BALL::GeneralizedBornModel Class Reference

Compute the electrostatics of a molecule in solution. More...

#include <generalizedBornCase.h>

List of all members.

Public Member Functions
void	clear ()
bool	setup (const AtomContainer &ac) throw (Exception::FileNotFound)
	We need an additional optioned version of that piece of code.
void	setScalingFactorFile (const String &filename)
	??? This should be done through Options!
void	setScalingFactors (const StringHashMap< float > &scaling_factors)
const StringHashMap< float > &	getScalingFactors () const
void	setSolventDC (float solvent_dc)
	??? Should be done by options
void	setSoluteDC (float solute_dc)
	??? Should be done by options
float	calculateEnergy ()
	Compute the total energy of the system.
float	calculateSolvationEnergy ()
	Compoute only the solvation energy (meaning the transfer energy which is a kind of a reaction field energy).
void	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	calculatePotential (const Atom &atom_i) const
	Calculate the total potential created by every other atom of the system at the position of atom_i.
bool	readScalingFactors (const String &inifile_name) throw (Exception::FileNotFound)

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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

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Member Function Documentation

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.