SZYBKI 1.3.3

Bug fixes

  • Until current release, molecular output files in the .oeb format had MMFF aromaticity. In practice, such a situation lead to the visual change between the input and output aromaticity of some molecules. Starting from now OpenEye aromaticity model is used in the .oeb output files.

SZYBKI 1.3.2

Bug fixes

  • A bug which occasionally caused errors in fixing a subset of atoms, was fixed.
  • When using PVM, Szybki now runs a mechanism for checking versions used by master and slaves. This mechanism prevents the situation of different versions of Szybki running on the master and slaves.
  • Molecules containing atoms for which MMFF types are not properly typed are not processed. In previous versions attempts were made to assign for such atom the closest MMFF type, however this procedure almost always lead to errors. This situation occurred for example in the case of bad pdb files. For proteins, better diagnostics (residue name and number, atom name) are included as output.
  • Reading protein data in .oeb binary format containing additional untagged information (FRED receptor files) is allowed. Until now using such a file in pvm mode caused a fatal error.

SZYBKI 1.3.1

Bug fixes

  • The combination of options -complex if1 and -ligands if2 run in the pvm mode caused incorrect behavior in the case when the preexisting ligand in the macromolecule (in the file if1) overlapped with one or more ligands from the input file if2.
  • Run time license for the shape toolkit is added. It is required when the combination of options -complex if1 and -ligands if2 is used.
  • Redundant warnings generated upon -protein_elec  none and -strip_water were removed.
  • Spelling in the log file was fixed.
  • Year 2008 was added to the Szybki banner.
  • In the documentation description for the -fix_smarts option an example was added which illustrates the adjustment of hydrogen atom positions.
  • Examples of log files generated upon ligand optimization in the partially flexible protein followed by a single point PB calculations are given.

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

SZYBKI 1.2.2

New features

  • Two new functions are added to the API:

    void SetResidueFlexibility(double dist); double GetResidueFlexibility() const;

    These allow the user to introduce and query for the flexibility of entire residues around the ligand.

Bug fixes

  • In the case when protein electrostatic model was set at OEProteinElectrostatics::NoElectrostatics and partial protein flexibility was allowed with the void SetSideChainsFlexibility(double) or void SetPolarHFlexibility(double) functions, Coulombic terms describing the interaction between the ligand and flexible protein atoms were included during optimization. This was inconsistent with the meaning of NoElectrostatics, therefore those Coulombic terms were eliminated in the current release
  • Using the function void SetSideChainsFlexibility(double) resulted occasionally in double counting of some residues. This bug was fixed.
  • Fixing atoms with a function bool FixAtoms(std::string) where the passed string is SMARTS pattern, was based on MMFF aromaticity types. Starting from the current release OE aromaticity model is used.