APBS  1.5
vacc.h File Reference

Contains declarations for class Vacc. More...

#include "apbscfg.h"
#include "maloc/maloc.h"
#include "mc/mc.h"
#include "generic/vhal.h"
#include "generic/valist.h"
#include "generic/vclist.h"
#include "generic/vatom.h"
#include "generic/vunit.h"
#include "generic/apolparm.h"
Include dependency graph for vacc.h:
This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Data Structures

struct  sVaccSurf
 Surface object list of per-atom surface points. More...
 
struct  sVacc
 Oracle for solvent- and ion-accessibility around a biomolecule. More...
 

Typedefs

typedef struct sVaccSurf VaccSurf
 Declaration of the VaccSurf class as the VaccSurf structure.
 
typedef struct sVacc Vacc
 Declaration of the Vacc class as the Vacc structure.
 

Functions

VEXTERNC unsigned long int Vacc_memChk (Vacc *thee)
 Get number of bytes in this object and its members. More...
 
VEXTERNC VaccSurfVaccSurf_ctor (Vmem *mem, double probe_radius, int nsphere)
 Allocate and construct the surface object; do not assign surface points to positions. More...
 
VEXTERNC int VaccSurf_ctor2 (VaccSurf *thee, Vmem *mem, double probe_radius, int nsphere)
 Construct the surface object using previously allocated memory; do not assign surface points to positions. More...
 
VEXTERNC void VaccSurf_dtor (VaccSurf **thee)
 Destroy the surface object and free its memory. More...
 
VEXTERNC void VaccSurf_dtor2 (VaccSurf *thee)
 Destroy the surface object. More...
 
VEXTERNC VaccSurfVaccSurf_refSphere (Vmem *mem, int npts)
 Set up an array of points for a reference sphere of unit radius. More...
 
VEXTERNC VaccSurfVacc_atomSurf (Vacc *thee, Vatom *atom, VaccSurf *ref, double probe_radius)
 Set up an array of points corresponding to the SAS due to a particular atom. More...
 
VEXTERNC VaccVacc_ctor (Valist *alist, Vclist *clist, double surf_density)
 Construct the accessibility object. More...
 
VEXTERNC int Vacc_ctor2 (Vacc *thee, Valist *alist, Vclist *clist, double surf_density)
 FORTRAN stub to construct the accessibility object. More...
 
VEXTERNC void Vacc_dtor (Vacc **thee)
 Destroy object. More...
 
VEXTERNC void Vacc_dtor2 (Vacc *thee)
 FORTRAN stub to destroy object. More...
 
VEXTERNC double Vacc_vdwAcc (Vacc *thee, double center[VAPBS_DIM])
 Report van der Waals accessibility. More...
 
VEXTERNC double Vacc_ivdwAcc (Vacc *thee, double center[VAPBS_DIM], double radius)
 Report inflated van der Waals accessibility. More...
 
VEXTERNC double Vacc_molAcc (Vacc *thee, double center[VAPBS_DIM], double radius)
 Report molecular accessibility. More...
 
VEXTERNC double Vacc_fastMolAcc (Vacc *thee, double center[VAPBS_DIM], double radius)
 Report molecular accessibility quickly. More...
 
VEXTERNC double Vacc_splineAcc (Vacc *thee, double center[VAPBS_DIM], double win, double infrad)
 Report spline-based accessibility. More...
 
VEXTERNC void Vacc_splineAccGrad (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, double *grad)
 Report gradient of spline-based accessibility. More...
 
VEXTERNC double Vacc_splineAccAtom (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom)
 Report spline-based accessibility for a given atom. More...
 
VEXTERNC void Vacc_splineAccGradAtomUnnorm (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *force)
 Report gradient of spline-based accessibility with respect to a particular atom (see Vpmg_splineAccAtom) More...
 
VEXTERNC void Vacc_splineAccGradAtomNorm (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *force)
 Report gradient of spline-based accessibility with respect to a particular atom normalized by the accessibility value due to that atom at that point (see Vpmg_splineAccAtom) More...
 
VEXTERNC void Vacc_splineAccGradAtomNorm4 (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *force)
 Report gradient of spline-based accessibility with respect to a particular atom normalized by a 4th order accessibility value due to that atom at that point (see Vpmg_splineAccAtom) More...
 
VEXTERNC void Vacc_splineAccGradAtomNorm3 (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *force)
 Report gradient of spline-based accessibility with respect to a particular atom normalized by a 3rd order accessibility value due to that atom at that point (see Vpmg_splineAccAtom) More...
 
VEXTERNC double Vacc_SASA (Vacc *thee, double radius)
 Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area. More...
 
VEXTERNC double Vacc_totalSASA (Vacc *thee, double radius)
 Return the total solvent accessible surface area (SASA) More...
 
VEXTERNC double Vacc_atomSASA (Vacc *thee, double radius, Vatom *atom)
 Return the atomic solvent accessible surface area (SASA) More...
 
VEXTERNC VaccSurfVacc_atomSASPoints (Vacc *thee, double radius, Vatom *atom)
 Get the set of points for this atom's solvent-accessible surface. More...
 
VEXTERNC void Vacc_atomdSAV (Vacc *thee, double radius, Vatom *atom, double *dSA)
 Get the derivatve of solvent accessible volume. More...
 
VEXTERNC void Vacc_atomdSASA (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA)
 Get the derivatve of solvent accessible area. More...
 
VEXTERNC void Vacc_totalAtomdSASA (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA)
 Testing purposes only. More...
 
VEXTERNC void Vacc_totalAtomdSAV (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA, Vclist *clist)
 Total solvent accessible volume. More...
 
VEXTERNC double Vacc_totalSAV (Vacc *thee, Vclist *clist, APOLparm *apolparm, double radius)
 Return the total solvent accessible volume (SAV) More...
 
VEXTERNC int Vacc_wcaEnergy (Vacc *thee, APOLparm *apolparm, Valist *alist, Vclist *clist)
 Return the WCA integral energy. More...
 
VEXTERNC int Vacc_wcaForceAtom (Vacc *thee, APOLparm *apolparm, Vclist *clist, Vatom *atom, double *force)
 Return the WCA integral force. More...
 
VEXTERNC int Vacc_wcaEnergyAtom (Vacc *thee, APOLparm *apolparm, Valist *alist, Vclist *clist, int iatom, double *value)
 Calculate the WCA energy for an atom. More...
 

Detailed Description

Contains declarations for class Vacc.

Version
$Id$
Author
Nathan A. Baker
Attention
*
* 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) 2010-2014 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
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* 

Definition in file vacc.h.