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.
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: Inputmoleculecontainschiralatomswithunspecifiedchirality. This warning may be generated when using the FreeForm part of the
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 torsionalcoordinates, and solid-bodyoptimization
have been added.
Missing documentation for the OEOptType.NEWTON constant, which
sets Newton type optimization, has been added.