| /** @defgroup Vacc Vacc class | |
| * @brief Solvent- and ion-accessibility oracle | |
| */ | |
| /** | |
| * @file vacc.h | |
| * @ingroup Vacc | |
| * @brief Contains declarations for class Vacc | |
| * @version $Id$ | |
| * @author Nathan A. Baker | |
| * | |
| * @attention | |
| * @verbatim | |
| * | |
| * 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) 2010-2020 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. | |
| * | |
| * @endverbatim | |
| */ | |
| /** | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @brief Surface object list of per-atom surface points | |
| */ | |
| struct sVaccSurf { | |
| Vmem *mem; /**< Memory object */ | |
| double *xpts; /**< Array of point x-locations */ | |
| double *ypts; /**< Array of point y-locations */ | |
| double *zpts; /**< Array of point z-locations */ | |
| char *bpts; /**< Array of booleans indicating whether a point is (1) or is | |
| * not (0) part of the surface */ | |
| double area; /**< Area spanned by these points */ | |
| int npts; /**< Length of thee->xpts, ypts, zpts arrays */ | |
| double probe_radius; /**< Probe radius (A) with which this surface was | |
| * constructed */ | |
| }; | |
| /** | |
| * @ingroup Vacc | |
| * @brief Declaration of the VaccSurf class as the VaccSurf structure | |
| */ | |
| typedef struct sVaccSurf VaccSurf; | |
| /** | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @brief Oracle for solvent- and ion-accessibility around a biomolecule | |
| */ | |
| struct sVacc { | |
| Vmem *mem; /**< Memory management object for this class */ | |
| Valist *alist; /**< Valist structure for list of atoms */ | |
| Vclist *clist; /**< Vclist structure for atom cell list */ | |
| int *atomFlags; /**< Array of boolean flags of length | |
| * Valist_getNumberAtoms(thee->alist) to prevent | |
| * double-counting atoms during calculations */ | |
| VaccSurf *refSphere; /**< Reference sphere for SASA calculations */ | |
| VaccSurf **surf; /**< Array of surface points for each atom; is not | |
| * initialized until needed (test against VNULL to | |
| * determine initialization state) */ | |
| Vset acc; /**< An integer array (to be treated as bitfields) of Vset type | |
| * with length equal to the number of vertices in the mesh */ | |
| double surf_density; /**< Minimum solvent accessible surface point density | |
| * (in pts/A^2) */ | |
| }; | |
| /** | |
| * @ingroup Vacc | |
| * @brief Declaration of the Vacc class as the Vacc structure | |
| */ | |
| typedef struct sVacc Vacc; | |
| /** @brief Get number of bytes in this object and its members | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns Number of bytes allocated for object | |
| */ | |
| VEXTERNC unsigned long int Vacc_memChk( | |
| Vacc *thee /**< Object for memory check */ | |
| ); | |
| /** | |
| * @brief Allocate and construct the surface object; do not assign surface | |
| * points to positions | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns Newly allocated and constructed surface object | |
| */ | |
| VEXTERNC VaccSurf* VaccSurf_ctor( | |
| Vmem *mem, /**< Memory manager (can be VNULL) */ | |
| double probe_radius, /**< Probe radius (in A) for this surface */ | |
| int nsphere /**< Number of points in sphere */ | |
| ); | |
| /** | |
| * @brief Construct the surface object using previously allocated memory; do | |
| * not assign surface points to positions | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns 1 if successful, 0 otherwise | |
| */ | |
| VEXTERNC int VaccSurf_ctor2( | |
| VaccSurf *thee, /**< Allocated memory */ | |
| Vmem *mem, /**< Memory manager (can be VNULL) */ | |
| double probe_radius, /**< Probe radius (in A) for this surface */ | |
| int nsphere /**< Number of points in sphere */ | |
| ); | |
| /** | |
| * @brief Destroy the surface object and free its memory | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| */ | |
| VEXTERNC void VaccSurf_dtor( | |
