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. | |
Get the derivatve of solvent accessible area.
| dpos | Acessibility object |
| radius | Atom position offset |
| atom | Probe radius (Å) |
| dSA | Atom of interest Array holding answers of calc |
Referenced by forceAPOL().
Get the derivatve of solvent accessible volume.
| radius | Acessibility object |
| atom | Probe radius (Å) |
| dSA | Atom of interest Array holding answers of calc |
Referenced by forceAPOL().
Return the atomic solvent accessible surface area (SASA).
| 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().

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

Set up an array of points corresponding to the SAS due to a particular atom.
| 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.
|
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().

Construct the accessibility object.
| 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().

FORTRAN stub to construct the accessibility object.
| 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().

| void Vacc_dtor | ( | Vacc ** | thee | ) |
Destroy object.
| thee | Pointer to memory location of object |
References Vacc_dtor2().
Referenced by initAPOL(), and Vpbe_dtor2().

| void Vacc_dtor2 | ( | Vacc * | thee | ) |
FORTRAN stub to destroy object.
| thee | Pointer to object |
References sVacc::alist, sVacc::atomFlags, sVacc::mem, sVacc::refSphere, sVacc::surf, VaccSurf_dtor(), and Valist_getNumberAtoms().
Referenced by Vacc_dtor().

| 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.
| 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().

| 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.
| 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.
| 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.
| 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().

| double Vacc_SASA | ( | Vacc * | thee, | |
| double | radius | |||
| ) |
Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area.
| 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(), Valist_getNumberAtoms(), and Vatom_getPosition().
Referenced by Vacc_atomSASA(), Vacc_atomSASPoints(), Vacc_fastMolAcc(), and Vacc_totalSASA().

| 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.
| 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().

| 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.
| 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().

| void Vacc_splineAccGrad | ( | Vacc * | thee, | |
| double | center[VAPBS_DIM], | |||
| double | win, | |||
| double | infrad, | |||
| double * | grad | |||
| ) |
Report gradient of spline-based accessibility.
| 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().

| 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.
| 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().

| 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).
| 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().

| 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).
| 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().

| 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.
| 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().

Testing purposes only.
| 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().

| void Vacc_totalAtomdSAV | ( | Vacc * | thee, | |
| double | dpos, | |||
| double | radius, | |||
| Vatom * | atom, | |||
| double * | dSA, | |||
| Vclist * | clist | |||
| ) |
Total solvent accessible volume.
| 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().

| double Vacc_totalSASA | ( | Vacc * | thee, | |
| double | radius | |||
| ) |
Return the total solvent accessible surface area (SASA).
| radius | Accessibility object Probe molecule radius (Å) |
References Vacc_SASA().
Referenced by initAPOL().

Return the total solvent accessible volume (SAV).
| 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().

| 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).
| center | Accessibility object Probe center coordinates |
Referenced by Vacc_molAcc(), Vfetk_fillArray(), and Vpmg_fillArray().
Return the WCA integral energy.
| 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, VRC_SUCCESS, and sAPOLparm::wcaEnergy.
Referenced by initAPOL().

| VPUBLIC int Vacc_wcaForceAtom | ( | Vacc * | thee, | |
| APOLparm * | apolparm, | |||
| Vclist * | clist, | |||
| Vatom * | atom, | |||
| double * | force | |||
| ) |
Return the WCA integral force.
| 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().

| VaccSurf* VaccSurf_ctor | ( | Vmem * | mem, | |
| double | probe_radius, | |||
| int | nsphere | |||
| ) |
Allocate and construct the surface object; do not assign surface points to positions.
| 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().

| 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.
| 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.
| thee | Object to be destroyed |
References VaccSurf_dtor2().
Referenced by Vacc_dtor2().

| void VaccSurf_dtor2 | ( | VaccSurf * | thee | ) |
Destroy the surface object.
| thee | Object to be destroyed |
References sVaccSurf::bpts, sVaccSurf::mem, 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.
| 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().

1.5.7.1