BALL::GeneralizedBornModel Class Reference

#include <BALL/SOLVATION/generalizedBornCase.h>

Classes
struct	Default
struct	Option

Public Member Functions
	GeneralizedBornModel () throw (Exception::FileNotFound)
	~GeneralizedBornModel ()
void	clear ()
bool	setup (const AtomContainer &ac) throw (Exception::FileNotFound)
	We need an additional optioned version of that piece of code. More...
void	setScalingFactorFile (const String &filename)
	??? This should be done through Options! More...
void	setScalingFactors (const StringHashMap< float > &scaling_factors)
const StringHashMap< float > &	getScalingFactors () const
void	setSolventDC (float solvent_dc)
	??? Should be done by options More...
void	setSoluteDC (float solute_dc)
	??? Should be done by options More...
float	calculateEnergy ()
	Compute the total energy of the system. More...
float	calculateSolvationEnergy ()
void	calculatePotential (HashMap< const Atom *, float > &p_hash) const
float	calculatePotential (const Atom &atom_i) const
bool	readScalingFactors (const String &inifile_name) throw (Exception::FileNotFound)

Detailed Description

Compute the electrostatics of a molecule in solution.

This implementation bases on

[1] "Modification of the Generalized Born Model Suitable for Macromolecules" Onufriev, Bashford, Case J. Phys. Chem. B 104:3712-3720, 2000

This paper uses techniques from

[2] "Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics" Still, Tempczyk, Hawley, Hendrickson J. Am. Chem. Soc. 112(16):6127-6129, 1990

[3] "Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt eff¤ects " Srinivasan, Trevathan, Beroza, Case Theor. Chem. Acc. 101(6):426-434, 1999

Definition at line 61 of file generalizedBornCase.h.

Constructor & Destructor Documentation

BALL::GeneralizedBornModel::GeneralizedBornModel	(		)
throw	(	Exception::FileNotFound
	)

BALL::GeneralizedBornModel::~GeneralizedBornModel

(

)

Member Function Documentation

float BALL::GeneralizedBornModel::calculateEnergy

(

)

Compute the total energy of the system.

void BALL::GeneralizedBornModel::calculatePotential

(

HashMap< const Atom *, float > &

p_hash

)

const

Calculate the total potential created by every other atom of the system for every atom and return a hashmap conteining the potential values.

float BALL::GeneralizedBornModel::calculatePotential

(

const Atom &

atom_i

)

const

Calculate the total potential created by every other atom of the system at the position of atom_i

float BALL::GeneralizedBornModel::calculateSolvationEnergy

(

)

Compoute only the solvation energy (meaning the transfer energy which is a kind of a reaction field energy)

void BALL::GeneralizedBornModel::clear

(

)

const StringHashMap<float>& BALL::GeneralizedBornModel::getScalingFactors

(

)

const

bool BALL::GeneralizedBornModel::readScalingFactors	(	const String &	inifile_name	)
throw	(	Exception::FileNotFound
	)

void BALL::GeneralizedBornModel::setScalingFactorFile

(

const String &

filename

)

??? This should be done through Options!

void BALL::GeneralizedBornModel::setScalingFactors

(

const StringHashMap< float > &

scaling_factors

)

void BALL::GeneralizedBornModel::setSoluteDC

(

float

solute_dc

)

??? Should be done by options

void BALL::GeneralizedBornModel::setSolventDC

(

float

solvent_dc

)

??? Should be done by options

bool BALL::GeneralizedBornModel::setup	(	const AtomContainer &	ac	)
throw	(	Exception::FileNotFound
	)

We need an additional optioned version of that piece of code.