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 | |
| VEXTERNC unsigned long int | Vacc_memChk (Vacc *thee) |
| Get number of bytes in this object and its members. | |
| VEXTERNC VaccSurf * | VaccSurf_ctor (Vmem *mem, double probe_radius, int nsphere) |
| Allocate and construct the surface object; do not assign surface points to positions. | |
| 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. | |
| VEXTERNC void | VaccSurf_dtor (VaccSurf **thee) |
| Destroy the surface object and free its memory. | |
| VEXTERNC void | VaccSurf_dtor2 (VaccSurf *thee) |
| Destroy the surface object. | |
| VEXTERNC VaccSurf * | VaccSurf_refSphere (Vmem *mem, int npts) |
| Set up an array of points for a reference sphere of unit radius. | |
| 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. | |
| VEXTERNC Vacc * | Vacc_ctor (Valist *alist, Vclist *clist, double surf_density) |
| Construct the accessibility object. | |
| VEXTERNC int | Vacc_ctor2 (Vacc *thee, Valist *alist, Vclist *clist, double surf_density) |
| FORTRAN stub to construct the accessibility object. | |
| VEXTERNC void | Vacc_dtor (Vacc **thee) |
| Destroy object. | |
| VEXTERNC void | Vacc_dtor2 (Vacc *thee) |
| FORTRAN stub to destroy object. | |
| VEXTERNC double | Vacc_vdwAcc (Vacc *thee, double center[VAPBS_DIM]) |
| Report van der Waals accessibility. | |
| VEXTERNC double | Vacc_ivdwAcc (Vacc *thee, double center[VAPBS_DIM], double radius) |
| Report inflated van der Waals accessibility. | |
| VEXTERNC double | Vacc_molAcc (Vacc *thee, double center[VAPBS_DIM], double radius) |
| Report molecular accessibility. | |
| VEXTERNC double | Vacc_fastMolAcc (Vacc *thee, double center[VAPBS_DIM], double radius) |
| Report molecular accessibility quickly. | |
| VEXTERNC double | Vacc_splineAcc (Vacc *thee, double center[VAPBS_DIM], double win, double infrad) |
| Report spline-based accessibility. | |
| VEXTERNC void | Vacc_splineAccGrad (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, double *grad) |
| Report gradient of spline-based accessibility. | |
| VEXTERNC double | Vacc_splineAccAtom (Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom) |
| Report spline-based accessibility for a given atom. | |
| 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) | |
| 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) | |
| 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) | |
| 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) | |
| VEXTERNC double | Vacc_SASA (Vacc *thee, double radius) |
| Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area. | |
| VEXTERNC double | Vacc_totalSASA (Vacc *thee, double radius) |
| Return the total solvent accessible surface area (SASA) | |
| VEXTERNC double | Vacc_atomSASA (Vacc *thee, double radius, Vatom *atom) |
| Return the atomic solvent accessible surface area (SASA) | |
| VEXTERNC VaccSurf * | Vacc_atomSASPoints (Vacc *thee, double radius, Vatom *atom) |
| Get the set of points for this atom's solvent-accessible surface. | |
| VEXTERNC void | Vacc_atomdSAV (Vacc *thee, double radius, Vatom *atom, double *dSA) |
| Get the derivatve of solvent accessible volume. | |
| VEXTERNC void | Vacc_atomdSASA (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA) |
| Get the derivatve of solvent accessible area. | |
| VEXTERNC void | Vacc_totalAtomdSASA (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA) |
| Testing purposes only. | |
| VEXTERNC void | Vacc_totalAtomdSAV (Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA, Vclist *clist) |
| Total solvent accessible volume. | |
| VEXTERNC double | Vacc_totalSAV (Vacc *thee, Vclist *clist, APOLparm *apolparm, double radius) |
| Return the total solvent accessible volume (SAV) | |
| VEXTERNC int | Vacc_wcaEnergy (Vacc *thee, APOLparm *apolparm, Valist *alist, Vclist *clist) |
| Return the WCA integral energy. | |
| VEXTERNC int | Vacc_wcaForceAtom (Vacc *thee, APOLparm *apolparm, Vclist *clist, Vatom *atom, double *force) |
| Return the WCA integral force. | |
| VEXTERNC int | Vacc_wcaEnergyAtom (Vacc *thee, APOLparm *apolparm, Valist *alist, Vclist *clist, int iatom, double *value) |
| Calculate the WCA energy for an atom. | |
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) |
Definition at line 811 of file vacc.c.


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) |
Definition at line 124 of file vacc.c.


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) |
Definition at line 195 of file vacc.c.


| 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) |
Definition at line 573 of file vacc.c.


| 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) |
Definition at line 544 of file vacc.c.


| 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) |
Definition at line 649 of file vacc.c.


| 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. |
Definition at line 464 of file vacc.c.


| 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 |
Definition at line 387 of file vacc.c.


| VEXTERNC void Vacc_splineAccGrad | ( | Vacc * | thee, |
| double | center[VAPBS_DIM], | ||
| double | win, | ||
| double | infrad, | ||
| double * | grad | ||
| ) |
Report gradient of spline-based accessibility.
| thee | Accessibility object |
| center | Probe center coordinates |
| win | Spline window (Å) |
| infrad | Inflation radius (Å) for ion access. |
| grad | 3-vector set to gradient of accessibility |
Definition at line 497 of file vacc.c.

| 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 |
Definition at line 289 of file vacc.c.


| 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 |
Definition at line 1040 of file vacc.c.

| 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 |
Definition at line 947 of file vacc.c.

| 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 |
Definition at line 338 of file vacc.c.

| 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) |
Definition at line 1428 of file vacc.c.


| 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 int Vacc_wcaEnergyAtom | ( | Vacc * | thee, |
| APOLparm * | apolparm, | ||
| Valist * | alist, | ||
| Vclist * | clist, | ||
| int | iatom, | ||
| double * | value | ||
| ) |
Calculate the WCA energy for an atom.
| thee | Accessibility object |
| apolparm | Apolar calculation parameters |
| alist | Atom list |
| clist | Cell list associated with Vacc object |
| iatom | Index for atom of interest |
| value | Set to energy value |
Definition at line 1505 of file vacc.c.


| 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 |
Definition at line 731 of file vacc.c.


| 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 |
Definition at line 746 of file vacc.c.

| 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 |
Definition at line 867 of file vacc.c.


1.7.2