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vacc.h File Reference

Contains declarations for class Vacc. More...

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

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Data Structures

struct  sVacc
 Oracle for solvent- and ion-accessibility around a biomolecule. More...

struct  sVaccSurf
 Surface object list of per-atom surface points. More...


Typedefs

typedef sVaccSurf VaccSurf
 Declaration of the VaccSurf class as the VaccSurf structure.

typedef sVacc Vacc
 Declaration of the Vacc class as the Vacc structure.


Functions

unsigned long int Vacc_memChk (Vacc *thee)
 Get number of bytes in this object and its members.

VaccSurfVaccSurf_ctor (Vmem *mem, double probe_radius, int nsphere)
 Allocate and construct the surface object; do not assign surface points to positions.

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.

void VaccSurf_dtor (VaccSurf **thee)
 Destroy the surface object and free its memory.

void VaccSurf_dtor2 (VaccSurf *thee)
 Destroy the surface object.

VaccSurfVaccSurf_refSphere (Vmem *mem, int npts)
 Set up an array of points for a reference sphere of unit radius.

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.

VaccVacc_ctor (Valist *alist, Vclist *clist, double surf_density)
 Construct the accessibility object.

int Vacc_ctor2 (Vacc *thee, Valist *alist, Vclist *clist, double surf_density)
 FORTRAN stub to construct the accessibility object.

void Vacc_dtor (Vacc **thee)
 Destroy object.

void Vacc_dtor2 (Vacc *thee)
 FORTRAN stub to destroy object.

double Vacc_vdwAcc (Vacc *thee, double center[VAPBS_DIM])
 Report van der Waals accessibility.

double Vacc_ivdwAcc (Vacc *thee, double center[VAPBS_DIM], double radius)
 Report inflated van der Waals accessibility.

double Vacc_molAcc (Vacc *thee, double center[VAPBS_DIM], double radius)
 Report molecular accessibility.

double Vacc_fastMolAcc (Vacc *thee, double center[VAPBS_DIM], double radius)
 Report molecular accessibility quickly.

double Vacc_splineAcc (Vacc *thee, double center[VAPBS_DIM], double win, double infrad)
 Report spline-based accessibility.

void Vacc_splineAccGrad (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, double *grad)
 Report gradient of spline-based accessibility.

double Vacc_splineAccAtom (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom)
 Report spline-based accessibility for a given atom.

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).

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).

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).

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).

double Vacc_SASA (Vacc *thee, double radius)
 Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area.

double Vacc_totalSASA (Vacc *thee, double radius)
 Return the total solvent accessible surface area (SASA).

double Vacc_atomSASA (Vacc *thee, double radius, Vatom *atom)
 Return the atomic solvent accessible surface area (SASA).

VaccSurfVacc_atomSASPoints (Vacc *thee, double radius, Vatom *atom)
 Get the set of points for this atom's solvent-accessible surface.

void Vacc_atomdSAV (Vacc *thee, double radius, Vatom *atom, double *dSA)
 Get the derivatve of solvent accessible volume.

void Vacc_atomdSASA (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA)
 Get the derivatve of solvent accessible area.

void Vacc_totalAtomdSASA (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA)
 Testing purposes only.

void Vacc_totalAtomdSAV (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA, Vclist *clist)
 Total solvent accessible volume.

double Vacc_totalSAV (Vacc *thee, Vclist *clist, APOLparm *apolparm, double radius)
 Return the total solvent accessible volume (SAV).

VPUBLIC int Vacc_wcaEnergy (Vacc *thee, APOLparm *apolparm, Valist *alist, Vclist *clist)
 Return the WCA integral energy.

VPUBLIC int Vacc_wcaForceAtom (Vacc *thee, APOLparm *apolparm, Vclist *clist, Vatom *atom, double *force)
 Return the WCA integral force.


Detailed Description

Contains declarations for class Vacc.

Version:
Id
vacc.h 1100 2007-06-25 17:02:52Z sobolevnrm
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.
 *
 * APBS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with APBS; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
 *
 * Linking APBS statically or dynamically with other modules is making a
 * combined work based on APBS. Thus, the terms and conditions of the GNU
 * General Public License cover the whole combination.
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 * SPECIAL GPL EXCEPTION
 * In addition, as a special exception, the copyright holders of APBS
 * give you permission to combine the APBS program with free software
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