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vpbe.h File Reference

Contains declarations for class Vpbe. More...

#include "maloc/maloc.h"
#include "apbs/vhal.h"
#include "apbs/vunit.h"
#include "apbs/vatom.h"
#include "apbs/vacc.h"
#include "apbs/vclist.h"

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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.

VpbeVpbe_ctor (Valist *alist, int ionNum, double *ionConc, double *ionRadii, double *ionQ, double T, 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 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

Contains declarations for class Vpbe.

Version:
Id
vpbe.h 1103 2007-07-05 21:06:44Z sdg0919
Author:
Nathan A. Baker
Attention:
 *
 * APBS -- Adaptive Poisson-Boltzmann Solver
 *
 * Nathan A. Baker (baker@biochem.wustl.edu)
 * Dept. of Biochemistry and Molecular Biophysics
 * Center for Computational Biology
 * Washington University in St. Louis
 *
 * Additional contributing authors listed in the code documentation.
 *
 * Copyright (c) 2002-2007.  Washington University in St. Louis.
 * All Rights Reserved.
 * Portions Copyright (c) 1999-2002.  The Regents of the University of
 * California.  
 * Portions Copyright (c) 1995.  Michael Holst.
 *
 * This file is part of APBS.
 *
 * APBS is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
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 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
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 * along with APBS; if not, write to the Free Software
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 *
 * Linking APBS statically or dynamically with other modules is making a
 * combined work based on APBS. Thus, the terms and conditions of the GNU
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 * In addition, as a special exception, the copyright holders of APBS
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