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polarSolvation.h
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// $Id: polarSolvation.h,v 1.2 2006/05/21 17:49:46 anker Exp $
#ifndef BALL_SCORING_COMPONENTS_POLARSOLVATION_H
#define BALL_SCORING_COMPONENTS_POLARSOLVATION_H
#include <BALL/SCORING/COMMON/scoringComponent.h>
#include <BALL/SOLVATION/poissonBoltzmann.h>
#include <BALL/SOLVATION/generalizedBornCase.h>
namespace BALL
{
class BALL_EXPORT PolarSolvation : public ScoringComponent
{
public:
enum CalculationMethod
{
CALCULATION__FRESNO,
CALCULATION__FULL_SLICK,
CALCULATION__FULL_CYCLE,
CALCULATION__FULL_CYCLE_FOCUSED,
CALCULATION__COULOMB,
CALCULATION__EEF1
};
enum AveragingMethod
{
AVERAGING__NONE,
AVERAGING__STATIC,
AVERAGING__RANDOM_FACTOR,
AVERAGING__RANDOM
};
struct BALL_EXPORT Option
{
static const char* POLAR_METHOD;
static const char* POLAR_GB;
static const char* POLAR_AVG;
static const char* POLAR_FOCUS_GRID_AROUND_LIGAND;
static const char* GB_SCALING_FILE;
static const char* UNITE_ATOMS;
static const char* VERBOSITY;
static const char* POLAR_OVERWRITE_RADII;
static const char* POLAR_OVERWRITE_CHARGES;
static const char* POLAR_RADIUS_RULES;
static const char* POLAR_CHARGE_RULES;
};
struct Default
{
static const Size POLAR_METHOD;
static const bool POLAR_GB;
static const Size POLAR_AVG;
static const bool POLAR_FOCUS_GRID_AROUND_LIGAND;
static const String GB_SCALING_FILE;
static const bool UNITE_ATOMS;
static const Size VERBOSITY;
static const bool POLAR_OVERWRITE_RADII;
static const bool POLAR_OVERWRITE_CHARGES;
static const String POLAR_RADIUS_RULES;
static const String POLAR_CHARGE_RULES;
};
PolarSolvation()
;
PolarSolvation(ScoringFunction& sf)
;
PolarSolvation(const PolarSolvation& fhb)
;
virtual ~PolarSolvation()
;
const PolarSolvation& operator = (const PolarSolvation& fr)
;
virtual void clear()
;
bool operator == (const PolarSolvation& fr) const
;
virtual bool setup();
void update(const vector<std::pair<Atom*, Atom*> >& /* pair_vector */);
virtual double updateScore();
private:
/*_
*/
Molecule desolv_protein_;
/*_
*/
Molecule desolv_ligand_;
/*_
*/
Size calculation_method_;
/*_
*/
Size averaging_;
/*_
*/
bool unite_atoms_;
/*_
*/
Size verbosity_;
/*_
*/
FDPB fdpb_;
/*_
*/
GeneralizedBornModel gbm_;
/*_
*/
bool use_gb_;
/*_
*/
float spacing_;
/*_
*/
float bulk_water_dc_;
/*_
*/
float vacuum_dc_;
/*_
*/
bool computeEnergyDifference_(System& system, float& energy)
;
/*_
*/
bool computeESEnergy_(System& system, float& energy)
;
/*_
*/
float computeESInteractionEnergy_(const Molecule& molecule, const
HashMap<const Atom*, float>& p_hash)
;
/*_
*/
bool computeFullCycle_(System& system, Molecule& protein,
Molecule& ligand, float& energy)
;
/*_
*/
Vector3 permuteComponentSigns_(Vector3 vector, Size permutation)
;
/*_ Condense hydrogens without radius but bearing charges on the heavy
atom they are attached to
*/
Size uniteAtoms_(Molecule& molecule)
;
};
} // namespace BALL
#endif // BALL_SCORING_COMPONENTS_POLARSOLVATION_H
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
BALL::FDPB
Definition poissonBoltzmann.h:37
BALL::GeneralizedBornModel
Definition generalizedBornCase.h:62
BALL::HashMap
HashMap class based on the STL map (containing serveral convenience functions).
