#include <BALL/SCORING/FUNCTIONS/PBScoring.h>

Inheritance diagram for BALL::PBScoring:

Public Member Functions
	PBScoring (AtomContainer &receptor, AtomContainer &reference_ligand, Options &options)

	PBScoring (AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options)

Public Member Functions inherited from BALL::ScoringFunction
	ScoringFunction ()

	ScoringFunction (const ScoringFunction &sf)

	ScoringFunction (AtomContainer &receptor, AtomContainer &ligand)

	ScoringFunction (AtomContainer &receptor, AtomContainer &ligand, const Options &options)

	ScoringFunction (AtomContainer &receptor, AtomContainer &ligand, Options &options)

	ScoringFunction (AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options)

virtual	~ScoringFunction ()

virtual void	clear ()

ScoringFunction &	operator= (const ScoringFunction &sf)

bool	setup ()

bool	setup (AtomContainer &receptor, AtomContainer &ligand)

bool	setup (AtomContainer &receptor, AtomContainer &ligand, const Options &options)

void	setMaximumNumberOfErrors (Size nr)

Size	getMaximumNumberOfErrors () const

void	setFirstMolecule (AtomContainer &molecule1)

AtomContainer *	getFirstMolecule () const

void	setSecondMolecule (AtomContainer &molecule2)

AtomContainer *	getSecondMolecule () const

void	setReceptor (AtomContainer &receptor)

AtomContainer *	getReceptor () const

void	setLigand (AtomContainer &ligand)

AtomContainer *	getLigand () const

void	setIntercept (double intercept)

double	getIntercept () const

void	setBaseFunction (ScoringBaseFunction &base_function)
	Set the instance of BaseFunction for the scoring function. More...

ScoringBaseFunction *	getBaseFunction () const

void	insertComponent (ScoringComponent *component)

void	insertComponent (ScoringComponent *component, float coefficient)

void	removeComponent (const ScoringComponent *component)

void	removeComponent (const String &name)

void	setCoefficient (const ScoringComponent *component, float coefficient)

void	setCoefficient (const String &name, float coefficient)

bool	getCoefficient (const ScoringComponent *component, float &coefficient) const

bool	getCoefficient (const String &name, float &coefficient) const

ScoringComponent *	getComponent (const String &name) const

ScoringComponent *	getComponent (const Size index) const

double	calculateScore ()

const HashSet< const Atom * > &	getUnassignedAtoms () const

HashSet< const Atom * > &	getUnassignedAtoms ()

double	getExpEnergyStddev ()

void	enableStoreInteractionsOnlyForPhContraints ()

String	convertTime (double seconds)

virtual void	update ()

virtual double	updateScore ()

virtual void	printResult (bool detail=0)

void	getScoreContributions (vector< double > &score_contributions, vector< String > &names)

String	getEquation ()

void	enableStoreInteractions (bool b=true)

String	getName ()

int	getBurialDepthScale ()

String	valueToString (double value)

void	unsetTrainingParameters ()

void	setNormalizationParameters (double stddev, double mean)

const HashGrid3< Atom * > *	getHashGrid ()

const Vector3 &	getLigandCenter () const

double	getLigandRadius () const

bool	storeInteractionsEnabled ()

virtual int	getNoNeighboringReceptorAtoms ()

int	getNoLigandAtoms ()

Options	getOptions ()

Options *	getOptionsToModify ()

void	createStaticLigandFragments ()

const vector< Bond * > *	getRotatableLigandBonds () const

const vector< StaticLigandFragment * > *	getStaticLigandFragments () const

bool	hasFlexibleResidues ()

void	setFlexibleResidues (const std::set< Residue * > &flexible_residues)

bool	assignRotamer (Residue residue, ResidueRotamerSet rotamer_set, const Rotamer *rotamer)

void	resetFlexibleResidues ()

Size	countNeighboringReceptorAtoms (const Atom atom, double distance_threshold, bool onePerCell=0, int number_of_overlaps=0) const

void	resetResiduePositions (Residue *residue, list< Vector3 > &old_positions)

double	getScore ()

const std::map< Atom , int >	getAtomFragmentMap ()

Protected Member Functions
void	setup ()

double	getES ()

Protected Member Functions inherited from BALL::ScoringFunction
void	setName (String name)

void	updateComponent (int id, AtomPairList *)

Vector3	calculateGeometricalCenter (AtomContainer s, int no_ligand_atoms=NULL)

double	calculateMoleculeRadius (AtomContainer *sys, Vector3 &center)

void	setupFlexibleResidues_ ()

virtual void	setupReferenceLigand ()

int	checkForAtomOverlaps (const AtomPairVector *pair_vector)

AtomPairVector *	createNonbondedPairVector (HashGrid3< Atom * > *hashgrid, int &overlaps, bool rec_lig, bool check_fragments=0, bool intra_fragment=0)

AtomPairVector *	createLigandNonbondedPairVector (bool intra_fragment, int &overlaps)

bool	hasPharmacophoreConstraints_ ()

void	clearStoredInteractions_ ()

double	calculateConstraintsScore ()

void	enableInteractionComponents_ (const list< String > &type_names)

Public Member Functions

Protected Member Functions