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* @brief The Poisson-Boltzmann master class
*
* Contains objects and parameters used in every PBE calculation,
* regardless of method.
*
*/
/**
* @file vpbe.h
* @ingroup Vpbe
* @brief Contains declarations for class Vpbe
* @version $Id$
* @author Nathan A. Baker
*
* @attention
* @verbatim
*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnnl.gov)
* Pacific Northwest National Laboratory
*
* Additional contributing authors listed in the code documentation.
*
* Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the
* Pacific Northwest National Laboratory, operated by Battelle Memorial
* Institute, Pacific Northwest Division for the U.S. Department of Energy.
*
* Portions Copyright (c) 2002-2010, Washington University in St. Louis.
* Portions Copyright (c) 2002-2010, Nathan A. Baker.
* Portions Copyright (c) 1999-2002, The Regents of the University of
* California.
* Portions Copyright (c) 1995, Michael Holst.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* Neither the name of the developer nor the names of its contributors may be
* used to endorse or promote products derived from this software without
* specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
* THE POSSIBILITY OF SUCH DAMAGE.
*
* @endverbatim
*/
#ifndef _VPBE_H_
#define _VPBE_H_
#include "apbscfg.h"
#include "maloc/maloc.h"
#include "generic/vhal.h"
#include "generic/vunit.h"
#include "generic/vatom.h"
#include "generic/vacc.h"
#include "generic/vclist.h"
/**
* @ingroup Vpbe
* @author Nathan Baker
* @brief Contains public data members for Vpbe class/module
*/
struct sVpbe {
Vmem *vmem; /**< Memory management object */
Valist *alist; /**< Atom (charge) list */
Vclist *clist; /**< Atom location cell list */
Vacc *acc; /**< Accessibility object */
double T; /**< Temperature (K) */
double soluteDiel; /**< Solute dielectric constant (unitless) */
double solventDiel; /**< Solvent dielectric constant (unitless) */
double solventRadius;
/**< Solvent probe radius (angstroms) for accessibility;
* determining defining volumes for the dielectric
* coefficient */
double bulkIonicStrength; /**< Bulk ionic strength (M) */
double maxIonRadius; /**< Max ion radius (A; used for calculating
* accessiblity and defining volumes for ionic
* strength coeffcients) */
int numIon; /**< Total number of ion species */
double ionConc[MAXION]; /**< Concentration (M) of each species */
double ionRadii[MAXION]; /**< Ionic radius (A) of each species */
double ionQ[MAXION]; /**< Charge (e) of each species */
double xkappa; /**< Debye-Huckel parameter (bulk) */
double deblen; /**< Debye length (bulk) */
double zkappa2; /**< Square of modified Debye-Huckel parameter (bulk) */
double zmagic; /**< Delta function scaling parameter */
double soluteCenter[3]; /**< Center of solute molecule (A) */
double soluteRadius; /**< Radius of solute molecule (A) */
double soluteXlen; /**< Solute length in x-direction */
double soluteYlen; /**< Solute length in y-direction */
double soluteZlen; /**< Solute length in z-direction */
double soluteCharge; /**< Charge of solute molecule (e) */
double smvolume; /**< Size-Modified PBE relative volume */
double smsize; /**< Size-Modified PBE size */
int ipkey; /**< PBE calculation type (this is a cached copy
* it should not be used directly in code) */
int paramFlag; /**< Check to see if the parameters have been set */
/*-------------------------------------------------------*/
/* Added by Michael Grabe */
/*-------------------------------------------------------*/
double z_mem; /**< Z value of the botton of the membrane (A) */
double L; /**< Length of the membrane (A) */
