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. | |
Contains objects and parameters used in every PBE calculation, regardless of method.
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Construct Vpbe object.
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FORTRAN stub to construct Vpbe objct.
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Object destructor.
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FORTRAN stub object destructor.
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Get bulk ionic strength.
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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.
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Get Debye-Huckel screening length.
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Get apolar coefficient.
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Get information about the counterion species present.
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Get maximum radius of ion species.
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Get coordinates of solute center.
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Get total solute charge.
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Get solute dielectric constant.
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Get sphere radius which bounds biomolecule.
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Get length of solute in x dimension.
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Get length of solute in y dimension.
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Get length of solute in z dimension.
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Get solvent dielectric constant.
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Get solvent molecule radius.
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Get temperature.
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Get accessibility oracle.
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Get atom list.
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Get Debye-Huckel parameter.
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Get modified squared Debye-Huckel parameter.
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Get charge scaling factor.
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Return the memory used by this structure (and its contents) in bytes.
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1.3.5