Vpbe class

The Poisson-Boltzmann master class. More...

Data Structures
struct	sVpbe
	Contains public data members for Vpbe class/module. More...
Files
file	vpbe.h
	Contains declarations for class Vpbe.
file	vpbe.c
	Class Vpbe methods.
Typedefs
typedef struct 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.
double	Vpbe_getzmem (Vpbe *thee)
	Get z position of the membrane bottom.
double	Vpbe_getLmem (Vpbe *thee)
	Get length of the membrane (A)aauthor Michael Grabe.
double	Vpbe_getmembraneDiel (Vpbe *thee)
	Get membrane dielectric constant.
double	Vpbe_getmemv (Vpbe *thee)
	Get membrane potential (kT).
Vpbe *	Vpbe_ctor (Valist alist, int ionNum, double ionConc, double ionRadii, double ionQ, double T, double soluteDiel, double solventDiel, double solventRadius, int focusFlag, double sdens, double z_mem, double L, double membraneDiel, double V)
	Construct Vpbe object.
int	Vpbe_ctor2 (Vpbe thee, Valist alist, int ionNum, double ionConc, double ionRadii, double *ionQ, double T, double soluteDiel, double solventDiel, double solventRadius, int focusFlag, double sdens, double z_mem, double L, double membraneDiel, double V)
	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	soluteDiel,
		double	solventDiel,
		double	solventRadius,
		int	focusFlag,
		double	sdens,
		double	z_mem,
		double	L,
		double	membraneDiel,
		double	V
	)

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

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)
	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

Referenced by initMG().

int Vpbe_ctor2	(	Vpbe *	thee,
		Valist *	alist,
		int	ionNum,
		double *	ionConc,
		double *	ionRadii,
		double *	ionQ,
		double	T,
		double	soluteDiel,
		double	solventDiel,
		double	solventRadius,
		int	focusFlag,
		double	sdens,
		double	z_mem,
		double	L,
		double	membraneDiel,
		double	V
	)

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

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)
	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

References sVpbe::acc, sVpbe::alist, sVpbe::bulkIonicStrength, sValist::center, sVpbe::clist, CLIST_AUTO_DOMAIN, sVpbe::deblen, sVpbe::ionConc, sVpbe::ionQ, sVpbe::ionRadii, sVpbe::ipkey, MAXION, sVpbe::maxIonRadius, sVpbe::numIon, sVpbe::paramFlag, sVpbe::smsize, sVpbe::smvolume, sVpbe::soluteCenter, sVpbe::soluteCharge, sVpbe::soluteDiel, sVpbe::soluteRadius, sVpbe::soluteXlen, sVpbe::soluteYlen, sVpbe::soluteZlen, sVpbe::solventDiel, sVpbe::solventRadius, sVpbe::T, Vacc_ctor(), Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getCharge(), Vatom_getPosition(), Vatom_getRadius(), Vclist_ctor(), sVpbe::vmem, sVpbe::xkappa, sVpbe::zkappa2, and sVpbe::zmagic.

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void Vpbe_dtor ( Vpbe ** thee )

Object destructor.

Author:: Nathan Baker

Parameters:

thee

Pointer to memory location of object to be destroyed

References Vpbe_dtor2().

Referenced by initMG(), killFE(), and killMG().

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void Vpbe_dtor2 ( Vpbe * thee )

FORTRAN stub object destructor.

Author:: Nathan Baker

Parameters:

thee

Pointer to object to be destroyed

References sVpbe::acc, sVpbe::clist, Vacc_dtor(), Vclist_dtor(), and sVpbe::vmem.

Referenced by Vpbe_dtor().

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double Vpbe_getBulkIonicStrength ( Vpbe * thee )

Get bulk ionic strength.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Bulk ionic strength (M)

Referenced by fillcoCoefMap(), fillcoCoefMolIon(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), Vfetk_ctor2(), Vfetk_energy(), Vpmg_ctor2(), Vpmg_energy(), Vpmg_fillco(), Vpmg_ibForce(), and Vpmg_qmEnergySMPBE().

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 .

References Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getCharge(), Vatom_getPosition(), Vpbe_getSoluteDiel(), Vpbe_getTemperature(), Vpbe_getValist(), Vunit_ec, Vunit_eps0, Vunit_kb, and Vunit_pi.

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double Vpbe_getDeblen ( Vpbe * thee )

Get Debye-Huckel screening length.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Debye-Huckel screening length (Å)

Referenced by initMG().