double membraneDiel; /**< Membrane dielectric constant */
double V; /**< Membrane potential */
int param2Flag; /**< Check to see if bcfl=3 parms have been set */
/*-------------------------------------------------------*/
};
/**
* @ingroup Vpbe
* @brief Declaration of the Vpbe class as the Vpbe structure
*/
typedef struct sVpbe Vpbe;
/* ///////////////////////////////////////////////////////////////////////////
// Class Vpbe: Inlineable methods (vpbe.c)
/////////////////////////////////////////////////////////////////////////// */
#if !defined(VINLINE_VPBE)
/** @brief Get atom list
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Pointer to internal Valist object
*/
VEXTERNC Valist* Vpbe_getValist(Vpbe *thee);
/** @brief Get accessibility oracle
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Pointer to internal Vacc object
*/
VEXTERNC Vacc* Vpbe_getVacc(Vpbe *thee);
/** @brief Get bulk ionic strength
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Bulk ionic strength (M)
*/
VEXTERNC double Vpbe_getBulkIonicStrength(Vpbe *thee);
/** @brief Get maximum radius of ion species
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Maximum radius (A)
*/
VEXTERNC double Vpbe_getMaxIonRadius(Vpbe *thee);
/** @brief Get temperature
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Temperature (K)
*/
VEXTERNC double Vpbe_getTemperature(Vpbe *thee);
/** @brief Get solute dielectric constant
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Solute dielectric constant
*/
VEXTERNC double Vpbe_getSoluteDiel(Vpbe *thee);
/** @brief Get apolar coefficient
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Apolar coefficent (kJ/mol/A^2)
*/
VEXTERNC double Vpbe_getGamma(Vpbe *thee);
/** @brief Get sphere radius which bounds biomolecule
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Sphere radius which bounds biomolecule (A)
*/
VEXTERNC double Vpbe_getSoluteRadius(Vpbe *thee);
/** @brief Get length of solute in x dimension
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Length of solute in x dimension (A)
*/
VEXTERNC double Vpbe_getSoluteXlen(Vpbe *thee);
/** @brief Get length of solute in y dimension
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Length of solute in y dimension (A)
*/
VEXTERNC double Vpbe_getSoluteYlen(Vpbe *thee);
/** @brief Get length of solute in z dimension
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Length of solute in z dimension (A)
*/
VEXTERNC double Vpbe_getSoluteZlen(Vpbe *thee);
/** @brief Get coordinates of solute center
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Pointer to 3*double array with solute center coordinates (A)
*/
VEXTERNC double* Vpbe_getSoluteCenter(Vpbe *thee);
/** @brief Get total solute charge
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Total solute charge (e)
*/
VEXTERNC double Vpbe_getSoluteCharge(Vpbe *thee);
/** @brief Get solvent dielectric constant
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Solvent dielectric constant
*/
VEXTERNC double Vpbe_getSolventDiel(Vpbe *thee);
/** @brief Get solvent molecule radius
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Solvent molecule radius (A)
*/
VEXTERNC double Vpbe_getSolventRadius(Vpbe *thee);
/** @brief Get Debye-Huckel parameter
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Bulk Debye-Huckel parameter (Å)
*/
VEXTERNC double Vpbe_getXkappa(Vpbe *thee);
/** @brief Get Debye-Huckel screening length
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Debye-Huckel screening length (Å)
*/
VEXTERNC double Vpbe_getDeblen(Vpbe *thee);
/** @brief Get modified squared Debye-Huckel parameter
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Modified squared Debye-Huckel parameter (\f$\AA^{-2}\f$)
