Two new API methods added: SetIntramolecularVdWCutoff and
Methods OESz::OESzybki::SetProteinVdWCutoff and
OESz::OESzybki::GetProteinVdWCutoff have become deprecated. They have
been replaced by OESz::OESzybki::SetIntermolecularVdWCutoff and
Steepest descent (OEOptType.SD) method added as an
optional optimizer instead of BFGS.
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That behavior has been replaced by retaining the initial charges, and zeroing the molecule’s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