BALL  1.4.1
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BALL::RotationalEntropyLoss Class Reference

#include <BALL/SCORING/COMPONENTS/rotationalEntropyLoss.h>

Inheritance diagram for BALL::RotationalEntropyLoss:
BALL::ScoringComponent

Classes

struct  Default
struct  Option

Public Types

enum  AlgorithmType { ALGORITHM__GUESS = 0, ALGORITHM__DATABASE = 1 }
enum  CalculationMethod {
  CALCULATION__ORIGINAL = 1, CALCULATION__BOEHM = 2, CALCULATION__GLYCOSIDIC_BONDS = 3, CALCULATION__FROZEN_GLYCOSIDIC_BONDS = 4,
  CALCULATION__GLYCOSIDIC_CONTRIBUTION = 5
}

Public Member Functions

Constructors and Destructors
 RotationalEntropyLoss ()
 RotationalEntropyLoss (ScoringFunction &sf)
 RotationalEntropyLoss (const RotationalEntropyLoss &fr)
virtual ~RotationalEntropyLoss ()
Assignment
const RotationalEntropyLossoperator= (const RotationalEntropyLoss &fr)
virtual void clear ()
Predicates.
bool operator== (const RotationalEntropyLoss &fr) const
Setup Methods
virtual bool setup ()
Accessors
virtual double calculateScore ()
- Public Member Functions inherited from BALL::ScoringComponent
 ScoringComponent ()
 ScoringComponent (const ScoringComponent &sc)
 ScoringComponent (ScoringFunction &sf)
virtual ~ScoringComponent ()
ScoringFunctiongetScoringFunction () const
void setScoringFunction (ScoringFunction &sf)
String getName () const
void setName (const String &name)
virtual double getScore () const

Private Member Functions

void cycleDFS_ (const Atom *atom, HashSet< const Atom * > &visited, HashSet< const Bond * > &tree, std::stack< const Bond * > &possible_cycle_bonds, HashSet< const Bond * > &cycle_bonds, int &cycle_count)
void heavyAtomsDFS_ (const Atom *atom, const Bond *bond, HashSet< const Atom * > &visited, int &heavy_atom_count, int &nonlip_heavy_atom_count)
void updateFrozenBonds_ ()
bool frozenBondsDFS_ (const Atom *atom, HashSet< const Atom * > &visited)

Private Attributes

std::vector< const Bond * > rotatable_bonds_
HashSet< const Bond * > glycosidic_bonds_
Size N_rot_
std::vector< boolis_frozen_
Size algorithm_type_
std::vector< std::pair< double,
double > > 
heavy_atom_fractions_
HashGrid3< const Atom * > * grid_
float grid_spacing_
Moleculereceptor_
Moleculeligand_
float bind_distance_offset_
Size calculation_method_
HashMap< const Atom *, Sizefresno_types_

Additional Inherited Members

- Protected Attributes inherited from BALL::ScoringComponent
ScoringFunctionscoring_function_
double score_

Detailed Description

SLICK rotational entropy loss contrbution { Definition:} {BALL/SCORING/COMPONENTS/rotationalEntropyLoss.h}

Definition at line 19 of file rotationalEntropyLoss.h.

Member Enumeration Documentation

Enumerator:
ALGORITHM__GUESS 
ALGORITHM__DATABASE 

Definition at line 25 of file rotationalEntropyLoss.h.

Enumerator:
CALCULATION__ORIGINAL 

The original Chemscore term.

CALCULATION__BOEHM 

The term developed by Böhm (N_rot)

CALCULATION__GLYCOSIDIC_BONDS 

The number of glycosidic bonds.

CALCULATION__FROZEN_GLYCOSIDIC_BONDS 

The number of frozen glycosidic bonds.

CALCULATION__GLYCOSIDIC_CONTRIBUTION 

The contribution of glycosidic bonds to the original term.

Definition at line 33 of file rotationalEntropyLoss.h.