| VaccSurf **thee /**< Object to be destroyed */ | |
| ); | |
| /** | |
| * @brief Destroy the surface object | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| */ | |
| VEXTERNC void VaccSurf_dtor2( | |
| VaccSurf *thee /**< Object to be destroyed */ | |
| ); | |
| /** | |
| * @brief Set up an array of points for a reference sphere of unit radius | |
| * | |
| * Generates approximately npts # of points (actual number stored in | |
| * thee->npts) somewhat uniformly distributed across a sphere of unit radius | |
| * centered at the origin. | |
| * | |
| * @note This routine was shamelessly ripped off from sphere.f from UHBD as | |
| * developed by Michael K. Gilson. | |
| * | |
| * @ingroup Vacc | |
| * @author Nathan Baker (original FORTRAN code by Mike Gilson) | |
| * @return Reference sphere surface object | |
| */ | |
| VEXTERNC VaccSurf* VaccSurf_refSphere( | |
| Vmem *mem, /**< Memory object */ | |
| int npts /**< Requested number of points on sphere */ | |
| ); | |
| /** | |
| * @brief Set up an array of points corresponding to the SAS due to a | |
| * particular atom. | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @return Atom sphere surface object | |
| */ | |
| VEXTERNC VaccSurf* Vacc_atomSurf( | |
| Vacc *thee, /**< Accessibility object for molecule */ | |
| Vatom *atom, /**< Atom for which the surface should be constructed */ | |
| VaccSurf *ref, /**< Reference sphere which sets the resolution for the | |
| * surface. @see VaccSurf_refSphere */ | |
| double probe_radius /**< Probe radius (in A) */ | |
| ); | |
| /** @brief Construct the accessibility object | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns Newly allocated Vacc object */ | |
| VEXTERNC Vacc* Vacc_ctor( | |
| Valist *alist, /**< Molecule for accessibility queries */ | |
| Vclist *clist, /**< Pre-constructed cell list for looking up atoms | |
| * near specific positions */ | |
| double surf_density /**< Minimum per-atom solvent accessible surface | |
| * point density (in pts/A^2)*/ | |
| ); | |
| /** @brief FORTRAN stub to construct the accessibility object | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns 1 if successful, 0 otherwise */ | |
| VEXTERNC int Vacc_ctor2( | |
| Vacc *thee, /**< Memory for Vacc objet */ | |
| Valist *alist, /**< Molecule for accessibility queries */ | |
| Vclist *clist, /**< Pre-constructed cell list for looking up atoms | |
| * near specific positions */ | |
| double surf_density /**< Minimum per-atom solvent accessible surface | |
| * point density (in pts/A^2)*/ | |
| ); | |
| /** @brief Destroy object | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| */ | |
| VEXTERNC void Vacc_dtor( | |
| Vacc **thee /**< Pointer to memory location of object */ | |
| ); | |
| /** @brief FORTRAN stub to destroy object | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| */ | |
| VEXTERNC void Vacc_dtor2( | |
| Vacc *thee /**< Pointer to object */ | |
| ); | |
| /** @brief Report van der Waals accessibility | |
| * | |
| * Determines if a point is within the union of the atomic spheres (with | |
| * radii equal to their van der Waals radii). | |
| * | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns Characteristic function value between 1.0 (accessible) and 0.0 | |
| * (inaccessible) | |
| */ | |
| VEXTERNC double Vacc_vdwAcc( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM] /**< Probe center coordinates */ | |
| ); | |
| /** @brief Report inflated van der Waals accessibility | |
| * | |
| * Determines if a point is within the union of the spheres centered at the | |
| * atomic centers with radii equal to the sum of the atomic van der Waals | |
| * radius and the probe radius. | |
| * | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns Characteristic function value between 1.0 (accessible) and 0.0 | |
| * (inaccessible) | |
| */ | |
| VEXTERNC double Vacc_ivdwAcc( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM], /**< Probe center coordinates */ | |
