Szybki TK 1.8.5¶

New features¶

OEForceFieldType.MMFF_IEFF and OEForceFieldType.MMFFS_IEFF protein-ligand potentials can be now combined with the PB solvent energetics and forces calculated with ESP partial charges that are read from the same molecular input as atomic multipoles.
The upper limit of the ligand size that might be charged with the AM1BCC partial charges when protein-ligand potential is set using OEForceFieldType.MMFF_AMBER or OEForceFieldType.MMFFS_AMBER types has increased from 100 to 150 heavy atoms.
OESetForceFieldDummyAtom can be used to ignore dummy atoms in forcefield calculations if only van der Waals and Coulombic components are included. Dummy atoms are ignored in MMFF force fields and cannot be used in intramolecular components.
OESzybkiResults.Clear has been added to reset the state of the OESzybkiResults object.

OESzybki will no longer crash when OESz::OESzybkiOptions::SetForceFieldType is called with the argument OEForceFieldType.MMFFS_AMBER and then followed by a call of OESz::OESzybkiOptions::SetUseCurrentCharges with true.

OESzybki.operator() will no longer lose SD data when operating on a single conformer OEMolBase.
OESzybkiResults is now cleared from whenever OESzybki.operator() fails. Clearing is done by the new method OESzybkiResults.Clear. A cleared OESzybkiResults will make OESzybkiResults.Print output: OESzybkiResults object does not have data to report.
OESz::OESzybki::GetForceFieldType now properly returns OEForceFieldType.MMFF_AMBER or OEForceFieldType.MMFF_IEFF. Previously, they could only be returned after a calculation was performed with the OESzybki object.
A CYS residue bonded by the sulfur to something other than another CYS residue is no longer treated as anionic by the AMBER charging system.
Final geometry of a ligand optimized with the MMFF_IEFF or MMFFS_IEFF potential has been updated with the transformed multipoles attached to atoms as generic data.
A potential memory leak when performing repeated protein-ligand minimizations has been fixed.

OEFuncType has been documented.
The Optimization of all conformers of a ligand section has a new example that demonstrates how to minimize all conformers in a ligand.