Solvation methods
[Molecular Modeling]

Classes
class	ClaverieParameter
	ClaverieParameter class. More...
class	ElectrostaticPotentialCalculator
	This class is used to compute the electrostatic potential for of a system. More...
class	Pair6_12InteractionEnergyProcessor
	Processor for the computation of the van-der-Waals interaction energy of a molecule with its surrounding. More...
class	Pair6_12RDFIntegrator
	6-12 pair potential integrator. More...
class	PairExpInteractionEnergyProcessor
	Processor for the computation of the van-derWaals interaction energy of a molecule. More...
class	PairExpRDFIntegrator
	6-exp pair potential integrator. More...
class	PCMCavFreeEnergyProcessor
	Processor for the computation of the cavitation free energy. More...
class	PierottiCavFreeEnergyProcessor
	Processor for the computation of the cavitation free energy. More...
class	FDPB
	Finite Difference Poisson Boltzmann Solver. More...
class	ReissCavFreeEnergyProcessor
	Processor for the computation of the cavitation free energy. More...
class	SolventAtomDescriptor
	This struct contains the information for one atom type of the solvent. More...
class	SolventAtomDescriptor
	This struct contains the information for one atom type of the solvent. More...
class	SolventDescriptor
	Solvent Description. More...
class	SolventParameter
	Parameter section for the solvent description. More...
class	UhligCavFreeEnergyProcessor
	Processor for the computation of the cavitation free energy. More...
Functions
BALL_EXPORT TRegularData3D< char > *	calculateSESGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
	calculateSESGrid
BALL_EXPORT TRegularData3D< char > *	calculateSASGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
	calculateSASGrid
BALL_EXPORT double	calculateOoiEnergy (AtomContainer &atoms)
	Calculate the solvation energy after Ooi et al.

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Detailed Description

This chapter contains all relevant information on the use of BALL solvation methods.

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Function Documentation

BALL_EXPORT double calculateOoiEnergy (  AtomContainer &  atoms  )

Calculate the solvation energy after Ooi et al. This function computes the solvation energy using the empirical surface model proposed by Ooi et al.(T. Ooi, M. Oobatake, G. Nemethy, H. A. Scheraga: Accessible surface areas as a measure off the thermodynamic parameters of hydration of peptides, Proc. Natl. Acad. Sci. USA, Vol. 84 (1987), pp. 3086-3090). The method is parameterized for proteins only. Calling the function with different structures probably yields results of arbitrary meaninglessness. The energy is returned in units of kJ/mol. Unparametrized atoms are simply ignored, which might lead to unreasonable values. Files: types and parameters are taken from data/solvation/Ooi.ini

BALL_EXPORT TRegularData3D<char>* calculateSASGrid (  const Vector3 &  lower, const Vector3 &  upper, float  spacing, const System &  system, float  probe_radius )

calculateSASGrid

BALL_EXPORT TRegularData3D<char>* calculateSESGrid (  const Vector3 &  lower, const Vector3 &  upper, float  spacing, const System &  system, float  probe_radius )

calculateSESGrid