BALL::GeneralizedBornModel Class Reference

#include <BALL/SOLVATION/generalizedBornCase.h>

Classes
struct	Default
class	GBParameters
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)

Private Member Functions
void	calculateBornRadii_ ()
float	calculateCreationEnergy_ () const
float	calculateTransferEnergy_ () const
float	f_GB_ (Size i, Size j) const
float	coulombIntegralApproximation_ (float distance, float scaled_radius_j, float radius_i) const

Private Attributes
AtomContainer *	ac_
std::vector< const Atom * >	atoms_
std::vector< float >	born_radii_
std::vector< std::pair< Size, Size > >	pair_list_
std::vector< float >	pair_distances_
std::vector< float >	pair_charges_
std::vector< std::vector< float > >	squared_distances_
float	dc_solute_
float	dc_solvent_
StringHashMap< float >	scaling_factors_
std::vector< float >	scaling_factor_
String	scaling_factor_filename_
float	lambda_
float	delta_
float	kappa_
float	rho_0_
float	to_kJ_mol_

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

void BALL::GeneralizedBornModel::calculateBornRadii_ ( )

private

Calculate the Born radii of all atoms

float BALL::GeneralizedBornModel::calculateCreationEnergy_ ( ) const

private

Calculate the energetic cost of creating a charge distribution in a uniform dielectric

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)

float BALL::GeneralizedBornModel::calculateTransferEnergy_ ( ) const

private

Calculate the energetic cost of transfering a solute into a dielectric medium.

void BALL::GeneralizedBornModel::clear

(

)

float BALL::GeneralizedBornModel::coulombIntegralApproximation_ ( float  distance, float  scaled_radius_j, float  radius_i  ) const

private

An approximation of the coulomb integral

float BALL::GeneralizedBornModel::f_GB_ ( Size  i, Size  j  ) const

private

A smooth function describing an approximation of the solute volume and several Born-dependent effects (including Coulomb integrals). There are several techniques in usage. We implement the on described in [1].

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.

Member Data Documentation

AtomContainer* BALL::GeneralizedBornModel::ac_

private

The atom container representing the molecule

Definition at line 225 of file generalizedBornCase.h.

std::vector<const Atom*> BALL::GeneralizedBornModel::atoms_

private

The atom list

Definition at line 229 of file generalizedBornCase.h.

std::vector<float> BALL::GeneralizedBornModel::born_radii_

private

The Born radii of all atoms

Definition at line 233 of file generalizedBornCase.h.

float BALL::GeneralizedBornModel::dc_solute_

private

Dielectric constants of the solute and the surrounding solvent

Definition at line 248 of file generalizedBornCase.h.

float BALL::GeneralizedBornModel::dc_solvent_

private

Definition at line 249 of file generalizedBornCase.h.

float BALL::GeneralizedBornModel::delta_

private

Downshift of the effictve Born radii for rectifying the energy increase caused by the lambda factor. More or less magic (see [1] for details) but allows to use the scaling_factors_ without reparamterizing them.

Definition at line 272 of file generalizedBornCase.h.

float BALL::GeneralizedBornModel::kappa_

private

Debye-Hueckel parameter describing salt effects (ionic strength) in units of 1/Angstrom.

Definition at line 277 of file generalizedBornCase.h.

float BALL::GeneralizedBornModel::lambda_

private

Scaling factor of integral part of effective Born radii calculation rectifying the underestimation of the radii caused by the vdW approximation (instead of real SAS calculations).

Definition at line 265 of file generalizedBornCase.h.

std::vector< float > BALL::GeneralizedBornModel::pair_charges_

private

Definition at line 243 of file generalizedBornCase.h.

std::vector< float > BALL::GeneralizedBornModel::pair_distances_

private

Distances between atoms of the pair list.

Definition at line 242 of file generalizedBornCase.h.

std::vector< std::pair<Size, Size> > BALL::GeneralizedBornModel::pair_list_

private

The pairs of atoms we have to look at. This list only inlcudes different atoms. Not suitable for self-energy calculations,

Definition at line 238 of file generalizedBornCase.h.

float BALL::GeneralizedBornModel::rho_0_

private

Radius offset (see [2] for details).

Definition at line 281 of file generalizedBornCase.h.

std::vector<float> BALL::GeneralizedBornModel::scaling_factor_

private

Definition at line 255 of file generalizedBornCase.h.

String BALL::GeneralizedBornModel::scaling_factor_filename_

private

Definition at line 259 of file generalizedBornCase.h.

StringHashMap<float> BALL::GeneralizedBornModel::scaling_factors_

private

Empirical scaling factor for the estimation of effective Born radii. See [3] for details.

Definition at line 254 of file generalizedBornCase.h.

std::vector< std::vector< float > > BALL::GeneralizedBornModel::squared_distances_

private

Definition at line 244 of file generalizedBornCase.h.

float BALL::GeneralizedBornModel::to_kJ_mol_

private

Definition at line 285 of file generalizedBornCase.h.