| double radius /**< Probe radius (Å) */ | |
| ); | |
| /** @brief Report molecular accessibility | |
| * | |
| * Determine accessibility of a probe (of radius radius) at a given point, | |
| * given a collection of atomic spheres. Uses molecular (Connolly) surface | |
| * definition. | |
| * | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns Characteristic function value between 1.0 (accessible) and 0.0 | |
| * (inaccessible) | |
| * @bug This routine has a slight bug which can generate very small | |
| * internal regions of high dielectric (thanks to John Mongan and | |
| * Jess Swanson for finding this) | |
| */ | |
| VEXTERNC double Vacc_molAcc( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM], /**< Probe center coordinates */ | |
| double radius /**< Probe radius (in Å) */ | |
| ); | |
| /** @brief Report molecular accessibility quickly | |
| * | |
| * Given a point which is INSIDE the collection of inflated van der Waals | |
| * spheres, but OUTSIDE the collection of non-inflated van der Waals spheres, | |
| * determine accessibility of a probe (of radius radius) at a given point, | |
| * given a collection of atomic spheres. Uses molecular (Connolly) surface | |
| * definition. | |
| * | |
| * @note THIS ASSUMES YOU HAVE TESTED THAT THIS POINT IS DEFINITELY INSIDE | |
| * THE INFLATED AND NON-INFLATED VAN DER WAALS SURFACES! | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns Characteristic function value between 1.0 (accessible) and 0.0 | |
| * (inaccessible) | |
| * @bug This routine has a slight bug which can generate very small | |
| * internal regions of high dielectric (thanks to John Mongan and | |
| * Jess Swanson for finding this) | |
| */ | |
| VEXTERNC double Vacc_fastMolAcc( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM], /**< Probe center coordinates */ | |
| double radius /**< Probe radius (in Å) */ | |
| ); | |
| /** @brief Report spline-based accessibility | |
| * | |
| * Determine accessibility at a given point, given a collection of atomic | |
| * spheres. Uses Benoit Roux (Im et al, Comp Phys Comm, 111, 59--75, 1998) | |
| * definition suitable for force evalation; basically a cubic spline. | |
| * | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns Characteristic function value between 1.0 (accessible) and 0.0 | |
| * (inaccessible) | |
| */ | |
| VEXTERNC double Vacc_splineAcc( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM], /**< Probe center coordinates */ | |
| double win, /**< Spline window (Å) */ | |
| double infrad /**< Inflation radius (Å) for ion access. */ | |
| ); | |
| /** @brief Report gradient of spline-based accessibility. | |
| * | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| */ | |
| VEXTERNC void Vacc_splineAccGrad( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM], /**< Probe center coordinates */ | |
| double win, /**< Spline window (Å) */ | |
| double infrad, /**< Inflation radius (Å) for ion access. */ | |
| double *grad /**< 3-vector set to gradient of accessibility */ | |
| ); | |
| /** @brief Report spline-based accessibility for a given atom | |
| * | |
| * Determine accessibility at a given point for a given atomic | |
| * spheres. Uses Benoit Roux (Im et al, Comp Phys Comm, 111, 59--75, 1998) | |
| * definition suitable for force evalation; basically a cubic spline. | |
| * | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @returns Characteristic function value between 1.0 (accessible) and 0.0 | |
| * (inaccessible) | |
| */ | |
| VEXTERNC double Vacc_splineAccAtom( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM], /**< Probe center coordinates */ | |
| double win, /**< Spline window (Å) */ | |
| double infrad, /**< Inflation radius (Å) for ion access. */ | |
| Vatom *atom /**< Atom */ | |
| ); | |
| /** @brief Report gradient of spline-based accessibility with respect to a | |
| * particular atom (see Vpmg_splineAccAtom) | |
