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

Inheritance diagram for BALL::SLICKEnergy:

Classes
struct	Default

struct	Option

Public Member Functions
Constructors and Destructors
	SLICKEnergy ()

	SLICKEnergy (Molecule &protein, Molecule &ligand)

	SLICKEnergy (Molecule &protein, Molecule &ligand, Options &options)

	SLICKEnergy (const SLICKEnergy &slick)

virtual	~SLICKEnergy ()

Assignment
const SLICKEnergy &	operator= (const SLICKEnergy &slick)

virtual void	clear ()

Setup Methods
bool	setup ()

Accessors specific to the SLICKEnergy scoring function
double	getCHPIScore () const

double	getHydrogenBondScore () const

double	getVDWScore () const

double	getPolarSolvationScore () const

double	getNonpolarSolvationScore () const

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 ()

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 ()

Additional Inherited Members
Static Public Member Functions inherited from BALL::ScoringFunction
static HashGrid3< Atom * > *	initializeHashGrid (AtomContainer *sys, Vector3 &center, double &resolution, int hashgrid_size)

static void	getDefaultOptions (Options &options)

Public Attributes inherited from BALL::ScoringFunction
list< Constraint * >	constraints

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)

virtual double	getES ()

void	enableAllComponents_ ()

void	fetchStaticLigandFragment (Atom *a1, int index)

int	countCovalentBonds (const Atom *atom, int threshold=-1)

virtual void	createAllLigandNonBondedPairs ()

virtual double	calculateStaticLigandFragmentEnergy ()

bool	isPeptideBond (const Bond *bond) const

Protected Attributes inherited from BALL::ScoringFunction
String	name_

Options	options_

AtomContainer *	receptor_

AtomContainer *	ligand_

double	score_

double	intercept_

ScoringBaseFunction *	base_function_

vector< ScoringComponent * >	scoring_components_

HashSet< const Atom * >	unassigned_atoms_

Size	max_number_of_errors_

Size	number_of_errors_

double	ligand_radius_

int	ligand_atoms_

Vector3	ligand_center_

HashGrid3< Atom * > *	hashgrid_

HashGrid3< Atom * > *	all_residues_hashgrid_

HashGrid3< Atom * > *	static_residues_hashgrid_

HashGrid3< Atom * > *	flexible_residues_hashgrid_

double	resolution_

std::map< Atom *, int >	atoms_to_fragments_

int	reference_neighbors_

int	neighboring_target_atoms_

int	misplaced_ligand_atoms_

int	hashgrid_search_radius_

double	nonbonded_cutoff_

double	nonbonded_cutoff_2_

bool	ignore_h_clashes_

int	overlaps_

int	ligand_intramol_overlaps_

double	allowed_intermolecular_overlap_

double	allowed_intramolecular_overlap_

double	neighbor_cutoff_2_

vector< StaticLigandFragment * >	static_ligand_fragments_

bool	store_interactions_

bool	store_interactions_phC_only_

AtomPairVector *	all_ligand_nonbonded_

double	conformation_scale_

bool	use_all_lig_nonb_

bool	use_static_lig_fragments_

int	burial_depth_scale_

double	exp_energy_stddev_

double	exp_energy_mean_

std::set< Residue * >	flexible_residues_

Result	result_

double	static_ligand_energy_

vector< Bond * >	rotatable_ligand_bonds_

list< list< Vector3 > >	flexres_org_positions_

Detailed Description

SLICKEnergy scoring function { Definition:} {BALL/SCORING/FUNCTIONS/slickEnergy.h}

Definition at line 27 of file slickEnergy.h.

Constructor & Destructor Documentation

BALL::SLICKEnergy::SLICKEnergy ( )

Default constructor.

BALL::SLICKEnergy::SLICKEnergy	(	Molecule &	protein,
		Molecule &	ligand
	)

Construct a SLICKEnergy with a system and pointers to protein and ligand

BALL::SLICKEnergy::SLICKEnergy	(	Molecule &	protein,
		Molecule &	ligand,
		Options &	options
	)

Construct a SLICKEnergy with a system and options.

BALL::SLICKEnergy::SLICKEnergy ( const SLICKEnergy & slick )

Copy constructor

virtual BALL::SLICKEnergy::~SLICKEnergy ( )

virtual

Destructor

Member Function Documentation

virtual void BALL::SLICKEnergy::clear ( )

virtual

Clear method.

Reimplemented from BALL::ScoringFunction.

double BALL::SLICKEnergy::getCHPIScore ( ) const

double BALL::SLICKEnergy::getHydrogenBondScore ( ) const

double BALL::SLICKEnergy::getNonpolarSolvationScore ( ) const

double BALL::SLICKEnergy::getPolarSolvationScore ( ) const

double BALL::SLICKEnergy::getVDWScore ( ) const

const SLICKEnergy& BALL::SLICKEnergy::operator= ( const SLICKEnergy & slick )

Assignment operator.

bool BALL::SLICKEnergy::setup ( )

Setup of scoring function

Classes

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation