BALL::RotationalEntropyLoss Class Reference

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

Inheritance diagram for BALL::RotationalEntropyLoss:

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 RotationalEntropyLoss &	operator= (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 ()
ScoringFunction *	getScoringFunction () 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< bool >	is_frozen_
Size	algorithm_type_
std::vector< std::pair< double, double > >	heavy_atom_fractions_
HashGrid3< const Atom * > *	grid_
float	grid_spacing_
Molecule *	receptor_
Molecule *	ligand_
float	bind_distance_offset_
Size	calculation_method_
HashMap< const Atom *, Size >	fresno_types_

Additional Inherited Members
Protected Attributes inherited from BALL::ScoringComponent
ScoringFunction *	scoring_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

enum BALL::RotationalEntropyLoss::AlgorithmType

Enumerator
ALGORITHM__GUESS
ALGORITHM__DATABASE

Definition at line 25 of file rotationalEntropyLoss.h.

enum BALL::RotationalEntropyLoss::CalculationMethod

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.