Szybki TK 1.5.0

New features

• Entropy calculations of a ligand in different environments can be performed based on the methods described in the recent paper of Wlodek et. al. ([Wlodek-2010]).

  New methods added to the public API are:

  • OESzybki::GetEntropy

  • GetSolutionEntropy

  • GetProteinBoundLigandEntropy

• Default VdW protein-ligand potential used for the optimization of a ligand inside the protein binding site is precalculated in the form of a lookup table. This is done for the purpose of speed. The exact VdW protein-ligand potential can be used with the new method:

  • SetExactVdWProteinLigand

  when boolean parameter passed is true. Passing false causes switching to the default form of the protein-ligand VdW. The function:

  • GetExactVdWProteinLigand

  allows the querying of which form of the VdW potential is used.

• Two functions have been added to the public API in szybki.h. The first new function allows the use of conformation-dependent AM1BCC charges for every conformation in the calculation of PB and Sheffield solvation energies, for protein-ligand Coulomb interactions, and in entropy calculations.

  • SetEveryConfAM1BCCCharges

  The second function returns true if AM1BCC are being calculated for every conformation, false otherwise.

  • GetEveryConfAM1BCCCharges

Bug fixes

• In a special situation of ligand optimization in the protein binding site with the use of the electrostatics model determined by the OEProteinElectrostatics::ExactCoulomb, constant, when the optimization was preceded by the Zap binding calculations with the same protein and the same ligand, Coulombic interaction resulted in zero value. This bug has been fixed.