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generalizedBornCase.h
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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: generalizedBornCase.h,v 1.1 2005/11/21 19:38:38 anker Exp $
//
#ifndef BALL_SOLVATION_GENERALIZED_BORN_H
#define BALL_SOLVATION_GENERALIZED_BORN_H
#ifndef BALL_COMMON_H
# include <BALL/common.h>
#endif
#ifndef BALL_KERNEL_PTE_H
# include <BALL/KERNEL/PTE.h>
#endif
#ifndef BALL_KERNEL_ATOMCONTAINER_H
# include <BALL/KERNEL/atomContainer.h>
#endif
#ifndef BALL_DATATYPE_STRINGHASHMAP_H
# include <BALL/DATATYPE/stringHashMap.h>
#endif
#ifndef BALL_FORMAT_INIFILE_H
# include <BALL/FORMAT/INIFile.h>
#endif
#ifndef BALL_FORMAT_PARAMETERSECTION_H
# include <BALL/FORMAT/parameterSection.h>
#endif
#include <map>
#include <set>
namespace BALL
{
class GeneralizedBornModel
{
public:
struct Option
{
static const String VERBOSITY;
static const String LAMBDA;
static const String DELTA;
static const String KAPPA;
static const String RHO_0;
static const String DC_SOLVENT;
static const String DC_SOLUTE;
static const String FILENAME;
};
struct Default
{
static const Size VERBOSITY;
static const float LAMBDA;
static const float DELTA;
static const float KAPPA;
static const float RHO_0;
static const float DC_SOLVENT;
static const float DC_SOLUTE;
static const String FILENAME;
};
GeneralizedBornModel();
~GeneralizedBornModel();
void clear();
bool setup(const AtomContainer& ac);
void setScalingFactorFile(const String& filename);
void setScalingFactors(const StringHashMap<float>& scaling_factors);
const StringHashMap<float>& getScalingFactors() const;
void setSolventDC(float solvent_dc);
void setSoluteDC(float solute_dc);
float calculateEnergy();
float calculateSolvationEnergy();
void calculatePotential(HashMap<const Atom*, float>& p_hash) const;
float calculatePotential(const Atom& atom_i) const;
bool readScalingFactors(const String& inifile_name);
private:
/* Parameters for the generalized Born model
*/
class GBParameters : public ParameterSection
{
public:
GBParameters();
~GBParameters();
bool extractSection(Parameters& parameters, const String& section_name);
const StringHashMap<float>& getScalingFactors() const;
float getSoluteDC() const;
float getSolventDC() const;
float getKappa() const;
private:
/*_
*/
StringHashMap<float> scaling_factors_;
/*_
*/
float dc_solute_;
/*_
*/
float dc_solvent_;
/*_
*/
float lambda_;
/*_
*/
float delta_;
/*_
*/
float kappa_;
/*_
*/
float rho_0_;
};
AtomContainer* ac_;
std::vector<const Atom*> atoms_;
std::vector<float> born_radii_;
std::vector< std::pair<Size, Size> > pair_list_;
std::vector< float > pair_distances_;
std::vector< float > pair_charges_;
std::vector< std::vector< float > > squared_distances_;
float dc_solute_;
float dc_solvent_;
StringHashMap<float> scaling_factors_;
std::vector<float> scaling_factor_;
String scaling_factor_filename_;
float lambda_;
float delta_;
float kappa_;
float rho_0_;
float to_kJ_mol_;
void calculateBornRadii_();
float calculateCreationEnergy_() const;
float calculateTransferEnergy_() const;
float f_GB_(Size i, Size j) const;
float coulombIntegralApproximation_(float distance, float scaled_radius_j,
float radius_i) const;
};
} // namespace BALL
#endif // BALL_SOLVATION_GENERALIZED_BORN_H
INIFile.h
PTE.h
atomContainer.h
BALL::AtomContainer
Definition atomContainer.h:32
BALL::Atom
Definition atom.h:90
BALL::GeneralizedBornModel::clear
void clear()
BALL::GeneralizedBornModel::setup
bool setup(const AtomContainer &ac)
BALL::GeneralizedBornModel::calculatePotential
void calculatePotential(HashMap< const Atom *, float > &p_hash) const
BALL::GeneralizedBornModel::setSolventDC
void setSolventDC(float solvent_dc)
??? Should be done by options
BALL::GeneralizedBornModel::calculateEnergy
float calculateEnergy()
Compute the total energy of the system.
