BALL::GeneralizedBornModel Class Reference
#include <BALL/SOLVATION/generalizedBornCase.h>
List of all members.
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
Constructor & Destructor Documentation
BALL::GeneralizedBornModel::~GeneralizedBornModel |
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Member Function Documentation
void BALL::GeneralizedBornModel::calculateBornRadii_ |
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[private] |
Calculate the Born radii of all atoms
float BALL::GeneralizedBornModel::calculateCreationEnergy_ |
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const [private] |
Calculate the energetic cost of creating a charge distribution in a uniform dielectric
float BALL::GeneralizedBornModel::calculateEnergy |
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Compute the total energy of the system.
float BALL::GeneralizedBornModel::calculatePotential |
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const Atom & |
atom_i |
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const |
Calculate the total potential created by every other atom of the system at the position of atom_i
void BALL::GeneralizedBornModel::calculatePotential |
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HashMap< const Atom *, float > & |
p_hash |
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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::calculateSolvationEnergy |
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Compoute only the solvation energy (meaning the transfer energy which is a kind of a reaction field energy)
float BALL::GeneralizedBornModel::calculateTransferEnergy_ |
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const [private] |
Calculate the energetic cost of transfering a solute into a dielectric medium.
void BALL::GeneralizedBornModel::clear |
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float BALL::GeneralizedBornModel::coulombIntegralApproximation_ |
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float |
distance, |
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float |
scaled_radius_j, |
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float |
radius_i | |
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An approximation of the coulomb integral
float BALL::GeneralizedBornModel::f_GB_ |
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Size |
i, |
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Size |
j | |
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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].
void BALL::GeneralizedBornModel::setScalingFactorFile |
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const String & |
filename |
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??? This should be done through Options!
void BALL::GeneralizedBornModel::setScalingFactors |
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const StringHashMap< float > & |
scaling_factors |
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void BALL::GeneralizedBornModel::setSoluteDC |
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float |
solute_dc |
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??? Should be done by options
void BALL::GeneralizedBornModel::setSolventDC |
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float |
solvent_dc |
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??? Should be done by options
We need an additional optioned version of that piece of code.
Member Data Documentation
The atom container representing the molecule
The Born radii of all atoms
Dielectric constants of the solute and the surrounding solvent
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.
Debye-Hueckel parameter describing salt effects (ionic strength) in units of 1/Angstrom.
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).
Distances between atoms of the pair list.
The pairs of atoms we have to look at. This list only inlcudes different* atoms. Not suitable for self-energy calculations,
Radius offset (see [2] for details).
Empirical scaling factor for the estimation of effective Born radii. See [3] for details.