*/
VEXTERNC double Vpbe_getZkappa2(Vpbe *thee);
/** @brief Get charge scaling factor
* @ingroup Vpbe
* @author Nathan Baker and Mike Holst
* @param thee Vpbe object
* @return Get factor for scaling charges (in e) to internal units
*/
VEXTERNC double Vpbe_getZmagic(Vpbe *thee);
/*--------------------------------------------------------------*/
/* Added by Michael Grabe */
/*--------------------------------------------------------------*/
/** @brief Get z position of the membrane bottom
* @ingroup Vpbe
* @author Michael Grabe
* @param thee Vpbe object
* @return z value of membrane (A)
*/
VEXTERNC double Vpbe_getzmem(Vpbe *thee);
/** @brief Get length of the membrane (A)
* @ingroup Vpbe
* aauthor Michael Grabe
* @param thee Vpbe object
* @return Length of the membrane (A)
*/
VEXTERNC double Vpbe_getLmem(Vpbe *thee);
/** @brief Get membrane dielectric constant
* @ingroup Vpbe
* @author Michael Grabe
* @param thee Vpbe object
* @return Membrane dielectric constant
*/
VEXTERNC double Vpbe_getmembraneDiel(Vpbe *thee);
/** @brief Get membrane potential (kT)
* @ingroup Vpbe
* @author Michael Grabe
* @param thee Vpbe object
*/
VEXTERNC double Vpbe_getmemv(Vpbe *thee);
/*--------------------------------------------------------------*/
#else /* if defined(VINLINE_VPBE) */
# define Vpbe_getValist(thee) ((thee)->alist)
# define Vpbe_getVacc(thee) ((thee)->acc)
# define Vpbe_getBulkIonicStrength(thee) ((thee)->bulkIonicStrength)
# define Vpbe_getTemperature(thee) ((thee)->T)
# define Vpbe_getSoluteDiel(thee) ((thee)->soluteDiel)
# define Vpbe_getSoluteCenter(thee) ((thee)->soluteCenter)
# define Vpbe_getSoluteRadius(thee) ((thee)->soluteRadius)
# define Vpbe_getSoluteXlen(thee) ((thee)->soluteXlen)
# define Vpbe_getSoluteYlen(thee) ((thee)->soluteYlen)
# define Vpbe_getSoluteZlen(thee) ((thee)->soluteZlen)
# define Vpbe_getSoluteCharge(thee) ((thee)->soluteCharge)
# define Vpbe_getSolventDiel(thee) ((thee)->solventDiel)
# define Vpbe_getSolventRadius(thee) ((thee)->solventRadius)
# define Vpbe_getMaxIonRadius(thee) ((thee)->maxIonRadius)
# define Vpbe_getXkappa(thee) ((thee)->xkappa)
# define Vpbe_getDeblen(thee) ((thee)->deblen)
# define Vpbe_getZkappa2(thee) ((thee)->zkappa2)
# define Vpbe_getZmagic(thee) ((thee)->zmagic)
/*------------------------------------------------------------*/
/* Added by Michael Grabe */
/*------------------------------------------------------------*/
# define Vpbe_getzmem(thee) ((thee)->z_mem)
# define Vpbe_getLmem(thee) ((thee)->L)
# define Vpbe_getmembraneDiel(thee) ((thee)->membraneDiel)
# define Vpbe_getmemv(thee) ((thee)->V)
/*------------------------------------------------------------*/
#endif /* if !defined(VINLINE_VPBE) */
/* ///////////////////////////////////////////////////////////////////////////
// Class Vpbe: Non-Inlineable methods (vpbe.c)
/////////////////////////////////////////////////////////////////////////// */
/** @brief Construct Vpbe object
* @ingroup Vpbe
* @author Nathan Baker and Mike Holst and Michael Grabe
* @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:
* \f[ \kappa^2 = \frac{8 \pi N_A e_c^2 I_s}{1000 \epsilon_w k_B T}
* \f]
* where the units are esu*esu/erg/mol. To obtain \f$\AA^{-2}\f$, we
* multiply by \f$10^{-16}\f$. Thus, in \f$\AA^{-2}\f$, where
* \f$k_B\f$ and \f$e_c\f$ are in gaussian rather than mks units, the
* proper value for kappa is:
* \f[ \kappa^2 = \frac{8 \pi N_A e_c^2 I_s}{1000 \epsilon_w k_b T}
* \times 10^{-16} \f]
* and the factor of \f$10^{-16}\f$ 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 \f$I_s\f$ is assumed to have
* been provided in moles per liter, which is moles per 1000 cm^3.
