7 #ifndef BALL_SOLVATION_GENERALIZED_BORN_H
8 #define BALL_SOLVATION_GENERALIZED_BORN_H
14 #ifndef BALL_KERNEL_PTE_H
18 #ifndef BALL_KERNEL_ATOMCONTAINER_H
22 #ifndef BALL_DATATYPE_STRINGHASHMAP_H
26 #ifndef BALL_FORMAT_INIFILE_H
30 #ifndef BALL_FORMAT_PARAMETERSECTION_H
184 float getSoluteDC()
const;
186 float getSolventDC()
const;
188 float getKappa()
const;
228 std::vector<const Atom*> atoms_;
232 std::vector<float> born_radii_;
237 std::vector< std::pair<Size, Size> > pair_list_;
241 std::vector< float > pair_distances_;
242 std::vector< float > pair_charges_;
243 std::vector< std::vector< float > > squared_distances_;
254 std::vector<float> scaling_factor_;
258 String scaling_factor_filename_;
288 void calculateBornRadii_();
293 float calculateCreationEnergy_()
const;
298 float calculateTransferEnergy_()
const;
309 float coulombIntegralApproximation_(
float distance,
float scaled_radius_j,
310 float radius_i)
const;
bool setup(const AtomContainer &ac)
void calculatePotential(HashMap< const Atom *, float > &p_hash) const
void setSolventDC(float solvent_dc)
??? Should be done by options
float calculateEnergy()
Compute the total energy of the system.
void setSoluteDC(float solute_dc)
??? Should be done by options
const StringHashMap< float > & getScalingFactors() const
float calculatePotential(const Atom &atom_i) const
float calculateSolvationEnergy()
void setScalingFactorFile(const String &filename)
??? This should be done through Options!
void setScalingFactors(const StringHashMap< float > &scaling_factors)
bool readScalingFactors(const String &inifile_name)
static const String LAMBDA
static const String KAPPA
static const String DC_SOLUTE
static const String DC_SOLVENT
static const String FILENAME
static const String RHO_0
static const String DELTA
static const String VERBOSITY
static const Size VERBOSITY
static const String FILENAME
static const float DC_SOLVENT
static const float LAMBDA
static const float DC_SOLUTE