Definition hashMap.h:74
BALL::Molecule
Definition molecule.h:31
BALL::PolarSolvation::PolarSolvation
PolarSolvation(ScoringFunction &sf)
BALL::PolarSolvation::update
void update(const vector< std::pair< Atom *, Atom * > > &)
BALL::PolarSolvation::setup
virtual bool setup()
BALL::PolarSolvation::CalculationMethod
CalculationMethod
Definition polarSolvation.h:23
BALL::PolarSolvation::CALCULATION__EEF1
@ CALCULATION__EEF1
Definition polarSolvation.h:47
BALL::PolarSolvation::CALCULATION__FRESNO
@ CALCULATION__FRESNO
Definition polarSolvation.h:27
BALL::PolarSolvation::CALCULATION__COULOMB
@ CALCULATION__COULOMB
Definition polarSolvation.h:43
BALL::PolarSolvation::CALCULATION__FULL_SLICK
@ CALCULATION__FULL_SLICK
Definition polarSolvation.h:31
BALL::PolarSolvation::CALCULATION__FULL_CYCLE
@ CALCULATION__FULL_CYCLE
Definition polarSolvation.h:35
BALL::PolarSolvation::CALCULATION__FULL_CYCLE_FOCUSED
@ CALCULATION__FULL_CYCLE_FOCUSED
Definition polarSolvation.h:39
BALL::PolarSolvation::AveragingMethod
AveragingMethod
Definition polarSolvation.h:54
BALL::PolarSolvation::AVERAGING__NONE
@ AVERAGING__NONE
Definition polarSolvation.h:57
BALL::PolarSolvation::AVERAGING__STATIC
@ AVERAGING__STATIC
Definition polarSolvation.h:62
BALL::PolarSolvation::AVERAGING__RANDOM_FACTOR
@ AVERAGING__RANDOM_FACTOR
Definition polarSolvation.h:67
BALL::PolarSolvation::AVERAGING__RANDOM
@ AVERAGING__RANDOM
Definition polarSolvation.h:73
BALL::PolarSolvation::~PolarSolvation
virtual ~PolarSolvation()
BALL::PolarSolvation::PolarSolvation
PolarSolvation(const PolarSolvation &fhb)
BALL::PolarSolvation::PolarSolvation
PolarSolvation()
BALL::PolarSolvation::updateScore
virtual double updateScore()
BALL::PolarSolvation::clear
virtual void clear()
BALL::ScoringComponent::ScoringComponent
ScoringComponent()
BALL::ScoringFunction
Definition scoringFunction.h:29
BALL::String
Definition string.h:57
BALL::System
Definition KERNEL/system.h:40
generalizedBornCase.h
BALL
Definition constants.h:13
BALL::Size
BALL_SIZE_TYPE Size
Definition COMMON/global.h:114
BALL::Vector3
TVector3< float > Vector3
Definition vector3.h:1084
poissonBoltzmann.h
scoringComponent.h
BALL::PolarSolvation::Default
Definition polarSolvation.h:129
BALL::PolarSolvation::Default::POLAR_CHARGE_RULES
static const String POLAR_CHARGE_RULES
Definition polarSolvation.h:173
BALL::PolarSolvation::Default::VERBOSITY
static const Size VERBOSITY
Definition polarSolvation.h:157
BALL::PolarSolvation::Default::POLAR_FOCUS_GRID_AROUND_LIGAND
static const bool POLAR_FOCUS_GRID_AROUND_LIGAND
Definition polarSolvation.h:145
BALL::PolarSolvation::Default::GB_SCALING_FILE
static const String GB_SCALING_FILE
Definition polarSolvation.h:149
BALL::PolarSolvation::Default::POLAR_AVG
static const Size POLAR_AVG
Definition polarSolvation.h:141
BALL::PolarSolvation::Default::UNITE_ATOMS
static const bool UNITE_ATOMS
Definition polarSolvation.h:153
BALL::PolarSolvation::Default::POLAR_METHOD
static const Size POLAR_METHOD
Definition polarSolvation.h:133
BALL::PolarSolvation::Default::POLAR_OVERWRITE_CHARGES
static const bool POLAR_OVERWRITE_CHARGES
Definition polarSolvation.h:165
BALL::PolarSolvation::Default::POLAR_RADIUS_RULES
static const String POLAR_RADIUS_RULES
Definition polarSolvation.h:169
BALL::PolarSolvation::Default::POLAR_OVERWRITE_RADII
static const bool POLAR_OVERWRITE_RADII
Definition polarSolvation.h:161
BALL::PolarSolvation::Default::POLAR_GB
static const bool POLAR_GB
Definition polarSolvation.h:137
BALL::PolarSolvation::Option
Definition polarSolvation.h:79
BALL::PolarSolvation::Option::POLAR_FOCUS_GRID_AROUND_LIGAND
static const char * POLAR_FOCUS_GRID_AROUND_LIGAND
Definition polarSolvation.h:95
BALL::PolarSolvation::Option::UNITE_ATOMS
static const char * UNITE_ATOMS
Definition polarSolvation.h:103
BALL::PolarSolvation::Option::POLAR_CHARGE_RULES
static const char * POLAR_CHARGE_RULES
Definition polarSolvation.h:123
BALL::PolarSolvation::Option::POLAR_GB
static const char * POLAR_GB
Definition polarSolvation.h:87
BALL::PolarSolvation::Option::GB_SCALING_FILE
static const char * GB_SCALING_FILE
Definition polarSolvation.h:99
BALL::PolarSolvation::Option::VERBOSITY
static const char * VERBOSITY
Definition polarSolvation.h:107
BALL::PolarSolvation::Option::POLAR_OVERWRITE_CHARGES
static const char * POLAR_OVERWRITE_CHARGES
Definition polarSolvation.h:115
BALL::PolarSolvation::Option::POLAR_OVERWRITE_RADII
static const char * POLAR_OVERWRITE_RADII
Definition polarSolvation.h:111
BALL::PolarSolvation::Option::POLAR_AVG
static const char * POLAR_AVG
Definition polarSolvation.h:91
BALL::PolarSolvation::Option::POLAR_RADIUS_RULES
static const char * POLAR_RADIUS_RULES
Definition polarSolvation.h:119
BALL::PolarSolvation::Option::POLAR_METHOD
static const char * POLAR_METHOD
Definition polarSolvation.h:83