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

Inheritance diagram for BALL::GridedPLP:

Public Member Functions
	GridedPLP (AtomContainer &receptor, AtomContainer &ligand, Options &options)

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

void	setLigand (AtomContainer *sys)

Public Member Functions inherited from BALL::DiffGridBasedScoring
	DiffGridBasedScoring (AtomContainer &receptor, AtomContainer &ligand, Options &options)

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

	~DiffGridBasedScoring ()

void	update ()

virtual double	updateScore ()

void	testOverlaps (Vector3 &position, HashGrid3< Atom * > *hashg=NULL)

Public Member Functions inherited from BALL::GridBasedScoring
	GridBasedScoring (AtomContainer &receptor, AtomContainer &ligand, Options &options)

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

virtual	~GridBasedScoring ()

void	defineGridSet (AtomContainer *sys, Vector3 &angstroem, double out_of_grid_penalty, bool enforce_grid_boundaries, double resolution, double interaction_no_scale=1)

void	defineGridSet (AtomContainer *sys, double out_of_grid_penalty, bool enforce_grid_boundaries, double resolution, double interaction_no_scale=1)

void	defineFlexibleResiduesGridSet ()

void	printResult ()

void	setAtomTypeNames (std::set< String > &types)

void	precalculateGrids (bool ony_flexRes_grids=false)

void	saveGridSetsToFile (String file, String receptor_name)

void	readAdditionalGridSetFromFile (String file)

void	replaceGridSetFromFile (String file)

void	loadFlexibleResidueScoreGrids (std::list< std::pair< const Residue , const Rotamer > > residue_list)

void	setupReferenceLigand ()

void	setCombineOperation (int i)

int	getNoNeighboringReceptorAtoms ()

std::vector< ScoreGridSet * > *	getScoreGridSets ()

void	validateGridSets ()

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	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 ()

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
AtomTypes &	getAtomTypes ()

void	setup ()

void	setAtomType (Atom *atom, const String &type_name)

double	getES ()

Protected Member Functions inherited from BALL::DiffGridBasedScoring
void	updatePrecalculatedScore (Size set)

Protected Member Functions inherited from BALL::GridBasedScoring
void	setup ()

double	calculateGridScore ()

void	defineReceptorGridSet (Vector3 &origin, Vector3 &size, double out_of_grid_penalty, bool enforce_grid_boundaries, double resolution=0.5, double interaction_no_scale=1)

std::map< String, int > *	getAtomTypesMap ()

String	getGridAtomTypeName (int grid_id)

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_ ()

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)

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
AtomTypes	atom_types_

Protected Attributes inherited from BALL::GridBasedScoring
GridSetsResult	gridsets_result_

int	combine_operation_

std::map< String, int >	atom_types_map_

std::vector< BALL::ScoreGridSet * >	grid_sets_

double	scoregrid_resolution_

bool	scoregrid_interpolation_

int	flex_gridset_id_

std::map< const Residue , ScoreGridSet >	flex_gridsets_

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_

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

Detailed Description

ScoringFunction using a grid-based version of Piecewise Linear Potential

Definition at line 15 of file gridedPLP.h.

Constructor & Destructor Documentation

BALL::GridedPLP::GridedPLP	(	AtomContainer &	receptor,
		AtomContainer &	ligand,
		Options &	options
	)

BALL::GridedPLP::GridedPLP	(	AtomContainer &	receptor,
		Vector3 &	hashgrid_origin,
		Options &	options
	)

Member Function Documentation

AtomTypes& BALL::GridedPLP::getAtomTypes ( )

protectedvirtual

Implements BALL::GridBasedScoring.

double BALL::GridedPLP::getES ( )

protectedvirtual

Reimplemented from BALL::ScoringFunction.

void BALL::GridedPLP::setAtomType	(	Atom *	atom,
		const String &	type_name
	)

protectedvirtual

Set the desired type of the given atom. This function can be overloaded when setting the atom's types type is done in a different way, like for example for Gehlhaar's ScoringFunction

Reimplemented from BALL::GridBasedScoring.

void BALL::GridedPLP::setLigand ( AtomContainer * sys )

virtual

Reimplemented from BALL::DiffGridBasedScoring.

void BALL::GridedPLP::setup ( )

protected

Member Data Documentation

AtomTypes BALL::GridedPLP::atom_types_

protected

Definition at line 33 of file gridedPLP.h.

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation