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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/vatom.h"
#include "apbs/vunit.h"

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Data Structures

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


Defines

#define VACCMAXNBOR   20
 Maximum number of neighbors used in an accessibility calculation.


Typedefs

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


Functions

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

VaccVacc_ctor (Valist *alist, double max_radius, int nx, int ny, int nz, int nsphere)
 Construct the accessibility object.

int Vacc_ctor2 (Vacc *thee, Valist *alist, double max_radius, int nx, int ny, int nz, int nsphere)
 FORTRAN stub to construct the accessibility object.

VaccVacc_ctorFocus (Valist *alist, double max_radius, int nx, int ny, int nz, int nsphere, double x_min, double y_min, double z_min, double x_max, double y_max, double z_max)
 FORTRAN stub to construct the accessibility object for a subdomain.

int Vacc_ctor2Focus (Vacc *thee, Valist *alist, double max_radius, int nx, int ny, int nz, int nsphere, double x_min, double y_min, double z_min, double x_max, double y_max, double z_max)
 FORTRAN stub to construct the accessibility object for a subdomain.

void Vacc_dtor (Vacc **thee)
 Destroy object.

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

double Vacc_vdwAcc (Vacc *thee, double center[3])
 Report van der Waals accessibility.

double Vacc_ivdwAcc (Vacc *thee, double center[3], double radius)
 Report inflated van der Waals accessibility.

double Vacc_molAcc (Vacc *thee, double center[3], double radius)
 Report molecular accessibility.

double Vacc_fastMolAcc (Vacc *thee, double center[3], double radius)
 Report molecular accessibility quickly.

double Vacc_splineAcc (Vacc *thee, double center[3], double win, double infrad)
 Report spline-based accessibility.

double Vacc_splineAccAtom (Vacc *thee, double center[3], double win, double infrad, int atomID)
 Report spline-based accessibility for a given atom.

void Vacc_splineAccGradAtom (Vacc *thee, double center[3], double win, double infrad, int atomID, 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).

double ** Vacc_sphere (Vacc *thee, int *npts)
 Set up an array of points for the reference sphere.

double Vacc_totalSASA (Vacc *thee, double radius)
 Calculates the solvent-accessible area of the entire molecules.

double Vacc_atomSASA (Vacc *thee, double radius, int iatom)
 Calculates the solvent-accessible area due to the specified atom.


Detailed Description

Contains declarations for class Vacc.

Version:
Id:
vacc.h,v 2.22 2004/01/19 21:01:37 apbs Exp
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) 2002-2004.  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
 *
 * 

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