#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 dependency graph for vacc.h:
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Go to the source code of this file.
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. | |
| VaccSurf * | VaccSurf_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. | |
| VaccSurf * | VaccSurf_refSphere (Vmem *mem, int npts) |
| Set up an array of points for a reference sphere of unit radius. | |
| VaccSurf * | Vacc_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. | |
| Vacc * | Vacc_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). | |
| 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). | |
| VaccSurf * | Vacc_atomSASPoints (Vacc *thee, double radius, Vatom *atom) |
| Get the set of points for this atom's solvent-accessible surface. | |
* * 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) 2002-2005. 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 * *
1.3.5