| * | |
| * Determine accessibility at a given point, given a collection of atomic | |
| * spheres. Uses Benoit Roux (Im et al, Comp Phys Comm, 111, 59--75, 1998) | |
| * definition suitable for force evalation; basically a cubic spline. | |
| * | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| */ | |
| VEXTERNC void Vacc_splineAccGradAtomUnnorm( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM], /**< Probe center coordinates */ | |
| double win, /**< Spline window (Å) */ | |
| double infrad, /**< Inflation radius (Å) for ion access. */ | |
| Vatom *atom, /**< Atom */ | |
| double *force /**< VAPBS_DIM-vector set to gradient of accessibility */ | |
| ); | |
| /** @brief 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) | |
| * | |
| * Determine accessibility at a given point, given a collection of atomic | |
| * spheres. Uses Benoit Roux (Im et al, Comp Phys Comm, 111, 59--75, 1998) | |
| * definition suitable for force evalation; basically a cubic spline. | |
| * | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| */ | |
| VEXTERNC void Vacc_splineAccGradAtomNorm( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM], /**< Probe center coordinates */ | |
| double win, /**< Spline window (Å) */ | |
| double infrad, /**< Inflation radius (Å) for ion access. */ | |
| Vatom *atom, /**< Atom */ | |
| double *force /**< VAPBS_DIM-vector set to gradient of accessibility */ | |
| ); | |
| /** @brief 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) | |
| * | |
| * @ingroup Vacc | |
| * @author Michael Schnieders | |
| */ | |
| VEXTERNC void Vacc_splineAccGradAtomNorm4( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM], /**< Probe center coordinates */ | |
| double win, /**< Spline window (Å) */ | |
| double infrad, /**< Inflation radius (Å) for ion access. */ | |
| Vatom *atom, /**< Atom */ | |
| double *force /**< VAPBS_DIM-vector set to gradient of accessibility */ | |
| ); | |
| /** @brief 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) | |
| * | |
| * @ingroup Vacc | |
| * @author Michael Schnieders | |
| */ | |
| VEXTERNC void Vacc_splineAccGradAtomNorm3( | |
| Vacc *thee, /**< Accessibility object */ | |
| double center[VAPBS_DIM], /**< Probe center coordinates */ | |
| double win, /**< Spline window (Å) */ | |
| double infrad, /**< Inflation radius (Å) for ion access. */ | |
| Vatom *atom, /**< Atom */ | |
| double *force /**< VAPBS_DIM-vector set to gradient of accessibility */ | |
| ); | |
| /** | |
| * @brief Build the solvent accessible surface (SAS) and calculate the | |
| * solvent accessible surface area | |
| * @ingroup Vacc | |
| * @note Similar to UHBD FORTRAN routine by Brock Luty | |
| * (returns UHBD's asas2) | |
| * @author Nathan Baker (original FORTRAN routine by Brock Luty) | |
| * @return Total solvent accessible area (A^2) | |
| */ | |
| VEXTERNC double Vacc_SASA( | |
| Vacc *thee, /**< Accessibility object */ | |
| double radius /**< Probe molecule radius (Å) */ | |
| ); | |
| /** | |
| * @brief Return the total solvent accessible surface area (SASA) | |
| * @ingroup Vacc | |
| * @note Alias for Vacc_SASA | |
| * @author Nathan Baker | |
| * @return Total solvent accessible area (A^2) | |
| */ | |
| VEXTERNC double Vacc_totalSASA( | |
| Vacc *thee, /**< Accessibility object */ | |
| double radius /**< Probe molecule radius (Å) */ | |
| ); | |
| /** | |
| * @brief Return the atomic solvent accessible surface area (SASA) | |
| * @ingroup Vacc | |
| * @note Alias for Vacc_SASA | |
| * @author Nathan Baker | |
| * @return Atomic solvent accessible area (A^2) | |
| */ | |
| VEXTERNC double Vacc_atomSASA( | |
| Vacc *thee, /**< Accessibility object */ | |
| double radius, /**< Probe molecule radius (Å) */ | |
| Vatom *atom /**< Atom of interest */ | |
| ); | |
| /** | |
| * @brief Get the set of points for this atom's solvent-accessible surface | |
| * @ingroup Vacc | |
