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class FDPB
{
%TypeHeaderCode
#include <BALL/SOLVATION/poissonBoltzmann.h>
%End
public:
enum ErrorCode
{
ERROR__NONE = -1,
ERROR__UNKNOWN = 0,
ERROR__NOT_IMPLEMENTED = 1,
ERROR__CANNOT_CREATE_ATOM_ARRAY,
ERROR__CANNOT_CREATE_SAS_GRID,
ERROR__CANNOT_CREATE_EPSILON_GRID,
ERROR__CANNOT_CREATE_KAPPA_GRID,
ERROR__CANNOT_CREATE_CHARGE_GRID,
ERROR__CANNOT_CREATE_PHI_GRID,
ERROR__SAS_GRID_REQUIRED,
ERROR__EPSILON_GRID_REQUIRED,
ERROR__ATOM_ARRAY_REQUIRED,
ERROR__PHI_GRID_REQUIRED,
ERROR__OUT_OF_MEMORY,
ERROR__UNKNOWN_DIELECTRIC_SMOOTHING_METHOD,
ERROR__UNKNOWN_CHARGE_DISTRIBUTION_METHOD,
ERROR__UNKNOWN_BOUNDARY_CONDITION_TYPE,
ERROR__NOT_A_VECTOR_IN_UPPER_LOWER,
ERROR__ILLEGAL_VALUE_FOR_LOWER_UPPER,
ERROR__SETUP_REQUIRED,
NUMBER_OF_ERRORS
};
struct Option
{
static const String& VERBOSITY;
static const String& PRINT_TIMING;
static const String& SPACING;
static const String& BORDER;
static const String& IONIC_STRENGTH;
static const String& SOLUTE_DC;
static const String& SOLVENT_DC;
static const String& PROBE_RADIUS;
static const String& ION_RADIUS;
static const String& TEMPERATURE;
static const String& BOUNDARY;
static const String& CHARGE_DISTRIBUTION;
static const String& DIELECTRIC_SMOOTHING;
static const String& OFFSET;
static const String& RMS_CRITERION;
static const String& MAX_CRITERION;
static const String& CHECK_AFTER_ITERATIONS;
static const String& MAX_ITERATIONS;
static const String& LOWER;
static const String& UPPER;
static const String& BOUNDING_BOX_LOWER;
static const String& BOUNDING_BOX_UPPER;
};
struct Boundary
{
static const String& ZERO;
static const String& DEBYE;
static const String& COULOMB;
static const String& DIPOLE;
static const String& FOCUSING;
};
struct ChargeDistribution
{
static const String& TRILINEAR;
static const String& UNIFORM;
};
struct DielectricSmoothing
{
static const String& NONE;
static const String& UNIFORM;
static const String& HARMONIC;
};
class Default
{
public:
static const int VERBOSITY;
static const bool PRINT_TIMING ;
static const float SPACING;
static const float BORDER;
static const float IONIC_STRENGTH;
static const float TEMPERATURE;
static const float PROBE_RADIUS;
static const float ION_RADIUS;
static const String BOUNDARY;
static const String CHARGE_DISTRIBUTION;
static const String DIELECTRIC_SMOOTHING;
static const float SOLVENT_DC;
static const float SOLUTE_DC;
static const float RMS_CRITERION;
static const float MAX_CRITERION;
static const int MAX_ITERATIONS;
static const int CHECK_AFTER_ITERATIONS;
};
class FastAtomStruct
{
public:
float q;
float r;
float x;
float y;
float z;
int index;
};
typedef struct FastAtomStruct FastAtom;
FDPB();
FDPB(const FDPB&);
FDPB(System&);
FDPB(Options&);
FDPB(System&, Options&);
~FDPB();
void destroy();
void destroyGrids();
bool setup(System&);
bool setup(System&, Options&);
bool setupEpsGrid(System&);
bool setupSASGrid(System&);
bool setupAtomArray(System&);
bool setupKappaGrid();
bool setupQGrid();
bool setupPhiGrid();
bool setupBoundary();
bool solve();
double getEnergy() const;
double getReactionFieldEnergy() const;
double calculateReactionFieldEnergy() const;
Size getNumberOfIterations() const;
Index getErrorCode() const;
static String getErrorMessage(Index);
Options options;
Options results;
RegularData3D* kappa_grid;
RegularData3D* q_grid;
RegularData3D* phi_grid;
};
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