Vacc class

Solvent- and ion-accessibility oracle. More...

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...
Files
file	vacc.h
	Contains declarations for class Vacc.
file	vacc.c
	Class Vacc methods.
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

Solvent- and ion-accessibility oracle.

Function Documentation

void Vacc_atomdSASA	(	Vacc *	thee,
		double	dpos,
		double	radius,
		Vatom *	atom,
		double *	dSA
	)

Get the derivatve of solvent accessible area.

Author:: Jason Wagoner, David Gohara, Nathan Baker

Parameters:

	dpos	Acessibility object
	radius	Atom position offset
	atom	Probe radius (Å)
	dSA	Atom of interest Array holding answers of calc

Referenced by forceAPOL().

void Vacc_atomdSAV	(	Vacc *	thee,
		double	radius,
		Vatom *	atom,
		double *	dSA
	)

Get the derivatve of solvent accessible volume.

Author:: Jason Wagoner, Nathan Baker

Parameters:

	radius	Acessibility object
	atom	Probe radius (Å)
	dSA	Atom of interest Array holding answers of calc

Referenced by forceAPOL().

double Vacc_atomSASA	(	Vacc *	thee,
		double	radius,
		Vatom *	atom
	)

Return the atomic solvent accessible surface area (SASA).

Note:: Alias for Vacc_SASA

Author:: Nathan Baker

Returns:: Atomic solvent accessible area (A^2)

Parameters:

	radius	Accessibility object
	atom	Probe molecule radius (Å) Atom of interest

References sVaccSurf::area, sVaccSurf::probe_radius, sVacc::refSphere, sVacc::surf, Vacc_atomSurf(), Vacc_SASA(), VaccSurf_dtor2(), and Vatom_getAtomID().

Referenced by fillcoCoefMolDielNoSmooth(), and initAPOL().

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VaccSurf* Vacc_atomSASPoints	(	Vacc *	thee,
		double	radius,
		Vatom *	atom
	)

Get the set of points for this atom's solvent-accessible surface.

Author:: Nathan Baker

Returns:: Pointer to VaccSurf object for this atom

Parameters:

	radius	Accessibility object
	atom	Probe molecule radius (Å) Atom of interest

References sVaccSurf::probe_radius, sVacc::refSphere, sVacc::surf, Vacc_atomSurf(), Vacc_SASA(), VaccSurf_dtor2(), and Vatom_getAtomID().

Referenced by fillcoCoefMolDielNoSmooth().

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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.

Author:: Nathan Baker

Returns:: Atom sphere surface object

Parameters:

	atom	Accessibility object for molecule
	ref	Atom for which the surface should be constructed
	probe_radius	Reference sphere which sets the resolution for the surface.

See also:: VaccSurf_refSphere Probe radius (in A)

References sVaccSurf::area, sVaccSurf::bpts, ivdwAccExclus(), sVacc::mem, sVaccSurf::npts, VaccSurf_ctor(), Vatom_getAtomID(), Vatom_getPosition(), Vatom_getRadius(), sVaccSurf::xpts, sVaccSurf::ypts, and sVaccSurf::zpts.

Referenced by forceAPOL(), Vacc_atomSASA(), Vacc_atomSASPoints(), and Vacc_SASA().

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Vacc* Vacc_ctor	(	Valist *	alist,
		Vclist *	clist,
		double	surf_density
	)

Construct the accessibility object.

Author:: Nathan Baker

Returns:: Newly allocated Vacc object

Parameters:

	clist	Molecule for accessibility queries
	surf_density	Pre-constructed cell list for looking up atoms near specific positions Minimum per-atom solvent accessible surface point density (in pts/A^2)

References Vacc_ctor2().

Referenced by initAPOL(), and Vpbe_ctor2().

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int Vacc_ctor2	(	Vacc *	thee,
		Valist *	alist,
		Vclist *	clist,
		double	surf_density
	)

FORTRAN stub to construct the accessibility object.

Author:: Nathan Baker

Returns:: 1 if successful, 0 otherwise

Parameters:

	alist	Memory for Vacc objet
	clist	Molecule for accessibility queries
	surf_density	Pre-constructed cell list for looking up atoms near specific positions Minimum per-atom solvent accessible surface point density (in pts/A^2)

References sVacc::mem, sVacc::surf, Vacc_allocate(), and Vacc_storeParms().

