67 #include "maloc/maloc.h" 68 #if defined(HAVE_MC_H) 77 #include "generic/apolparm.h" 133 #if !defined(VINLINE_VACC) 146 # define Vacc_memChk(thee) (Vmem_bytes((thee)->mem)) VEXTERNC Vacc * Vacc_ctor(Valist *alist, Vclist *clist, double surf_density)
Construct the accessibility object.
Contains declarations for class Valist.
VEXTERNC int Vacc_wcaEnergyAtom(Vacc *thee, APOLparm *apolparm, Valist *alist, Vclist *clist, int iatom, double *value)
Calculate the WCA energy for an atom.
VEXTERNC void Vacc_totalAtomdSASA(Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA)
Testing purposes only.
VEXTERNC double Vacc_atomSASA(Vacc *thee, double radius, Vatom *atom)
Return the atomic solvent accessible surface area (SASA)
Oracle for solvent- and ion-accessibility around a biomolecule.
VEXTERNC void Vacc_dtor(Vacc **thee)
Destroy object.
VEXTERNC unsigned long int Vacc_memChk(Vacc *thee)
Get number of bytes in this object and its members.
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 acc...
VEXTERNC double Vacc_ivdwAcc(Vacc *thee, double center[VAPBS_DIM], double radius)
Report inflated van der Waals 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_splineAccAt...
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 o...
VEXTERNC void VaccSurf_dtor2(VaccSurf *thee)
Destroy the surface object.
VEXTERNC int Vacc_wcaEnergy(Vacc *thee, APOLparm *apolparm, Valist *alist, Vclist *clist)
Return the WCA integral energy.
VEXTERNC VaccSurf * VaccSurf_refSphere(Vmem *mem, int npts)
Set up an array of points for a reference sphere of unit radius.
VEXTERNC double Vacc_totalSASA(Vacc *thee, double radius)
Return the total solvent accessible surface area (SASA)
VEXTERNC int Vacc_wcaForceAtom(Vacc *thee, APOLparm *apolparm, Vclist *clist, Vatom *atom, double *force)
Return the WCA integral force.
VEXTERNC void Vacc_dtor2(Vacc *thee)
FORTRAN stub to destroy object.
Contains a collection of useful constants and conversion factors.
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 o...
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 double Vacc_vdwAcc(Vacc *thee, double center[VAPBS_DIM])
Report van der Waals accessibility.
Contains declarations for class Vatom.
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 double Vacc_totalSAV(Vacc *thee, Vclist *clist, APOLparm *apolparm, double radius)
Return the total solvent accessible volume (SAV)
VEXTERNC void Vacc_atomdSASA(Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA)
Get the derivatve of solvent accessible area.
VEXTERNC void Vacc_totalAtomdSAV(Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA, Vclist *clist)
Total solvent accessible volume.
VEXTERNC double Vacc_fastMolAcc(Vacc *thee, double center[VAPBS_DIM], double radius)
Report molecular accessibility quickly.
VEXTERNC double Vacc_SASA(Vacc *thee, double radius)
Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area...
Contains generic macro definitions for APBS.
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 posit...
#define VAPBS_DIM
Our dimension.
VEXTERNC VaccSurf * Vacc_atomSASPoints(Vacc *thee, double radius, Vatom *atom)
Get the set of points for this atom's solvent-accessible surface.
Surface object list of per-atom surface points.
VEXTERNC void VaccSurf_dtor(VaccSurf **thee)
Destroy the surface object and free its memory.
VEXTERNC double Vacc_molAcc(Vacc *thee, double center[VAPBS_DIM], double radius)
Report molecular accessibility.
VEXTERNC int Vacc_ctor2(Vacc *thee, Valist *alist, Vclist *clist, double surf_density)
FORTRAN stub to construct the accessibility object.
Contains public data members for Vatom class/module.
Container class for list of atom objects.
Contains declarations for class Vclist.
VEXTERNC void Vacc_atomdSAV(Vacc *thee, double radius, Vatom *atom, double *dSA)
Get the derivatve of solvent accessible volume.
VEXTERNC double Vacc_splineAcc(Vacc *thee, double center[VAPBS_DIM], double win, double infrad)
Report spline-based accessibility.
Parameter structure for APOL-specific variables from input files.
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.