APBS
1.5
|
Solvent- and ion-accessibility oracle. More...
Files | |
file | vacc.c |
Class Vacc methods. | |
file | vacc.h |
Contains declarations for class Vacc. | |
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... | |
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 | |
VEXTERNC unsigned long int | Vacc_memChk (Vacc *thee) |
Get number of bytes in this object and its members. More... | |
VEXTERNC VaccSurf * | VaccSurf_ctor (Vmem *mem, double probe_radius, int nsphere) |
Allocate and construct the surface object; do not assign surface points to positions. More... | |
VEXTERNC 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. More... | |
VEXTERNC void | VaccSurf_dtor (VaccSurf **thee) |
Destroy the surface object and free its memory. More... | |
VEXTERNC void | VaccSurf_dtor2 (VaccSurf *thee) |
Destroy the surface object. More... | |
VEXTERNC VaccSurf * | VaccSurf_refSphere (Vmem *mem, int npts) |
Set up an array of points for a reference sphere of unit radius. More... | |
VEXTERNC 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. More... | |
VEXTERNC Vacc * | Vacc_ctor (Valist *alist, Vclist *clist, double surf_density) |
Construct the accessibility object. More... | |
VEXTERNC int | Vacc_ctor2 (Vacc *thee, Valist *alist, Vclist *clist, double surf_density) |
FORTRAN stub to construct the accessibility object. More... | |
VEXTERNC void | Vacc_dtor (Vacc **thee) |
Destroy object. More... | |
VEXTERNC void | Vacc_dtor2 (Vacc *thee) |
FORTRAN stub to destroy object. More... | |
VEXTERNC double | Vacc_vdwAcc (Vacc *thee, double center[VAPBS_DIM]) |
Report van der Waals accessibility. More... | |
VEXTERNC double | Vacc_ivdwAcc (Vacc *thee, double center[VAPBS_DIM], double radius) |
Report inflated van der Waals accessibility. More... | |
VEXTERNC double | Vacc_molAcc (Vacc *thee, double center[VAPBS_DIM], double radius) |
Report molecular accessibility. More... | |
VEXTERNC double | Vacc_fastMolAcc (Vacc *thee, double center[VAPBS_DIM], double radius) |
Report molecular accessibility quickly. More... | |
VEXTERNC double | Vacc_splineAcc (Vacc *thee, double center[VAPBS_DIM], double win, double infrad) |
Report spline-based accessibility. More... | |
VEXTERNC void | Vacc_splineAccGrad (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, double *grad) |
Report gradient of spline-based accessibility. More... | |
VEXTERNC double | Vacc_splineAccAtom (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom) |
Report spline-based accessibility for a given atom. More... | |
VEXTERNC 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) More... | |
VEXTERNC 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) More... | |
VEXTERNC 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) More... | |
VEXTERNC 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) More... | |
VEXTERNC double | Vacc_SASA (Vacc *thee, double radius) |
Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area. More... | |
VEXTERNC double | Vacc_totalSASA (Vacc *thee, double radius) |
Return the total solvent accessible surface area (SASA) More... | |
VEXTERNC double | Vacc_atomSASA (Vacc *thee, double radius, Vatom *atom) |
Return the atomic solvent accessible surface area (SASA) More... | |
VEXTERNC VaccSurf * | Vacc_atomSASPoints (Vacc *thee, double radius, Vatom *atom) |
Get the set of points for this atom's solvent-accessible surface. More... | |
VEXTERNC void | Vacc_atomdSAV (Vacc *thee, double radius, Vatom *atom, double *dSA) |
Get the derivatve of solvent accessible volume. More... | |
VEXTERNC void | Vacc_atomdSASA (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA) |
Get the derivatve of solvent accessible area. More... | |
VEXTERNC void | Vacc_totalAtomdSASA (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA) |
Testing purposes only. More... | |
VEXTERNC void | Vacc_totalAtomdSAV (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA, Vclist *clist) |
Total solvent accessible volume. More... | |
VEXTERNC double | Vacc_totalSAV (Vacc *thee, Vclist *clist, APOLparm *apolparm, double radius) |
Return the total solvent accessible volume (SAV) More... | |
VEXTERNC int | Vacc_wcaEnergy (Vacc *thee, APOLparm *apolparm, Valist *alist, Vclist *clist) |
Return the WCA integral energy. More... | |
VEXTERNC int | Vacc_wcaForceAtom (Vacc *thee, APOLparm *apolparm, Vclist *clist, Vatom *atom, double *force) |
Return the WCA integral force. More... | |
VEXTERNC int | Vacc_wcaEnergyAtom (Vacc *thee, APOLparm *apolparm, Valist *alist, Vclist *clist, int iatom, double *value) |
Calculate the WCA energy for an atom. More... | |
Solvent- and ion-accessibility oracle.
