Szybki TK 1.8.2¶
- OEEstimateSolvFreeEnergy and OEEstimateConfFreeEnergies added to perform FreeForm calculations. Their usage requires passing instances of the following classes:
- OEOpt::OEFunc1::CheckVariablesValidity added for checking the validity of arguments for the function to be optimized. The users of the all classes derived from OEFunc1 can implement it according to specific features of their objective functions.
- OESz::OESzybki::GetSolutionEntropy and OESz::OESzybki::GetProteinBoundLigandEntropy have been officially deprecated. OESzybki::GetEntropy that returns double values by reference has also been deprecated. Users should switch to using the OESzybkiEnsembleResults object instead.
Major bug fixes¶
- Dangling pointer in the implementation of the OESzybki::UnsetProtein has been found and fixed.
- Setting up a Newton-Raphson optimization on large systems can easily exhaust the amount of memory needed because of the O(n^2) Hessian matrix. If memory exhaustion is detected, the calculation will now error out instead of crashing.
- An exception has been added to catch the memory exhaustion upon Hessian allocation used for Newton-Raphson optimization of large systems. That could happen on some platforms with limited memory (for example Win32).
Minor bug fixes¶
- Removed unbounded stack allocations.
- Verbose mode of some protein-ligand optimization could not report the number of cycles at the very end of optimization.
- Warning is issued upon the attempt to remove Coulomb terms from the combined force field Amber-MMFF (and Amber-MMFFS) with methods OESz::OESzybki::SetRemoveCoulombTerms and OESz::OESzybkiOptions::SetRemoveCoulombTerms.
- Unnecessary and confusing warning Warning: Solid-body optimization allowed only for ligand in fixed protein is eliminated when OESzybkiOptions::SetRunType is used with the OERunType::SolidBodyOpt argument.
- Examples added to demonstrate how to do an entropy estimation.
- Examples have been updated to use non-deprecated APIs.