCharges`	`OESzybkiSolventOptions::SetChargeEngine`
`OESz::OESzybki::SetExactVdWProteinLigand`	`OESzybkiProteinOptions::SetExactVdWProteinLigand`
`OESz::OESzybkiOptions::SetExactVdWProteinLigand`	`OESzybkiProteinOptions::SetExactVdWProteinLigand`
`OESz::OESzybki::GetExactVdWProteinLigand`	`OESzybkiProteinOptions::GetExactVdWProteinLigand`
`OESz::OESzybkiOptions::GetExactVdWProteinLigand`	`OESzybkiProteinOptions::GetExactVdWProteinLigand`
`OESz::OESzybki::SetProteinDielectric`	`OESzybkiProteinOptions::SetProteinDielectric`
`OESz::OESzybkiOptions::SetProteinDielectric`	`OESzybkiProteinOptions::SetProteinDielectric`
`OESz::OESzybki::GetProteinDielectric`	`OESzybkiProteinOptions::GetProteinDielectric`
`OESz::OESzybkiOptions::GetProteinDielectric`	`OESzybkiProteinOptions::GetProteinDielectric`
`OESz::OESzybki::SetProteinFlexibilityRange`	`OESzybkiProteinOptions::SetProteinFlexibilityRange`
`OESz::OESzybkiOptions::SetProteinFlexibilityRange`	`OESzybkiProteinOptions::SetProteinFlexibilityRange`
`OESz::OESzybki::GetProteinFlexibilityRange`	`OESzybkiProteinOptions::GetProteinFlexibilityRange`
`OESz::OESzybkiOptions::GetProteinFlexibilityRange`	`OESzybkiProteinOptions::GetProteinFlexibilityRange`
`OESz::OESzybki::SetIntermolecularVdWCutoff`	`OESzybkiProteinOptions::SetIntermolecularVdWCutoff`
`OESz::OESzybkiOptions::SetIntermolecularVdWCutoff`	`OESzybkiProteinOptions::SetIntermolecularVdWCutoff`
`OESz::OESzybki::GetIntermolecularVdWCutoff`	`OESzybkiProteinOptions::GetIntermolecularVdWCutoff`
`OESz::OESzybkiOptions::GetIntermolecularVdWCutoff`	`OESzybkiProteinOptions::GetIntermolecularVdWCutoff`
`OESz::OESzybki::SetProteinElectrostaticModel`	`OESzybkiProteinOptions::SetProteinElectrostaticModel`
`OESz::OESzybkiOptions::SetProteinElectrostaticModel`	`OESzybkiProteinOptions::SetProteinElectrostaticModel`
`OESz::OESzybki::GetProteinElectrostaticModel`	`OESzybkiProteinOptions::GetProteinElectrostaticModel`
`OESz::OESzybkiOptions::GetProteinElectrostaticModel`	`OESzybkiProteinOptions::GetProteinElectrostaticModel`
`OESz::OESzybki::SetProteinFlexibilityType`	`OESzybkiProteinOptions::SetProteinFlexibilityType`
`OESz::OESzybkiOptions::SetProteinFlexibilityType`	`OESzybkiProteinOptions::SetProteinFlexibilityType`
`OESz::OESzybki::GetProteinFlexibilityType`	`OESzybkiProteinOptions::GetProteinFlexibilityType`
`OESz::OESzybkiOptions::GetProteinFlexibilityType`	`OESzybkiProteinOptions::GetProteinFlexibilityType`

Minor bug fixes¶

User-defined partial charges set for the MMFFS_AMBER or MMFF_AMBER force field calculations had previously not been preserved. They are now passed to the optimized molecule.
Changing the protein flexibility type from range-defined to a list of residues for an OESzybkiOptions object previously required creating a copy of the object. This issue has been fixed.
Atomic radii for IEFF/PB calculations were previously restricted to the Bondi type. Although the default is still Bondi, ZAP7 and ZAP9 radii are now available.