Constructor & Destructor Documentation

BALL::RotationalEntropyLoss::RotationalEntropyLoss ( )

Default constructor.

BALL::RotationalEntropyLoss::RotationalEntropyLoss ( ScoringFunction sf)

Constructor.

BALL::RotationalEntropyLoss::RotationalEntropyLoss ( const RotationalEntropyLoss fr)

Copy constructor

virtual BALL::RotationalEntropyLoss::~RotationalEntropyLoss ( )
virtual

Destructor.

Member Function Documentation

virtual double BALL::RotationalEntropyLoss::calculateScore ( )
virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ScoringComponent.

virtual void BALL::RotationalEntropyLoss::clear ( )
virtual

Clear method.

Reimplemented from BALL::ScoringComponent.

void BALL::RotationalEntropyLoss::cycleDFS_ ( const Atom atom,
HashSet< const Atom * > &  visited,
HashSet< const Bond * > &  tree,
std::stack< const Bond * > &  possible_cycle_bonds,
HashSet< const Bond * > &  cycle_bonds,
int &  cycle_count 
)
private
bool BALL::RotationalEntropyLoss::frozenBondsDFS_ ( const Atom atom,
HashSet< const Atom * > &  visited 
)
private
void BALL::RotationalEntropyLoss::heavyAtomsDFS_ ( const Atom atom,
const Bond bond,
HashSet< const Atom * > &  visited,
int &  heavy_atom_count,
int &  nonlip_heavy_atom_count 
)
private
const RotationalEntropyLoss& BALL::RotationalEntropyLoss::operator= ( const RotationalEntropyLoss fr)

Assignment.

bool BALL::RotationalEntropyLoss::operator== ( const RotationalEntropyLoss fr) const
virtual bool BALL::RotationalEntropyLoss::setup ( )
virtual

Setup method.

Reimplemented from BALL::ScoringComponent.

void BALL::RotationalEntropyLoss::updateFrozenBonds_ ( )
private

Member Data Documentation

Size BALL::RotationalEntropyLoss::algorithm_type_
private

Definition at line 195 of file rotationalEntropyLoss.h.

float BALL::RotationalEntropyLoss::bind_distance_offset_
private

Definition at line 221 of file rotationalEntropyLoss.h.

Size BALL::RotationalEntropyLoss::calculation_method_
private

Definition at line 225 of file rotationalEntropyLoss.h.

HashMap<const Atom*, Size> BALL::RotationalEntropyLoss::fresno_types_
private

Definition at line 229 of file rotationalEntropyLoss.h.

HashSet<const Bond*> BALL::RotationalEntropyLoss::glycosidic_bonds_
private

Definition at line 181 of file rotationalEntropyLoss.h.

HashGrid3<const Atom*>* BALL::RotationalEntropyLoss::grid_
private

Definition at line 205 of file rotationalEntropyLoss.h.

float BALL::RotationalEntropyLoss::grid_spacing_
private

Definition at line 209 of file rotationalEntropyLoss.h.

std::vector< std::pair<double, double> > BALL::RotationalEntropyLoss::heavy_atom_fractions_
private

Definition at line 200 of file rotationalEntropyLoss.h.

std::vector<bool> BALL::RotationalEntropyLoss::is_frozen_
private

Definition at line 190 of file rotationalEntropyLoss.h.

Molecule* BALL::RotationalEntropyLoss::ligand_
private

Definition at line 217 of file rotationalEntropyLoss.h.

Size BALL::RotationalEntropyLoss::N_rot_
private

Definition at line 185 of file rotationalEntropyLoss.h.

Molecule* BALL::RotationalEntropyLoss::receptor_
private

Definition at line 213 of file rotationalEntropyLoss.h.

std::vector<const Bond*> BALL::RotationalEntropyLoss::rotatable_bonds_
private

Definition at line 177 of file rotationalEntropyLoss.h.