Szybki TK 1.8.1

New features

  • OENewtonOpt added for Newton-Raphson optimization.
  • OESzybkiOptions class added for setting all options of the OESzybki object during construction. All new functionality, starting from the mentioned above Newton-Raphson optimization, will only be available through the OESzybkiOptions class. All the OESzybki methods with the same name as their OESzybkiOptions counterpart are deprecated and will be removed in Szybki TK.
  • OEOptimizer2 abstract base class added to allow optimizers that use analytical second derivatives.
  • Newton-Raphson optimization method added as an option for minimization. For this release it is restricted however to the MMFF94/MMFF94S force field and Sheffield solvation model. It is available only for optimization in Cartesian coordinates.
  • The string representation of the gradient norm by the OECheckpoint1 object and by the OESzybkiResults::Print method will be in scientific notation to provide better precision.
  • The following methods have been added to OESzybkiResults:
  • Efficiency of diagonalization of Hessian matrix is improved.
  • Added two new example programs showing how to use Newton-Raphson optimization.
  • The C++ Szybki toolkit now links against the new oemath library.
  • All C++ examples have been renamed to better represent their utility.

Major bug fixes

  • Calculation of PB solvent forces will no longer run out of memory and crash due to violent moves of the optimizer.
  • OESzybki::LoadPotentialGrid and OESzybki::SavePotentialGrid will no longer crash due to the length of the file name passed.
  • OESzybki will no longer allow a solid-body optimization in partially flexible protein as this was never an intended feature.

Minor bug fixes

Documentation fixes