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

References sVpbe::ionConc, sVpbe::ionQ, sVpbe::ionRadii, and sVpbe::numIon.

Referenced by Vfetk_ctor2(), Vpmg_ctor2(), Vpmg_ibForce(), and Vpmg_qmEnergySMPBE().

double Vpbe_getLmem ( Vpbe * thee )

Get length of the membrane (A)aauthor Michael Grabe.

Parameters:

thee

Vpbe object

Returns:: Length of the membrane (A)

Referenced by bcCalc().

double Vpbe_getMaxIonRadius ( Vpbe * thee )

Get maximum radius of ion species.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Maximum radius (A)

Referenced by fillcoCoefMolIon(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), and Vpmg_ibForce().

double Vpbe_getmembraneDiel ( Vpbe * thee )

Get membrane dielectric constant.

Author:: Michael Grabe

Parameters:

thee

Vpbe object

Returns:: Membrane dielectric constant

Referenced by bcCalc().

double Vpbe_getmemv ( Vpbe * thee )

Get membrane potential (kT).

Author:: Michael Grabe

Parameters:

thee

Vpbe object

Referenced by bcCalc().

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)

Referenced by focusFillBound().

double Vpbe_getSoluteCharge ( Vpbe * thee )

Get total solute charge.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Total solute charge (e)

Referenced by focusFillBound().

double Vpbe_getSoluteDiel ( Vpbe * thee )

Get solute dielectric constant.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Solute dielectric constant

Referenced by fillcoCoefMolDielNoSmooth(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), Vpbe_getCoulombEnergy1(), Vpmg_dbForce(), Vpmg_fillArray(), Vpmg_fillco(), and Vpmg_polarizEnergy().

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)

Referenced by focusFillBound().

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

Referenced by bcCalc(), fillcoCoefMolDielNoSmooth(), fillcoCoefMolDielSmooth(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), focusFillBound(), Vpmg_dbForce(), Vpmg_fillArray(), Vpmg_fillco(), Vpmg_polarizEnergy(), and Vpmg_solveLaplace().

double Vpbe_getSolventRadius ( Vpbe * thee )

Get solvent molecule radius.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Solvent molecule radius (A)

Referenced by fillcoCoefMolDielNoSmooth(), and Vpmg_dbForce().

double Vpbe_getTemperature ( Vpbe * thee )

Get temperature.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Temperature (K)

Referenced by focusFillBound(), Vpbe_getCoulombEnergy1(), Vpmg_dbForce(), and Vpmg_polarizEnergy().

Vacc* Vpbe_getVacc ( Vpbe * thee )

Get accessibility oracle.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Pointer to internal Vacc object

Referenced by Vpmg_fillArray().

Valist* Vpbe_getValist ( Vpbe * thee )

Get atom list.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Pointer to internal Valist object

Referenced by Vfetk_getAtomColor(), Vfetk_loadMesh(), and Vpbe_getCoulombEnergy1().

double Vpbe_getXkappa ( Vpbe * thee )

Get Debye-Huckel parameter.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Bulk Debye-Huckel parameter (Å)

Referenced by bcCalc(), and focusFillBound().

double Vpbe_getZkappa2 ( Vpbe * thee )

Get modified squared Debye-Huckel parameter.

Author:: Nathan Baker

Parameters:

thee

Vpbe object

Returns:: Modified squared Debye-Huckel parameter ( $\AA^{-2}$ )

Referenced by Vfetk_ctor2(), Vpmg_ctor2(), Vpmg_ibForce(), Vpmg_qmEnergySMPBE(), and Vpmg_solve().

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

Referenced by fillcoChargeMap(), fillcoChargeSpline1(), fillcoChargeSpline2(), fillcoPermanentMultipole(), Vfetk_PDE_delta(), Vfetk_PDE_Ju(), Vpmg_dbForce(), Vpmg_dielEnergy(), Vpmg_fillArray(), Vpmg_ibForce(), and Vpmg_qfEnergyVolume().

double Vpbe_getzmem ( Vpbe * thee )

Get z position of the membrane bottom.

Author:: Michael Grabe

Parameters:

thee

Vpbe object

Returns:: z value of membrane (A)

Referenced by bcCalc().

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

References sVpbe::acc, and Vacc_memChk().

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Vpbe class

Data Structures

Files

Typedefs

Functions

Detailed Description

Function Documentation