#include "maloc/maloc.h"
#include "apbs/vhal.h"
#include "apbs/valist.h"
#include "apbs/vatom.h"
#include "apbs/vunit.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 | 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. | |
Vacc * | Vacc_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. | |
Vacc * | Vacc_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. |
* * 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 * *