#include <BALL/SCORING/COMMON/gridBasedScoring.h>

Inheritance diagram for BALL::GridBasedScoring:

Classes
struct	Default

struct	GridSetsResult

struct	Option

Public Member Functions
	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	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 ()

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	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)

virtual AtomTypes &	getAtomTypes ()=0

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

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

String	getGridAtomTypeName (int grid_id)

virtual void	updatePrecalculatedScore (Size set)=0

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)

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
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_

Friends
class	ScoreGridSet

class	PharmacophoreConstraint

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

Definition at line 21 of file gridBasedScoring.h.

Constructor & Destructor Documentation

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

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

virtual BALL::GridBasedScoring::~GridBasedScoring ( )

virtual

Member Function Documentation

double BALL::GridBasedScoring::calculateGridScore ( )

protected

calculates the score for the interaction between the receptor and the current ligand conformation by use of the precalculated GridSets

void BALL::GridBasedScoring::defineFlexibleResiduesGridSet ( )

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

creates a new ScoreGridSet and appends it to the existing ones.
See class ScoreGridSet for documentation of the other parameters

Parameters

angstroem the size of the grid in Angstroem (since this might be more comfortable when supplying a molecule)

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

create a new ScoreGridSet and appends it to the existing ones.
The size of this ScoreGridSet is automatically set in such a way that it is large enough to encompass all nonbonded interactions with the given AtomContainer (dependend on nonbonded_cutoff_, which is set by use of an Option object in the ScoringFunction constructor)

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

protected

creates a new ScoreGridSet for receptor_ according to dimensions/properties of ScoringFunction::hashgrid_
See class ScoreGridSet for documentation of the other parameters

Parameters

size	the number of grid cell on each axis

virtual AtomTypes& BALL::GridBasedScoring::getAtomTypes ( )

protectedpure virtual

Implemented in BALL::GridedPLP, and BALL::GridedMM.

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

protected

String BALL::GridBasedScoring::getGridAtomTypeName ( int grid_id )

protected

Get the atom-type name for the specified grid (as stored in atom_types_map_)

int BALL::GridBasedScoring::getNoNeighboringReceptorAtoms ( )

virtual

Returns the average number of receptor atoms neighboring each ligand atom as determined by the last call of calculateGridScore() (which is called by update()).

Reimplemented from BALL::ScoringFunction.

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

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

Load precalculated ScoreGridSets for the given residues from files.
The values stored in those grids are automatically added to the ScoreGridSets that holds the scores for all flexible residues.

void BALL::GridBasedScoring::precalculateGrids ( bool ony_flexRes_grids = false )

precalculate one Grid for each desired AtomType and one Grid for the electrostatic (q1/distance)

void BALL::GridBasedScoring::printResult ( )

void BALL::GridBasedScoring::readAdditionalGridSetFromFile ( String file )

restores GridSet from the given file and appends it to the current ScoreGridSets

void BALL::GridBasedScoring::replaceGridSetFromFile ( String file )

deletes all existing ScoreGridSet and creates a new one from a given file

void BALL::GridBasedScoring::saveGridSetsToFile	(	String	file,
		String	receptor_name
	)

saves all previously calculated Grids to the specified file

virtual void BALL::GridBasedScoring::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 in BALL::GridedPLP.

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

sets the atom_types that are to be used

void BALL::GridBasedScoring::setCombineOperation ( int i )

defines how the Scores computed for on all ScoreGridSets are to be combined
0 = addition
1 = average
2 = minimum
3 = maximum

void BALL::GridBasedScoring::setup ( )

protected

void BALL::GridBasedScoring::setupReferenceLigand ( )

virtual

Use the current ligand as reference ligand. Thus, the average number of neighboring target atoms per reference ligand atom is calculated and can later be compared to the value for a ligand candidate, so that its depth of burial is thereby estimated.

Reimplemented from BALL::ScoringFunction.

virtual void BALL::GridBasedScoring::updatePrecalculatedScore ( Size set )

protectedpure virtual

update all nonbonded atom-pair lists and precalculate the score

Parameters

set	the id of the ScoreGrid, whose HashGrid is to be used

Implemented in BALL::DiffGridBasedScoring.

void BALL::GridBasedScoring::validateGridSets ( )

Friends And Related Function Documentation

friend class PharmacophoreConstraint

friend

Definition at line 160 of file gridBasedScoring.h.

friend class ScoreGridSet

friend

Definition at line 159 of file gridBasedScoring.h.

Member Data Documentation

std::map<String, int> BALL::GridBasedScoring::atom_types_map_

protected

maps each AtomType that is to be used to the ID of its Grid (position within ScoreGridSet.score_grids)

Definition at line 137 of file gridBasedScoring.h.

int BALL::GridBasedScoring::combine_operation_

protected

see setCombineOperation()

Definition at line 134 of file gridBasedScoring.h.

int BALL::GridBasedScoring::flex_gridset_id_

protected

index of the ScoreGridSet for the flexible residues of the receptor (if there are any)

Definition at line 153 of file gridBasedScoring.h.

std::map<const Residue*, ScoreGridSet*> BALL::GridBasedScoring::flex_gridsets_

protected

Stores one ScoreGridSets for each flexible sidechain.
These ScoreGridSets are not used directly during updateScore() (and therefore they are not put into grid_sets_), but their scores are added to the one ScoreGridSet that holds the score-sums of all flexible residues by loadFlexibleResidueScoreGrids().

Definition at line 157 of file gridBasedScoring.h.

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

protected

stores all calculated GridSets

Definition at line 140 of file gridBasedScoring.h.

GridSetsResult BALL::GridBasedScoring::gridsets_result_

protected

saves the final and all intermediate results of the last call of updateScore()

Definition at line 111 of file gridBasedScoring.h.

bool BALL::GridBasedScoring::scoregrid_interpolation_

protected

determines whether or not interpolation should be used in order to calculated the score from the precalculated ScoreGridSets.

Definition at line 150 of file gridBasedScoring.h.

double BALL::GridBasedScoring::scoregrid_resolution_

protected

the resolution of the ScoreGrids in units of Angstroem (not to be confused with ScoringFunction::resolution_, which is the resolution of the _Hash_Grid !!)

Definition at line 147 of file gridBasedScoring.h.

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation