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 | |
| VEXTERNC Valist * | Vpbe_getValist (Vpbe *thee) |
| Get atom list. | |
| VEXTERNC Vacc * | Vpbe_getVacc (Vpbe *thee) |
| Get accessibility oracle. | |
| VEXTERNC double | Vpbe_getBulkIonicStrength (Vpbe *thee) |
| Get bulk ionic strength. | |
| VEXTERNC double | Vpbe_getMaxIonRadius (Vpbe *thee) |
| Get maximum radius of ion species. | |
| VEXTERNC double | Vpbe_getTemperature (Vpbe *thee) |
| Get temperature. | |
| VEXTERNC double | Vpbe_getSoluteDiel (Vpbe *thee) |
| Get solute dielectric constant. | |
| VEXTERNC double | Vpbe_getGamma (Vpbe *thee) |
| Get apolar coefficient. | |
| VEXTERNC double | Vpbe_getSoluteRadius (Vpbe *thee) |
| Get sphere radius which bounds biomolecule. | |
| VEXTERNC double | Vpbe_getSoluteXlen (Vpbe *thee) |
| Get length of solute in x dimension. | |
| VEXTERNC double | Vpbe_getSoluteYlen (Vpbe *thee) |
| Get length of solute in y dimension. | |
| VEXTERNC double | Vpbe_getSoluteZlen (Vpbe *thee) |
| Get length of solute in z dimension. | |
| VEXTERNC double * | Vpbe_getSoluteCenter (Vpbe *thee) |
| Get coordinates of solute center. | |
| VEXTERNC double | Vpbe_getSoluteCharge (Vpbe *thee) |
| Get total solute charge. | |
| VEXTERNC double | Vpbe_getSolventDiel (Vpbe *thee) |
| Get solvent dielectric constant. | |
| VEXTERNC double | Vpbe_getSolventRadius (Vpbe *thee) |
| Get solvent molecule radius. | |
| VEXTERNC double | Vpbe_getXkappa (Vpbe *thee) |
| Get Debye-Huckel parameter. | |
| VEXTERNC double | Vpbe_getDeblen (Vpbe *thee) |
| Get Debye-Huckel screening length. | |
| VEXTERNC double | Vpbe_getZkappa2 (Vpbe *thee) |
| Get modified squared Debye-Huckel parameter. | |
| VEXTERNC double | Vpbe_getZmagic (Vpbe *thee) |
| Get charge scaling factor. | |
| VEXTERNC double | Vpbe_getzmem (Vpbe *thee) |
| Get z position of the membrane bottom. | |
| VEXTERNC double | Vpbe_getLmem (Vpbe *thee) |
| Get length of the membrane (A)aauthor Michael Grabe. | |
| VEXTERNC double | Vpbe_getmembraneDiel (Vpbe *thee) |
| Get membrane dielectric constant. | |
| VEXTERNC double | Vpbe_getmemv (Vpbe *thee) |
| Get membrane potential (kT) | |
| VEXTERNC 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. | |
| VEXTERNC 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. | |
| VEXTERNC int | Vpbe_getIons (Vpbe *thee, int *nion, double ionConc[MAXION], double ionRadii[MAXION], double ionQ[MAXION]) |
| Get information about the counterion species present. | |
| VEXTERNC void | Vpbe_dtor (Vpbe **thee) |
| Object destructor. | |
| VEXTERNC void | Vpbe_dtor2 (Vpbe *thee) |
| FORTRAN stub object destructor. | |
| VEXTERNC double | Vpbe_getCoulombEnergy1 (Vpbe *thee) |
| Calculate coulombic energy of set of charges. | |
| VEXTERNC unsigned long int | Vpbe_memChk (Vpbe *thee) |
| Return the memory used by this structure (and its contents) in bytes. | |
The Poisson-Boltzmann master class.
Contains objects and parameters used in every PBE calculation, regardless of method.
| VEXTERNC 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.
, we multiply by
. Thus, in
, where
and
are in gaussian rather than mks units, the proper value for kappa is:
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. | alist | Atom list |
| ionNum | Number of counterion species |
| ionConc | Array containing counterion concentrations (M) |
| ionRadii | Array containing counterion radii (A) |
| ionQ | Array containing counterion charges (e) |
| T | Temperature for Boltzmann distribution (K) |
| soluteDiel | Solute internal dielectric constant |
| solventDiel | Solvent dielectric constant |
| solventRadius | Solvent probe radius for surfaces that use it (A) |
| focusFlag | 1 if focusing operation, 0 otherwise |
| sdens | Vacc sphere density |
| z_mem | Membrane location (A) |
| L | Membrane thickness (A) |
| membraneDiel | Membrane dielectric constant |
| V | Transmembrane potential (V) |
| VEXTERNC 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.
, we multiply by
. Thus, in
, where
and
are in gaussian rather than mks units, the proper value for kappa is:
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. | thee | Pointer to memory allocated for Vpbe object |
| alist | Atom list |
| ionNum | Number of counterion species |
| ionConc | Array containing counterion concentrations (M) |
| ionRadii | Array containing counterion radii (A) |
| ionQ | Array containing counterion charges (e) |
| T | Temperature for Boltzmann distribution (K) |
| soluteDiel | Solute internal dielectric constant |
| solventDiel | Solvent dielectric constant |
| solventRadius | Solvent probe radius for surfaces that use it (A) |
| focusFlag | 1 if focusing operation, 0 otherwise |
| sdens | Vacc sphere density |
| z_mem | Membrane location (A) |
| L | Membrane thickness (A) |
| membraneDiel | Membrane dielectric constant |
| V | Transmembrane potential (V) |
Definition at line 257 of file vpbe.c.

| VEXTERNC void Vpbe_dtor | ( | Vpbe ** | thee ) |
| VEXTERNC void Vpbe_dtor2 | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getBulkIonicStrength | ( | Vpbe * | thee ) |
| VEXTERNC 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.
| thee | Vpbe object |
. Definition at line 474 of file vpbe.c.

| VEXTERNC double Vpbe_getDeblen | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getGamma | ( | Vpbe * | thee ) |
Get apolar coefficient.
| thee | Vpbe object |
| VEXTERNC int Vpbe_getIons | ( | Vpbe * | thee, |
| int * | nion, | ||
| double | ionConc[MAXION], | ||
| double | ionRadii[MAXION], | ||
| double | ionQ[MAXION] | ||
| ) |
Get information about the counterion species present.
| 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) |
Definition at line 528 of file vpbe.c.

| VEXTERNC double Vpbe_getLmem | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getMaxIonRadius | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getmembraneDiel | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getmemv | ( | Vpbe * | thee ) |
| VEXTERNC double* Vpbe_getSoluteCenter | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getSoluteCharge | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getSoluteDiel | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getSoluteRadius | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getSoluteXlen | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getSoluteYlen | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getSoluteZlen | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getSolventDiel | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getSolventRadius | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getTemperature | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getXkappa | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getZkappa2 | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getZmagic | ( | Vpbe * | thee ) |
| VEXTERNC double Vpbe_getzmem | ( | Vpbe * | thee ) |
| VEXTERNC unsigned long int Vpbe_memChk | ( | Vpbe * | thee ) |
1.7.2