* @return Pointer to newly allocated Vpbe object
*/
VEXTERNC Vpbe* Vpbe_ctor(
Valist *alist, /**< Atom list */
int ionNum, /**< Number of counterion species */
double *ionConc, /**< Array containing counterion concentrations (M) */
double *ionRadii, /**< Array containing counterion radii (A) */
double *ionQ, /**< Array containing counterion charges (e) */
double T, /**< Temperature for Boltzmann distribution (K) */
double soluteDiel, /**< Solute internal dielectric constant */
double solventDiel, /**< Solvent dielectric constant */
double solventRadius, /**< Solvent probe radius for surfaces that use it (A) */
int focusFlag, /**< 1 if focusing operation, 0 otherwise */
double sdens, /**< Vacc sphere density */
double z_mem, /**< Membrane location (A) */
double L, /**< Membrane thickness (A) */
double membraneDiel, /**< Membrane dielectric constant */
double V /**< Transmembrane potential (V) */
);
/** @brief FORTRAN stub to construct Vpbe objct
* @ingroup Vpbe
* @author Nathan Baker and Mike Holst and Michael Grabe
* @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:
* \f[ \kappa^2 = \frac{8 \pi N_A e_c^2 I_s}{1000 eps_w k_B T} \f]
* where the units are esu*esu/erg/mol. To obtain \f$\AA^{-2}\f$, we
* multiply by \f$10^{-16}\f$.
* Thus, in \f$\AA^{-2}\f$, where \f$k_B\f$ and \f$e_c\f$ are in
* gaussian rather than mks units, the proper value for kappa is:
* \f[ \kappa^2 = \frac{8 pi N_A e_c^2 I_s}{1000 eps_w k_b T} \times
* 10^{-16} \f]
* and the factor of \f$10^{-16}\f$ 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 \f$I_s\f$ is assumed to have
* been provided in moles per liter, which is moles per 1000 cm^3.
* @bug The focusing flag is currently not used!!
* @return 1 if successful, 0 otherwise
*/
VEXTERNC int Vpbe_ctor2(
Vpbe *thee, /**< Pointer to memory allocated for Vpbe object */
Valist *alist, /**< Atom list */
int ionNum, /**< Number of counterion species */
double *ionConc, /**< Array containing counterion concentrations (M) */
double *ionRadii, /**< Array containing counterion radii (A) */
double *ionQ, /**< Array containing counterion charges (e) */
double T, /**< Temperature for Boltzmann distribution (K) */
double soluteDiel, /**< Solute internal dielectric constant */
double solventDiel, /**< Solvent dielectric constant */
double solventRadius, /**< Solvent probe radius for surfaces that use it (A) */
int focusFlag, /**< 1 if focusing operation, 0 otherwise */
double sdens, /**< Vacc sphere density */
double z_mem, /**< Membrane location (A) */
double L, /**< Membrane thickness (A) */
double membraneDiel, /**< Membrane dielectric constant */
double V /**< Transmembrane potential (V) */
);
/** @brief Get information about the counterion species present
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Pointer to Vpbe object
* @param nion Set to the number of counterion species
* @param ionConc Array to store counterion species' concentrations (M)
* @param ionRadii Array to store counterion species' radii (A)
* @param ionQ Array to store counterion species' charges (e)
* @return Number of ions
*/
VEXTERNC int Vpbe_getIons(Vpbe *thee, int *nion, double ionConc[MAXION],
double ionRadii[MAXION], double ionQ[MAXION]);
/** @brief Object destructor
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Pointer to memory location of object to be destroyed
*/
VEXTERNC void Vpbe_dtor(Vpbe **thee);
/** @brief FORTRAN stub object destructor
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Pointer to object to be destroyed
*/
VEXTERNC void Vpbe_dtor2(Vpbe *thee);
/** @brief 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.
*
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return Coulombic energy in units of \f$k_B T\f$.
*/
VEXTERNC double Vpbe_getCoulombEnergy1(Vpbe *thee);
/** @brief Return the memory used by this structure (and its contents)
* in bytes
* @ingroup Vpbe
* @author Nathan Baker
* @param thee Vpbe object
* @return The memory used by this structure and its contents in bytes
*/
VEXTERNC unsigned long int Vpbe_memChk(Vpbe *thee);
#endif /* ifndef _VPBE_H_ */
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