Szybki TK 1.8.1¶
OENewtonOptadded for Newton-Raphson optimization.
OESzybkiOptionsclass added for setting all options of the
OESzybkiobject during construction. All new functionality, starting from the mentioned above Newton-Raphson optimization, will only be available through the
OESzybkiOptionsclass. All the
OESzybkimethods with the same name as their
OESzybkiOptionscounterpart are deprecated and will be removed in Szybki TK.
OEOptimizer2abstract 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 following methods have been added to
Efficiency of diagonalization of Hessian matrix is improved.
Added two new example programs showing how to use Newton-Raphson optimization.
Major bug fixes¶
Calculation of PB solvent forces will no longer run out of memory and crash due to violent moves of the optimizer.
OESzybkiwill no longer allow a solid-body optimization in partially flexible protein as this was never an intended feature.