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
Valist *	Vpbe_getValist (Vpbe *thee)
	Get atom list.
Vacc *	Vpbe_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, double sdens)
	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, double sdens)
	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.
unsigned long 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,

double sdens

)

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:
$\kappa^2 = \frac{8 \pi N_A e_c^2 I_s}{1000 \epsilon_w k_B T}$
where the units are esu*esu/erg/mol. To obtain $\AA^{-2}$ , we multiply by $10^{-16}$ . Thus, in $\AA^{-2}$ , where $k_B$ and $e_c$ are in gaussian rather than mks units, the proper value for kappa is:
$\kappa^2 = \frac{8 \pi N_A e_c^2 I_s}{1000 \epsilon_w k_b T} \times 10^{-16}$
and the factor of $10^{-16}$ 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 $I_s$ 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

sdens Vacc sphere density

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,

double sdens

)

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:
$\kappa^2 = \frac{8 \pi N_A e_c^2 I_s}{1000 eps_w k_B T}$
where the units are esu*esu/erg/mol. To obtain $\AA^{-2}$ , we multiply by $10^{-16}$ . Thus, in $\AA^{-2}$ , where $k_B$ and $e_c$ are in gaussian rather than mks units, the proper value for kappa is:
$\kappa^2 = \frac{8 pi N_A e_c^2 I_s}{1000 eps_w k_b T} \times 10^{-16}$
and the factor of $10^{-16}$ 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 $I_s$ 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

Bug:
The focusing flag is currently not used!!

Parameters:

sdens Vacc sphere density

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 $k_B T$ .

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 ( $\AA^{-2}$ )

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

unsigned long 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

Generated on Tue Dec 6 10:05:59 2005 for APBS by

1.3.5

Vpbe class

Files

Data Structures

Typedefs

Functions

Detailed Description

Function Documentation