BALL::GeneralizedBornModel::~GeneralizedBornModel
~GeneralizedBornModel()
BALL::GeneralizedBornModel::GeneralizedBornModel
GeneralizedBornModel()
BALL::GeneralizedBornModel::setSoluteDC
void setSoluteDC(float solute_dc)
??? Should be done by options
BALL::GeneralizedBornModel::calculatePotential
float calculatePotential(const Atom &atom_i) const
BALL::GeneralizedBornModel::calculateSolvationEnergy
float calculateSolvationEnergy()
BALL::GeneralizedBornModel::setScalingFactorFile
void setScalingFactorFile(const String &filename)
??? This should be done through Options!
BALL::GeneralizedBornModel::setScalingFactors
void setScalingFactors(const StringHashMap< float > &scaling_factors)
BALL::GeneralizedBornModel::readScalingFactors
bool readScalingFactors(const String &inifile_name)
BALL::GeneralizedBornModel::getScalingFactors
const StringHashMap< float > & getScalingFactors() const
BALL::HashMap
HashMap class based on the STL map (containing serveral convenience functions).
Definition hashMap.h:74
BALL::ParameterSection
Definition parameterSection.h:40
BALL::Parameters
Definition parameters.h:25
BALL::StringHashMap
Definition stringHashMap.h:42
BALL::String
Definition string.h:57
common.h
BALL
Definition constants.h:13
BALL::Size
BALL_SIZE_TYPE Size
Definition COMMON/global.h:114
parameterSection.h
stringHashMap.h
BALL::GeneralizedBornModel::Default
Definition generalizedBornCase.h:93
BALL::GeneralizedBornModel::Default::VERBOSITY
static const Size VERBOSITY
Definition generalizedBornCase.h:95
BALL::GeneralizedBornModel::Default::FILENAME
static const String FILENAME
Definition generalizedBornCase.h:116
BALL::GeneralizedBornModel::Default::DC_SOLVENT
static const float DC_SOLVENT
Definition generalizedBornCase.h:110
BALL::GeneralizedBornModel::Default::LAMBDA
static const float LAMBDA
Definition generalizedBornCase.h:98
BALL::GeneralizedBornModel::Default::DC_SOLUTE
static const float DC_SOLUTE
Definition generalizedBornCase.h:113
BALL::GeneralizedBornModel::Default::KAPPA
static const float KAPPA
Definition generalizedBornCase.h:104
BALL::GeneralizedBornModel::Default::DELTA
static const float DELTA
Definition generalizedBornCase.h:101
BALL::GeneralizedBornModel::Default::RHO_0
static const float RHO_0
Definition generalizedBornCase.h:107
BALL::GeneralizedBornModel::Option
Definition generalizedBornCase.h:66
BALL::GeneralizedBornModel::Option::LAMBDA
static const String LAMBDA
Definition generalizedBornCase.h:71
BALL::GeneralizedBornModel::Option::KAPPA
static const String KAPPA
Definition generalizedBornCase.h:77
BALL::GeneralizedBornModel::Option::DC_SOLUTE
static const String DC_SOLUTE
Definition generalizedBornCase.h:86
BALL::GeneralizedBornModel::Option::DC_SOLVENT
static const String DC_SOLVENT
Definition generalizedBornCase.h:83
BALL::GeneralizedBornModel::Option::FILENAME
static const String FILENAME
Definition generalizedBornCase.h:89
BALL::GeneralizedBornModel::Option::RHO_0
static const String RHO_0
Definition generalizedBornCase.h:80
BALL::GeneralizedBornModel::Option::DELTA
static const String DELTA
Definition generalizedBornCase.h:74
BALL::GeneralizedBornModel::Option::VERBOSITY
static const String VERBOSITY
Definition generalizedBornCase.h:68