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 | 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 | |
| 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). | |
| 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). | |
| VaccSurf * | Vacc_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 1366 2009-04-22 18:37:13Z sdg0919
- 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) 2002-2009, Washington University in St. Louis. * Portions Copyright (c) 2002-2009. 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 Washington University in St. Louis 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. * *