Referenced by Vacc_ctor().

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void Vacc_dtor ( Vacc ** thee )

Destroy object.

Author:: Nathan Baker

Parameters:

thee

Pointer to memory location of object

References Vacc_dtor2().

Referenced by initAPOL(), and Vpbe_dtor2().

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void Vacc_dtor2 ( Vacc * thee )

FORTRAN stub to destroy object.

Author:: Nathan Baker

Parameters:

thee

Pointer to object

References sVacc::alist, sVacc::atomFlags, sVacc::mem, sVacc::refSphere, sVacc::surf, VaccSurf_dtor(), and Valist_getNumberAtoms().

Referenced by Vacc_dtor().

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double Vacc_fastMolAcc	(	Vacc *	thee,
		double	center[VAPBS_DIM],
		double	radius
	)

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!

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)

Parameters:

	center	Accessibility object
	radius	Probe center coordinates Probe radius (in Å)

References sVclistCell::atoms, sVacc::clist, sVclistCell::natoms, sVaccSurf::npts, sVacc::surf, Vacc_SASA(), Vatom_getAtomID(), Vclist_getCell(), sVaccSurf::xpts, sVaccSurf::ypts, and sVaccSurf::zpts.

Referenced by Vacc_molAcc().

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double Vacc_ivdwAcc	(	Vacc *	thee,
		double	center[VAPBS_DIM],
		double	radius
	)

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.

Author:: Nathan Baker

Returns:: Characteristic function value between 1.0 (accessible) and 0.0 (inaccessible)

Parameters:

	center	Accessibility object
	radius	Probe center coordinates Probe radius (Å)

Referenced by Vacc_molAcc(), Vacc_totalSAV(), Vacc_wcaForceAtom(), Vfetk_fillArray(), and Vpmg_fillArray().

unsigned long int Vacc_memChk ( Vacc * thee )

Get number of bytes in this object and its members.

Author:: Nathan Baker

Returns:: Number of bytes allocated for object

Parameters:

thee

Object for memory check

References sVacc::mem.

Referenced by Vpbe_memChk().

double Vacc_molAcc	(	Vacc *	thee,
		double	center[VAPBS_DIM],
		double	radius
	)

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.

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)

Parameters:

	center	Accessibility object
	radius	Probe center coordinates Probe radius (in Å)

References Vacc_fastMolAcc(), Vacc_ivdwAcc(), and Vacc_vdwAcc().

Referenced by Vfetk_fillArray(), and Vpmg_fillArray().

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double Vacc_SASA	(	Vacc *	thee,
		double	radius
	)

Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area.

Note:: Similar to UHBD FORTRAN routine by Brock Luty (returns UHBD's asas2)

Author:: Nathan Baker (original FORTRAN routine by Brock Luty)

Returns:: Total solvent accessible area (A^2)

Parameters:

radius

Accessibility object Probe molecule radius (Å)

References sVacc::alist, sVaccSurf::area, sVacc::mem, sVaccSurf::probe_radius, sVacc::refSphere, sVacc::surf, Vacc_atomSurf(), VaccSurf_dtor2(), Valist_getAtom(), and Valist_getNumberAtoms().

Referenced by fillcoCoefMolDielNoSmooth(), Vacc_atomSASA(), Vacc_atomSASPoints(), Vacc_fastMolAcc(), and Vacc_totalSASA().

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double Vacc_splineAcc	(	Vacc *	thee,
		double	center[VAPBS_DIM],
		double	win,
		double	infrad
	)

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.

Author:: Nathan Baker

Returns:: Characteristic function value between 1.0 (accessible) and 0.0 (inaccessible)

Parameters:

	center	Accessibility object
	win	Probe center coordinates
	infrad	Spline window (Å) Inflation radius (Å) for ion access.

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

Referenced by Vfetk_fillArray(), and Vpmg_fillArray().

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double Vacc_splineAccAtom	(	Vacc *	thee,
		double	center[VAPBS_DIM],
		double	win,
		double	infrad,
		Vatom *	atom
	)

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.

Author:: Nathan Baker

Returns:: Characteristic function value between 1.0 (accessible) and 0.0 (inaccessible)

Parameters:

	center	Accessibility object
	win	Probe center coordinates
	infrad	Spline window (Å)
	atom	Inflation radius (Å) for ion access. Atom

References Vatom_getPosition(), and Vatom_getRadius().

