Szybki TK 1.8.6¶

Major bug fixes¶

A memory issue that caused periodic crash of JVM in a situation when torsion optimization was performed and Coulomb terms were removed from the MMFF94 or MMFF94S force field in Java-wrapped code has been fixed.
Possible memory corruption in the IEFF force field has been fixed.
Previously, making the protein partially flexible and selecting a run type of either OERunType.SinglePoint or OERunType.TorsionsOpt had been causing crashes. These bugs have both been fixed.
The order of the residue names generated in the logging output for flexible polar hydrogens for the Protein-Ligand IEFF-MMFF calculation will now be consistent between runs. Previously, the order of the residue names could change in subsequent runs.
A discontinuity in the flat-bottom harmonic potential has been fixed. The potential function generated by the method OESzybki.SetHarmonicConstraints had a discontinuity in the primary function and its first derivative that caused the optimizer to over-constrain optimizations with harmonic constraints with flat-bottom. The class OEHarmonicPotential has been reimplemented.

Language in the warning regarding the input of atoms with unspecified chirality is improved. It now reads: Input molecule contains chiral atoms with unspecified chirality. This warning may be generated when using the FreeForm part of the Szybki TK.
OEEstimateConfFreeEnergies now accepts an input ensemble containing a molecule with 20 or more rotatable bonds. Previously, encountering such a molecule resulted in a warning and then that molecule was skipped.

Documentation for constants describing optimization in torsional coordinates and translational-rotational coordinates (OERunType.TorsionsOpt and OERunType.SolidBodyOpt has been expanded. Specifically, short descriptions of the terms torsional coordinates, and solid-body optimization have been added.
Missing documentation for the OEOptType.NEWTON constant, which sets Newton type optimization, has been added.