vacc.c File Reference

Class Vacc methods. More...

#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.

Detailed Description

Class Vacc methods.

Author:: Nathan Baker

Version:

Id: vacc.c 1367 2009-04-24 17:11:03Z 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.
 *
 *

Function Documentation

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.

Returns:: 1 if accessible (outside the inflated van der Waals radius), 0 otherwise

Author:: Nathan Baker

Parameters:

	center	Accessibility object
	radius	Position to test
	atomID	Radius of probe ID of atom to ignore

References sVclistCell::atoms, sVacc::clist, sVatom::id, sVclistCell::natoms, sVatom::position, sVatom::radius, Vclist_getCell(), and Vclist_maxRadius().

Referenced by Vacc_atomSurf().

Here is the call graph for this function:

VPRIVATE double splineAcc	(	Vacc *	thee,
		double	center[VAPBS_DIM],
		double	win,
		double	infrad,
		VclistCell *	cell
	)

Fast spline-based surface computation subroutine.

Returns:: Spline value

Author:: Todd Dolinsky and Nathan Baker

Parameters:

	center	Accessibility object
	win	Point at which the acc is to be evaluated
	infrad	Spline window
	cell	Radius to inflate atomic radius Cell of atom objects