Set up an array of points corresponding to the SAS due to a particular atom.
thee | Accessibility object for molecule |
atom | Atom for which the surface should be constructed |
ref | Reference sphere which sets the resolution for the surface. |
probe_radius | Probe radius (in A) |
Construct the accessibility object.
alist | Molecule for accessibility queries |
clist | Pre-constructed cell list for looking up atoms near specific positions |
surf_density | Minimum per-atom solvent accessible surface point density (in pts/A^2) |
FORTRAN stub to construct the accessibility object.
thee | Memory for Vacc objet |
alist | Molecule for accessibility queries |
clist | Pre-constructed cell list for looking up atoms near specific positions |
surf_density | Minimum per-atom solvent accessible surface point density (in pts/A^2) |
VEXTERNC void Vacc_dtor | ( | Vacc ** | thee | ) |
VEXTERNC void Vacc_dtor2 | ( | Vacc * | thee | ) |
VEXTERNC 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.
thee | Accessibility object |
center | Probe center coordinates |
radius | Probe radius (in Å) |
VEXTERNC 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.
thee | Accessibility object |
center | Probe center coordinates |
radius | Probe radius (Å) |
VEXTERNC unsigned long int Vacc_memChk | ( | Vacc * | thee | ) |
VEXTERNC 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.
thee | Accessibility object |
center | Probe center coordinates |
radius | Probe radius (in Å) |
VEXTERNC double Vacc_SASA | ( | Vacc * | thee, |
double | radius | ||
) |
Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area.
thee | Accessibility object |
radius | Probe molecule radius (Å) |
VEXTERNC 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.
thee | Accessibility object |
center | Probe center coordinates |
win | Spline window (Å) |
infrad | Inflation radius (Å) for ion access. |
VEXTERNC 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.
thee | Accessibility object |
center | Probe center coordinates |
win | Spline window (Å) |
infrad | Inflation radius (Å) for ion access. |
atom | Atom |
VEXTERNC void Vacc_splineAccGrad | ( | Vacc * | thee, |
double | center[VAPBS_DIM], | ||
double | win, | ||
double | infrad, | ||
double * | grad | ||
) |
VEXTERNC 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.
thee | Accessibility object |
center | Probe center coordinates |
win | Spline window (Å) |
infrad | Inflation radius (Å) for ion access. |
atom | Atom |
force | VAPBS_DIM-vector set to gradient of accessibility |
VEXTERNC 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)
thee | Accessibility object |
center | Probe center coordinates |
win | Spline window (Å) |
infrad | Inflation radius (Å) for ion access. |
atom | Atom |
force | VAPBS_DIM-vector set to gradient of accessibility |
VEXTERNC 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)
thee | Accessibility object |
center | Probe center coordinates |
win | Spline window (Å) |
infrad | Inflation radius (Å) for ion access. |
atom | Atom |
force | VAPBS_DIM-vector set to gradient of accessibility |
VEXTERNC 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.
thee | Accessibility object |
center | Probe center coordinates |
win | Spline window (Å) |
infrad | Inflation radius (Å) for ion access. |
atom | Atom |
force | VAPBS_DIM-vector set to gradient of accessibility |
VEXTERNC double Vacc_totalSASA | ( | Vacc * | thee, |
double | radius | ||
) |
Return the total solvent accessible volume (SAV)
thee | Accessibility object |
clist | Clist for acc object |
apolparm | Apolar parameters – could be VNULL if none required for this calculation. If VNULL, then default settings are used |
radius | Probe molecule radius (Å) |
VEXTERNC 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).
thee | Accessibility object |
center | Probe center coordinates |
VEXTERNC VaccSurf* VaccSurf_ctor | ( | Vmem * | mem, |
double | probe_radius, | ||
int | nsphere | ||
) |
Allocate and construct the surface object; do not assign surface points to positions.
mem | Memory manager (can be VNULL) |
probe_radius | Probe radius (in A) for this surface |
nsphere | Number of points in sphere |
VEXTERNC 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.
thee | Allocated memory |
mem | Memory manager (can be VNULL) |
probe_radius | Probe radius (in A) for this surface |
nsphere | Number of points in sphere |
VEXTERNC void VaccSurf_dtor | ( | VaccSurf ** | thee | ) |
VEXTERNC void VaccSurf_dtor2 | ( | VaccSurf * | thee | ) |
VEXTERNC 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.
mem | Memory object |
npts | Requested number of points on sphere |