Files | |
file | vacc.h |
Contains declarations for class Vacc. | |
Data Structures | |
struct | sVacc |
Oracle for solvent- and ion-accessibility around a biomolecule. More... | |
Defines | |
#define | VACCMAXNBOR 20 |
Maximum number of neighbors used in an accessibility calculation. | |
Typedefs | |
typedef sVacc | Vacc |
Declaration of the Vacc class as the Vacc structure. | |
Functions | |
int | Vacc_memChk (Vacc *thee) |
Get number of bytes in this object and its members. | |
Vacc * | Vacc_ctor (Valist *alist, double max_radius, int nx, int ny, int nz, int nsphere) |
Construct the accessibility object. | |
int | Vacc_ctor2 (Vacc *thee, Valist *alist, double max_radius, int nx, int ny, int nz, int nsphere) |
FORTRAN stub to construct the accessibility object. | |
Vacc * | Vacc_ctorFocus (Valist *alist, double max_radius, int nx, int ny, int nz, int nsphere, double x_min, double y_min, double z_min, double x_max, double y_max, double z_max) |
FORTRAN stub to construct the accessibility object for a subdomain. | |
int | Vacc_ctor2Focus (Vacc *thee, Valist *alist, double max_radius, int nx, int ny, int nz, int nsphere, double x_min, double y_min, double z_min, double x_max, double y_max, double z_max) |
FORTRAN stub to construct the accessibility object for a subdomain. | |
void | Vacc_dtor (Vacc **thee) |
Destroy object. | |
void | Vacc_dtor2 (Vacc *thee) |
FORTRAN stub to destroy object. | |
double | Vacc_vdwAcc (Vacc *thee, double center[3]) |
Report van der Waals accessibility. | |
double | Vacc_ivdwAcc (Vacc *thee, double center[3], double radius) |
Report inflated van der Waals accessibility. | |
double | Vacc_molAcc (Vacc *thee, double center[3], double radius) |
Report molecular accessibility. | |
double | Vacc_fastMolAcc (Vacc *thee, double center[3], double radius) |
Report molecular accessibility quickly. | |
double | Vacc_splineAcc (Vacc *thee, double center[3], double win, double infrad) |
Report spline-based accessibility. | |
double | Vacc_splineAccAtom (Vacc *thee, double center[3], double win, double infrad, int atomID) |
Report spline-based accessibility for a given atom. | |
void | Vacc_splineAccGradAtom (Vacc *thee, double center[3], double win, double infrad, int atomID, 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). | |
double ** | Vacc_sphere (Vacc *thee, int *npts) |
Set up an array of points for the reference sphere. | |
double | Vacc_totalSASA (Vacc *thee, double radius) |
Calculates the solvent-accessible area of the entire molecules. | |
double | Vacc_atomSASA (Vacc *thee, double radius, int iatom) |
Calculates the solvent-accessible area due to the specified atom. |
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Calculates the solvent-accessible area due to the specified atom.
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Construct the accessibility object.
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FORTRAN stub to construct the accessibility object.
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FORTRAN stub to construct the accessibility object for a subdomain.
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FORTRAN stub to construct the accessibility object for a subdomain.
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Destroy object.
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FORTRAN stub to destroy object.
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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.
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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.
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Get number of bytes in this object and its members.
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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.
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Set up an array of points for the reference sphere. Generates approximately npts # of points (actual number stored in npts) somewhat uniformly distributed across a sphere of unit radius centered at the origin. Returns an (npts x 3) double array, which the user is responsible for destroying.
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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.
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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.
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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.
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Calculates the solvent-accessible area of the entire molecules.
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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).
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