Files | |
| file | vacc.h |
| Contains declarations for class Vacc. | |
Data Structures | |
| struct | sVacc |
| Oracle for solvent- and ion-accessibility around a biomolecule. More... | |
| struct | sVaccSurf |
| Surface object list of per-atom surface points. More... | |
Typedefs | |
| typedef sVaccSurf | VaccSurf |
| Declaration of the VaccSurf class as the VaccSurf structure. | |
| typedef 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). | |
| 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. | |
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Return the atomic solvent accessible surface area (SASA).
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Get the set of points for this atom's solvent-accessible surface.
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Set up an array of points corresponding to the SAS due to a particular atom.
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Construct the accessibility object.
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FORTRAN stub to construct the accessibility object.
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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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Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area.
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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.
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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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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.
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Return the total solvent accessible surface area (SASA).
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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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Allocate and construct the surface object; do not assign surface points to positions.
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Construct the surface object using previously allocated memory; do not assign surface points to positions.
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Destroy the surface object and free its memory.
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Destroy the surface object.
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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.
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1.3.5