APBS
1.4.1
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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"
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 VaccSurf * | VaccSurf_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 VaccSurf * | VaccSurf_refSphere (Vmem *mem, int npts) |
Set up an array of points for a reference sphere of unit radius. More... | |
VEXTERNC 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. More... | |
VEXTERNC Vacc * | Vacc_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 VaccSurf * | Vacc_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... | |
Contains declarations for class Vacc.
* * 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) 2010-2012 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 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF * THE POSSIBILITY OF SUCH DAMAGE. * *
Definition in file vacc.h.