Referenced by splineAcc().

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void Vacc_splineAccGrad	(	Vacc *	thee,
		double	center[VAPBS_DIM],
		double	win,
		double	infrad,
		double *	grad
	)

Report gradient of spline-based accessibility.

Author:: Nathan Baker

Parameters:

	center	Accessibility object
	win	Probe center coordinates
	infrad	Spline window (Å)
	grad	Inflation radius (Å) for ion access. 3-vector set to gradient of accessibility

References sVacc::atomFlags, sVclistCell::atoms, sVacc::clist, sVatom::id, sVclistCell::natoms, splineAcc(), Vacc_splineAccGradAtomNorm(), Vclist_getCell(), and Vclist_maxRadius().

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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).

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.

Author:: Nathan Baker

Parameters:

	center	Accessibility object
	win	Probe center coordinates
	infrad	Spline window (Å)
	atom	Inflation radius (Å) for ion access.
	force	Atom VAPBS_DIM-vector set to gradient of accessibility

References Vatom_getPosition(), and Vatom_getRadius().

Referenced by Vacc_splineAccGrad(), and Vpmg_splineSelect().

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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).

Author:: Michael Schnieders

Parameters:

	center	Accessibility object
	win	Probe center coordinates
	infrad	Spline window (Å)
	atom	Inflation radius (Å) for ion access.
	force	Atom VAPBS_DIM-vector set to gradient of accessibility

References Vatom_getPosition(), and Vatom_getRadius().

Referenced by Vpmg_splineSelect().

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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).

Author:: Michael Schnieders

Parameters:

	center	Accessibility object
	win	Probe center coordinates
	infrad	Spline window (Å)
	atom	Inflation radius (Å) for ion access.
	force	Atom VAPBS_DIM-vector set to gradient of accessibility

References Vatom_getPosition(), and Vatom_getRadius().

Referenced by Vpmg_splineSelect().

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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).

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.

Author:: Nathan Baker

Parameters:

	center	Accessibility object
	win	Probe center coordinates
	infrad	Spline window (Å)
	atom	Inflation radius (Å) for ion access.
	force	Atom VAPBS_DIM-vector set to gradient of accessibility

References Vatom_getPosition(), and Vatom_getRadius().

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void Vacc_totalAtomdSASA	(	Vacc *	thee,
		double	dpos,
		double	radius,
		Vatom *	atom,
		double *	dSA
	)

Testing purposes only.

Author:: David Gohara, Nathan Baker

Parameters:

	dpos	Acessibility object
	radius	Atom position offset
	atom	Probe radius (Å)
	dSA	Atom of interest Array holding answers of calc

References sVacc::refSphere, Vatom_getAtomID(), Vatom_getPosition(), and Vatom_getRadius().

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void Vacc_totalAtomdSAV	(	Vacc *	thee,
		double	dpos,
		double	radius,
		Vatom *	atom,
		double *	dSA,
		Vclist *	clist
	)

Total solvent accessible volume.

Author:: David Gohara, Nathan Baker

Parameters:

	dpos	Acessibility object
	radius	Atom position offset
	atom	Probe radius (Å)
	dSA	Atom of interest
	clist	Array holding answers of calc clist for this calculation

References sVacc::refSphere, Vacc_totalSAV(), Vatom_getAtomID(), Vatom_getPosition(), and Vatom_getRadius().

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double Vacc_totalSASA	(	Vacc *	thee,
		double	radius
	)

Return the total solvent accessible surface area (SASA).

Note:: Alias for Vacc_SASA

Author:: Nathan Baker

Returns:: Total solvent accessible area (A^2)

Parameters:

radius

Accessibility object Probe molecule radius (Å)

References Vacc_SASA().

Referenced by initAPOL().

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double Vacc_totalSAV	(	Vacc *	thee,
		Vclist *	clist,
		APOLparm *	apolparm,
		double	radius
	)

Return the total solvent accessible volume (SAV).

Note:: Alias for Vacc_SAV

Author:: David Gohara

Returns:: Total solvent accessible volume (A^3)

Parameters:

	clist	Accessibility object
	apolparm	Clist for acc object
	radius	Apolar parameters -- could be VNULL if none required for this calculation. If VNULL, then default settings are used Probe molecule radius (Å)

References sAPOLparm::grid, sVclist::lower_corner, sAPOLparm::setgrid, sVclist::upper_corner, and Vacc_ivdwAcc().

