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Vpbe class

The Poisson-Boltzmann master class. More...


Files

file  vpbe.h
 Contains declarations for class Vpbe.


Data Structures

struct  sVpbe
 Contains public data members for Vpbe class/module. More...


Typedefs

typedef sVpbe Vpbe
 Declaration of the Vpbe class as the Vpbe structure.


Functions

ValistVpbe_getValist (Vpbe *thee)
 Get atom list.

VaccVpbe_getVacc (Vpbe *thee)
 Get accessibility oracle.

double Vpbe_getBulkIonicStrength (Vpbe *thee)
 Get bulk ionic strength.

double Vpbe_getMaxIonRadius (Vpbe *thee)
 Get maximum radius of ion species.

double Vpbe_getTemperature (Vpbe *thee)
 Get temperature.

double Vpbe_getSoluteDiel (Vpbe *thee)
 Get solute dielectric constant.

double Vpbe_getGamma (Vpbe *thee)
 Get apolar coefficient.

double Vpbe_getSoluteRadius (Vpbe *thee)
 Get sphere radius which bounds biomolecule.

double Vpbe_getSoluteXlen (Vpbe *thee)
 Get length of solute in x dimension.

double Vpbe_getSoluteYlen (Vpbe *thee)
 Get length of solute in y dimension.

double Vpbe_getSoluteZlen (Vpbe *thee)
 Get length of solute in z dimension.

double * Vpbe_getSoluteCenter (Vpbe *thee)
 Get coordinates of solute center.

double Vpbe_getSoluteCharge (Vpbe *thee)
 Get total solute charge.

double Vpbe_getSolventDiel (Vpbe *thee)
 Get solvent dielectric constant.

double Vpbe_getSolventRadius (Vpbe *thee)
 Get solvent molecule radius.

double Vpbe_getXkappa (Vpbe *thee)
 Get Debye-Huckel parameter.

double Vpbe_getDeblen (Vpbe *thee)
 Get Debye-Huckel screening length.

double Vpbe_getZkappa2 (Vpbe *thee)
 Get modified squared Debye-Huckel parameter.

double Vpbe_getZmagic (Vpbe *thee)
 Get charge scaling factor.

Vpbe * Vpbe_ctor (Valist *alist, int ionNum, double *ionConc, double *ionRadii, double *ionQ, double T, double gamma, double soluteDiel, double solventDiel, double solventRadius, int focusFlag)
 Construct Vpbe object.

int Vpbe_ctor2 (Vpbe *thee, Valist *alist, int ionNum, double *ionConc, double *ionRadii, double *ionQ, double T, double gamma, double soluteDiel, double solventDiel, double solventRadius, int focusFlag)
 FORTRAN stub to construct Vpbe objct.

int Vpbe_getIons (Vpbe *thee, int *nion, double ionConc[MAXION], double ionRadii[MAXION], double ionQ[MAXION])
 Get information about the counterion species present.

void Vpbe_dtor (Vpbe **thee)
 Object destructor.

void Vpbe_dtor2 (Vpbe *thee)
 FORTRAN stub object destructor.

double Vpbe_getCoulombEnergy1 (Vpbe *thee)
 Calculate coulombic energy of set of charges.

int Vpbe_memChk (Vpbe *thee)
 Return the memory used by this structure (and its contents) in bytes.


Detailed Description

The Poisson-Boltzmann master class.

Contains objects and parameters used in every PBE calculation, regardless of method.


Function Documentation

Vpbe* Vpbe_ctor Valist   alist,
int    ionNum,
double *    ionConc,
double *    ionRadii,
double *    ionQ,
double    T,
double    gamma,
double    soluteDiel,
double    solventDiel,
double    solventRadius,
int    focusFlag
 

Construct Vpbe object.

Author:
Nathan Baker and Mike Holst
Note:
This is partially based on some of Mike Holst's PMG code. Here are a few of the original function comments: kappa is defined as follows:

where the units are esu*esu/erg/mol. To obtain , we multiply by . Thus, in , where and are in gaussian rather than mks units, the proper value for kappa is:

and the factor of results from converting cm^2 to angstroms^2, noting that the 1000 in the denominator has converted m^3 to cm^3, since the ionic strength is assumed to have been provided in moles per liter, which is moles per 1000 cm^3.

Parameters:
alist  Atom list
ionNum  Number of counterion species
ionConc  Array containing counterion species' concentrations (M)
ionRadii  Array containing counterion species' radii (A)
ionQ  Array containing counterion species' charges (e)
T  temperature (K)
gamma  Apolar coefficient (kJ/mol/A^2)
soluteDiel  Solute dielectric constant
solventDiel  Solvent dielectric constant
solventRadius  Solvent radius
focusFlag  1 if Focusing operation, 0 otherwise
Returns:
Pointer to newly allocated Vpbe object

int Vpbe_ctor2 Vpbe   thee,
Valist   alist,
int    ionNum,
double *    ionConc,
double *    ionRadii,
double *    ionQ,
double    T,
double    gamma,
double    soluteDiel,
double    solventDiel,
double    solventRadius,
int    focusFlag
 

FORTRAN stub to construct Vpbe objct.

