#include "apbscfg.h"
#include "apbs/vacc.h"
#include "apbs/apolparm.h"
#include "mc/mc.h"
Include dependency graph for vacc.c:
Functions | |
VPUBLIC unsigned long int | Vacc_memChk (Vacc *thee) |
Get number of bytes in this object and its members. | |
VPRIVATE int | ivdwAccExclus (Vacc *thee, double center[3], double radius, int atomID) |
Determines if a point is within the union of the spheres centered at the atomic centers with radii equal to the sum of their van der Waals radii and the probe radius. Does not include contributions from the specified atom. | |
VPUBLIC Vacc * | Vacc_ctor (Valist *alist, Vclist *clist, double surf_density) |
Construct the accessibility object. | |
VPRIVATE int | Vacc_storeParms (Vacc *thee, Valist *alist, Vclist *clist, double surf_density) |
VPRIVATE int | Vacc_allocate (Vacc *thee) |
VPUBLIC int | Vacc_ctor2 (Vacc *thee, Valist *alist, Vclist *clist, double surf_density) |
FORTRAN stub to construct the accessibility object. | |
VPUBLIC void | Vacc_dtor (Vacc **thee) |
Destroy object. | |
VPUBLIC void | Vacc_dtor2 (Vacc *thee) |
FORTRAN stub to destroy object. | |
VPUBLIC void | Vacc_splineAccGradAtomNorm (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *grad) |
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). | |
VPUBLIC void | Vacc_splineAccGradAtomUnnorm (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *grad) |
Report gradient of spline-based accessibility with respect to a particular atom (see Vpmg_splineAccAtom). | |
VPUBLIC double | Vacc_splineAccAtom (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom) |
Report spline-based accessibility for a given atom. | |
VPRIVATE double | splineAcc (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, VclistCell *cell) |
Fast spline-based surface computation subroutine. | |
VPUBLIC double | Vacc_splineAcc (Vacc *thee, double center[VAPBS_DIM], double win, double infrad) |
Report spline-based accessibility. | |
VPUBLIC void | Vacc_splineAccGrad (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, double *grad) |
Report gradient of spline-based accessibility. | |
VPUBLIC double | Vacc_molAcc (Vacc *thee, double center[VAPBS_DIM], double radius) |
Report molecular accessibility. | |
VPUBLIC double | Vacc_fastMolAcc (Vacc *thee, double center[VAPBS_DIM], double radius) |
Report molecular accessibility quickly. | |
VPUBLIC double | Vacc_SASA (Vacc *thee, double radius) |
Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area. | |
VPUBLIC double | Vacc_totalSASA (Vacc *thee, double radius) |
Return the total solvent accessible surface area (SASA). | |
VPUBLIC double | Vacc_atomSASA (Vacc *thee, double radius, Vatom *atom) |
Return the atomic solvent accessible surface area (SASA). | |
VPUBLIC VaccSurf * | VaccSurf_ctor (Vmem *mem, double probe_radius, int nsphere) |
Allocate and construct the surface object; do not assign surface points to positions. | |
VPUBLIC 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. | |
VPUBLIC void | VaccSurf_dtor (VaccSurf **thee) |
Destroy the surface object and free its memory. | |
VPUBLIC void | VaccSurf_dtor2 (VaccSurf *thee) |
Destroy the surface object. | |
VPUBLIC VaccSurf * | Vacc_atomSurf (Vacc *thee, Vatom *atom, VaccSurf *ref, double prad) |
Set up an array of points corresponding to the SAS due to a particular atom. | |
VPUBLIC VaccSurf * | VaccSurf_refSphere (Vmem *mem, int npts) |
Set up an array of points for a reference sphere of unit radius. | |
VPUBLIC VaccSurf * | Vacc_atomSASPoints (Vacc *thee, double radius, Vatom *atom) |
Get the set of points for this atom's solvent-accessible surface. | |
VPUBLIC void | Vacc_splineAccGradAtomNorm4 (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *grad) |
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). | |
VPUBLIC void | Vacc_splineAccGradAtomNorm3 (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *grad) |
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). | |
VPUBLIC void | Vacc_atomdSAV (Vacc *thee, double srad, Vatom *atom, double *dSA) |
Get the derivatve of solvent accessible volume. | |
VPUBLIC void | Vacc_atomdSASA (Vacc *thee, double dpos, double srad, Vatom *atom, double *dSA) |
Get the derivatve of solvent accessible area. | |
VPUBLIC void | Vacc_totalAtomdSASA (Vacc *thee, double dpos, double srad, Vatom *atom, double *dSA) |
Testing purposes only. | |
VPUBLIC void | Vacc_totalAtomdSAV (Vacc *thee, double dpos, double srad, Vatom *atom, double *dSA, Vclist *clist) |
Total solvent accessible volume. | |
VPUBLIC double | Vacc_totalSAV (Vacc *thee, Vclist *clist, APOLparm *apolparm, double radius) |
Return the total solvent accessible volume (SAV). | |
VPUBLIC int | Vacc_wcaEnergy (Vacc *acc, 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. |
* * 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) 2002-2007. 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 * * Linking APBS statically or dynamically with other modules is making a * combined work based on APBS. Thus, the terms and conditions of the GNU * General Public License cover the whole combination. * * SPECIAL GPL EXCEPTION * In addition, as a special exception, the copyright holders of APBS * give you permission to combine the APBS program with free software * programs and libraries that are released under the GNU LGPL or with * code included in releases of ISIM, Ion Simulator Interface, PMV, PyMOL * SMOL, VMD, and Vision. Such combined software may be linked with APBS and * redistributed together in original or modified form as mere aggregation * without requirement that the entire work be under the scope of the GNU * General Public License. This special exception permission is also extended * to any software listed in the SPECIAL GPL EXCEPTION clauses by the PMG, * FEtk, MC, or MALOC libraries. * * Note that people who make modified versions of APBS are not obligated * to grant this special exception for their modified versions; it is * their choice whether to do so. The GNU General Public License gives * permission to release a modified version without this exception; this * exception also makes it possible to release a modified version which * carries forward this exception. * *
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Determines if a point is within the union of the spheres centered at the atomic centers with radii equal to the sum of their van der Waals radii and the probe radius. Does not include contributions from the specified atom.
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Fast spline-based surface computation subroutine.
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Allocate (and clear) space for storage |
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Check and store parameters passed to constructor |
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