SZYBKI 1.3.0

New features

  • Optimization using conjugate gradient method was added as an alternative to the default quasi-Newton method with the BFGS Hessian update scheme. In Szybki toolkit this is done by the usage of a new function void SetOptimizerType(unsigned int type). In Szybki application a flag -conj has been added for that purpose.
  • Default value of the protein dielectric constant is 1. Previous default value for that parameter was 2, however it was not consistent with the default value of MMFF94 force field.
  • Protein-electrostatic models in Szybki application are selected with descriptive strings. Available options are:
    • None - no electrostatic potential used (default option)
    • ExactCoulomb - exact MMFF Coulomb potential
    • GridCoulomb - MMFF Coulomb potential on grid
    • PB - PP solvent forces used at every step

Bug fixes

  • A bug causing crash in the case of combined usage of partial protein flexibility and protein electrostatic model OEProteinElectrostatics::SolventPBForces was fixed.
  • A bug causing different behavior and/or occasional crash depending of the order of calls: SetProtein(const OEChem::OEMolBase&), SetRunType(unsigned int) and SetResidueFlexibility(double) has been fixed.
  • Modification of the potential function after the usage of coordinate adaptors could occasionally result in crash, for example when function FixAtoms() was followed by SetRemoveCoulombTerms(). This bug was fixed.
  • Running in the pvm mode requires now setting the PVM_PATH variable, which points at the directory where the Szybki script is located. For example if Szybki was untarred in the directory mydir, then using bash shell one can set the above variable with: export PVM_PATH=mydir/openeye/bin