Referenced by initAPOL(), and Vacc_totalAtomdSAV().

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double Vacc_vdwAcc	(	Vacc *	thee,
		double	center[VAPBS_DIM]
	)

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).

Author:: Nathan Baker

Returns:: Characteristic function value between 1.0 (accessible) and 0.0 (inaccessible)

Parameters:

center

Accessibility object Probe center coordinates

Referenced by Vacc_molAcc(), Vfetk_fillArray(), and Vpmg_fillArray().

VPUBLIC int Vacc_wcaEnergy	(	Vacc *	thee,
		APOLparm *	apolparm,
		Valist *	alist,
		Vclist *	clist
	)

Return the WCA integral energy.

Author:: David Gohara

Returns:: WCA energy (kJ/mol)

Parameters:

	apolparm	Accessibility object
	alist	Apolar calculation parameters
	clist	Alist for acc object Clist for acc object

References sAPOLparm::bconc, sAPOLparm::setwat, Valist_getNumberAtoms(), VRC_FAILURE, and VRC_SUCCESS.

Referenced by initAPOL().

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VPUBLIC int Vacc_wcaForceAtom	(	Vacc *	thee,
		APOLparm *	apolparm,
		Vclist *	clist,
		Vatom *	atom,
		double *	force
	)

Return the WCA integral force.

Author:: David Gohara

Returns:: WCA energy (kJ/mol/A)

Parameters:

	apolparm	Accessibility object
	clist	Apolar calculation parameters
	atom	Clist for acc object
	force	Current atom Force for atom

References sAPOLparm::bconc, sVatom::epsilon, sAPOLparm::grid, sVclist::lower_corner, sVatom::radius, sAPOLparm::setgrid, sAPOLparm::setwat, sAPOLparm::srad, sVclist::upper_corner, Vacc_ivdwAcc(), Vatom_getPosition(), VRC_FAILURE, VRC_SUCCESS, sAPOLparm::watepsilon, and sAPOLparm::watsigma.

Referenced by forceAPOL().

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VaccSurf* VaccSurf_ctor	(	Vmem *	mem,
		double	probe_radius,
		int	nsphere
	)

Allocate and construct the surface object; do not assign surface points to positions.

Author:: Nathan Baker

Returns:: Newly allocated and constructed surface object

Parameters:

	probe_radius	Memory manager (can be VNULL)
	nsphere	Probe radius (in A) for this surface Number of points in sphere

References VaccSurf_ctor2().

Referenced by Vacc_atomSurf(), and VaccSurf_refSphere().

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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.

Author:: Nathan Baker

Returns:: 1 if successful, 0 otherwise

Parameters:

	mem	Allocated memory
	probe_radius	Memory manager (can be VNULL)
	nsphere	Probe radius (in A) for this surface Number of points in sphere

References sVaccSurf::area, sVaccSurf::bpts, sVaccSurf::mem, sVaccSurf::npts, sVaccSurf::probe_radius, sVaccSurf::xpts, sVaccSurf::ypts, and sVaccSurf::zpts.

Referenced by VaccSurf_ctor().

void VaccSurf_dtor ( VaccSurf ** thee )

Destroy the surface object and free its memory.

Author:: Nathan Baker

Parameters:

thee

Object to be destroyed

References VaccSurf_dtor2().

Referenced by Vacc_dtor2().

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void VaccSurf_dtor2 ( VaccSurf * thee )

Destroy the surface object.

Author:: Nathan Baker

Parameters:

thee

Object to be destroyed

References sVaccSurf::bpts, sVaccSurf::npts, sVaccSurf::xpts, sVaccSurf::ypts, and sVaccSurf::zpts.

Referenced by Vacc_atomSASA(), Vacc_atomSASPoints(), Vacc_SASA(), and VaccSurf_dtor().

VaccSurf* VaccSurf_refSphere	(	Vmem *	mem,
		int	npts
	)

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.

Author:: Nathan Baker (original FORTRAN code by Mike Gilson)

Returns:: Reference sphere surface object

Parameters:

npts

Memory object Requested number of points on sphere

References sVaccSurf::bpts, sVaccSurf::npts, VaccSurf_ctor(), Vunit_pi, sVaccSurf::xpts, sVaccSurf::ypts, and sVaccSurf::zpts.

Referenced by Vacc_storeParms().

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