Szybki TK 1.8.5¶
OEForceFieldType.MMFFS_IEFFprotein-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.MMFFS_AMBERtypes has increased from 100 to 150 heavy atoms.
OESetForceFieldDummyAtomcan 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.Clearhas been added to reset the state of the OESzybkiResults object.
Major bug fixes¶
OESzybki will no longer crash when
OESz::OESzybkiOptions::SetForceFieldTypeis called with the argument
OEForceFieldType.MMFFS_AMBERand then followed by a call of
Minor bug fixes¶
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 object does not have data to report.
OESz::OESzybki::GetForceFieldTypenow properly returns
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.
OEFuncTypehas 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.