| * @author Nathan Baker | |
| * @return Pointer to VaccSurf object for this atom | |
| */ | |
| VEXTERNC VaccSurf* Vacc_atomSASPoints( | |
| Vacc *thee, /**< Accessibility object */ | |
| double radius, /**< Probe molecule radius (Å) */ | |
| Vatom *atom /**< Atom of interest */ | |
| ); | |
| /** | |
| * @brief Get the derivatve of solvent accessible volume | |
| * @ingroup Vacc | |
| * @author Jason Wagoner, Nathan Baker | |
| */ | |
| VEXTERNC void Vacc_atomdSAV( | |
| Vacc *thee, /**< Acessibility object */ | |
| double radius, /**< Probe radius (Å) */ | |
| Vatom *atom, /**< Atom of interest */ | |
| double *dSA /**< Array holding answers of calc */ | |
| ); | |
| /** | |
| * @brief Get the derivatve of solvent accessible area | |
| * @ingroup Vacc | |
| * @author Jason Wagoner, David Gohara, Nathan Baker | |
| */ | |
| VEXTERNC void Vacc_atomdSASA( | |
| Vacc *thee, /**< Acessibility object */ | |
| double dpos, /**< Atom position offset */ | |
| double radius, /**< Probe radius (Å) */ | |
| Vatom *atom, /**< Atom of interest */ | |
| double *dSA /**< Array holding answers of calc */ | |
| ); | |
| /** | |
| * @brief Testing purposes only | |
| * @ingroup Vacc | |
| * @author David Gohara, Nathan Baker | |
| */ | |
| VEXTERNC void Vacc_totalAtomdSASA( | |
| Vacc *thee, /**< Acessibility object */ | |
| double dpos, /**< Atom position offset */ | |
| double radius, /**< Probe radius (Å) */ | |
| Vatom *atom, /**< Atom of interest */ | |
| double *dSA /**< Array holding answers of calc */ | |
| ); | |
| /** | |
| * @brief Total solvent accessible volume | |
| * @ingroup Vacc | |
| * @author David Gohara, Nathan Baker | |
| */ | |
| VEXTERNC void Vacc_totalAtomdSAV( | |
| Vacc *thee, /**< Acessibility object */ | |
| double dpos, /**< Atom position offset */ | |
| double radius, /**< Probe radius (Å) */ | |
| Vatom *atom, /**< Atom of interest */ | |
| double *dSA, /**< Array holding answers of calc */ | |
| Vclist *clist /**< clist for this calculation */ | |
| ); | |
| /** | |
| * @brief Return the total solvent accessible volume (SAV) | |
| * @ingroup Vacc | |
| * @note Alias for Vacc_SAV | |
| * @author David Gohara | |
| * @return Total solvent accessible volume (A^3) | |
| */ | |
| VEXTERNC double Vacc_totalSAV( | |
| Vacc *thee, /**< Accessibility object */ | |
| Vclist *clist, /**< Clist for acc object */ | |
| APOLparm *apolparm, /**< Apolar parameters -- could be VNULL if none required for this calculation. | |
| * If VNULL, then default settings are used */ | |
| double radius /**< Probe molecule radius (Å) */ | |
| ); | |
| /** | |
| * @brief Return the WCA integral energy | |
| * @ingroup Vacc | |
| * @author David Gohara | |
| * @return Success flag | |
| */ | |
| VEXTERNC int Vacc_wcaEnergy( | |
| Vacc *thee, /**< Accessibility object */ | |
| APOLparm *apolparm, /**< Apolar calculation parameters */ | |
| Valist *alist, /**< Alist for acc object */ | |
| Vclist *clist /**< Clist for acc object */ | |
| ); | |
| /** | |
| * @brief Return the WCA integral force | |
| * @ingroup Vacc | |
| * @author David Gohara | |
| * @return WCA energy (kJ/mol/A) | |
| */ | |
| VEXTERNC int Vacc_wcaForceAtom(Vacc *thee, /**< Accessibility object */ | |
| APOLparm *apolparm, /**< Apolar calculation parameters */ | |
| Vclist *clist, /**< Clist for acc object */ | |
| Vatom *atom, /**< Current atom */ | |
| double *force /**< Force for atom */ | |
| ); | |
| /** @brief Calculate the WCA energy for an atom | |
| @ingroup Vacc | |
| @author Dave Gohara and Nathan Baker | |
| @return Success flag | |
| */ | |
| VEXTERNC int Vacc_wcaEnergyAtom( | |
| Vacc *thee, /**< Accessibility object */ | |
| APOLparm *apolparm, /**< Apolar calculation parameters */ | |
| Valist *alist, /**< Atom list */ | |
| Vclist *clist, /**< Cell list associated with Vacc object */ | |
| int iatom, /**< Index for atom of interest */ | |
| double *value /**< Set to energy value */ | |
| ); | |