Szybki TK 1.7.2

New features

  • Two new API methods added: SetIntramolecularVdWCutoff and GetIntramolecularVdWCutoff
  • Methods OESz::OESzybki::SetProteinVdWCutoff and OESz::OESzybki::GetProteinVdWCutoff have become deprecated. They have been replaced by OESz::OESzybki::SetIntermolecularVdWCutoff and OESz::OESzybki::GetIntermolecularVdWCutoff respectively.
  • Steepest descent (OEOptType::SD) method added as an optional optimizer instead of BFGS.

Major bug fixes

Minor bug fixes

  • Reusing the OESzybki object after ligand entropy estimation in the protein environment, for other, non-entropy runs of a ligand inside the same protein, required an extra call to OESzybki::SetProtein in order to set correctly the new protein-electrostatic model correctly. This is not needed anymore.
  • In the rare case when ligand is moved out from the protein binding site during entropy estimation the run is terminated with the proper warning. Previously, in such a case the attempts were done to reoptimize the ligand and rebuild the Hessian. Such a strategy was wrong because even if formally successful, it would lead to physically meaningless results. The situation described here can happen when the ligand is poorly docked, or if the X-ray structure used as input is very inaccurate.
  • When the method OESz::OESzybki::SetUseCurrentCharges was used which causes the use of input charges for PB or Sheffield calculations, the molecule which was processed with the OESzybki::operator() methods, on exit received the mmff94 charges. That behavior has been replaced by retaining the initial charges, and zeroing the molecule’s partial charges when the input molecule had none.
  • Error message for the case when the input structure generates infinite initial gradients is more informative.