Author:
Nathan Baker and Mike Holst
Note:
This is partially based on some of Mike Holst's PMG code. Here are a few of the original function comments: kappa is defined as follows:

where the units are esu*esu/erg/mol. To obtain , we multiply by . Thus, in , where and are in gaussian rather than mks units, the proper value for kappa is:

and the factor of results from converting cm^2 to angstroms^2, noting that the 1000 in the denominator has converted m^3 to cm^3, since the ionic strength is assumed to have been provided in moles per liter, which is moles per 1000 cm^3.

Parameters:
thee  Pointer to memory allocated for Vpbe object
alist  Atom list
ionNum  Number of counterion species
ionConc  Array containing counterion species' concentrations (M)
ionRadii  Array containing counterion species' radii (A)
ionQ  Array containing counterion species' charges (e)
T  temperature (K)
gamma  Apolar coefficient (kJ/mol/A^2)
soluteDiel  Solute dielectric constant
solventDiel  Solvent dielectric constant
solventRadius  Solvent radius
focusFlag  1 if Focusing operation, 0 otherwise
Returns:
1 if successful, 0 otherwise

void Vpbe_dtor Vpbe **    thee
 

Object destructor.

Author:
Nathan Baker
Parameters:
thee  Pointer to memory location of object to be destroyed

void Vpbe_dtor2 Vpbe   thee
 

FORTRAN stub object destructor.

Author:
Nathan Baker
Parameters:
thee  Pointer to object to be destroyed

double Vpbe_getBulkIonicStrength Vpbe   thee
 

Get bulk ionic strength.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Bulk ionic strength (M)

double Vpbe_getCoulombEnergy1 Vpbe   thee
 

Calculate coulombic energy of set of charges.

Perform an inefficient double sum to calculate the Coulombic energy of a set of charges in a homogeneous dielectric (with permittivity equal to the protein interior) and zero ionic strength. Result is returned in units of k_B T. The sum can be restriction to charges present in simplices of specified color (pcolor); if (color == -1) no restrictions are used.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Coulombic energy in units of .

double Vpbe_getDeblen Vpbe   thee
 

Get Debye-Huckel screening length.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Debye-Huckel screening length (Å)

double Vpbe_getGamma Vpbe   thee
 

Get apolar coefficient.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Apolar coefficent (kJ/mol/A^2)

int Vpbe_getIons Vpbe   thee,
int *    nion,
double    ionConc[MAXION],
double    ionRadii[MAXION],
double    ionQ[MAXION]
 

Get information about the counterion species present.

Author:
Nathan Baker
Parameters:
thee  Pointer to Vpbe object
nion  Set to the number of counterion species
ionConc  Array to store counterion species' concentrations (M)
ionRadii  Array to store counterion species' radii (A)
ionQ  Array to store counterion species' charges (e)
Returns:
Number of ions

double Vpbe_getMaxIonRadius Vpbe   thee
 

Get maximum radius of ion species.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Maximum radius (A)

double* Vpbe_getSoluteCenter Vpbe   thee
 

Get coordinates of solute center.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Pointer to 3*double array with solute center coordinates (A)

double Vpbe_getSoluteCharge Vpbe   thee
 

Get total solute charge.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Total solute charge (e)

double Vpbe_getSoluteDiel Vpbe   thee
 

Get solute dielectric constant.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Solute dielectric constant

double Vpbe_getSoluteRadius Vpbe   thee
 

Get sphere radius which bounds biomolecule.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Sphere radius which bounds biomolecule (A)

double Vpbe_getSoluteXlen Vpbe   thee
 

Get length of solute in x dimension.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Length of solute in x dimension (A)

double Vpbe_getSoluteYlen Vpbe   thee
 

Get length of solute in y dimension.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Length of solute in y dimension (A)

double Vpbe_getSoluteZlen Vpbe   thee
 

Get length of solute in z dimension.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Length of solute in z dimension (A)

double Vpbe_getSolventDiel Vpbe   thee
 

Get solvent dielectric constant.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Solvent dielectric constant

double Vpbe_getSolventRadius Vpbe   thee
 

Get solvent molecule radius.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Solvent molecule radius (A)

double Vpbe_getTemperature Vpbe   thee
 

Get temperature.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Temperature (K)

Vacc* Vpbe_getVacc Vpbe   thee
 

Get accessibility oracle.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Pointer to internal Vacc object

Valist* Vpbe_getValist Vpbe   thee
 

Get atom list.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Pointer to internal Valist object

double Vpbe_getXkappa Vpbe   thee
 

Get Debye-Huckel parameter.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Bulk Debye-Huckel parameter (Å)

double Vpbe_getZkappa2 Vpbe   thee
 

Get modified squared Debye-Huckel parameter.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
Modified squared Debye-Huckel parameter ( )

double Vpbe_getZmagic Vpbe   thee
 

Get charge scaling factor.

Author:
Nathan Baker and Mike Holst
Parameters:
thee  Vpbe object
Returns:
Get factor for scaling charges (in e) to internal units

int Vpbe_memChk Vpbe   thee
 

Return the memory used by this structure (and its contents) in bytes.

Author:
Nathan Baker
Parameters:
thee  Vpbe object
Returns:
The memory used by this structure and its contents in bytes


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