#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 ()=default
void	update ()
virtual double	updateScore ()
void	testOverlaps (Vector3 &position, HashGrid3< Atom * > *hashg=nullptr)
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.
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_ {nullptr}
AtomContainer *	ligand_ {nullptr}
double	score_ {0.0}
double	intercept_ {0.0}
ScoringBaseFunction *	base_function_ {nullptr}
vector< ScoringComponent * >	scoring_components_ {}
HashSet< const Atom * >	unassigned_atoms_ {}
Size	max_number_of_errors_ {0}
Size	number_of_errors_ {0}
double	ligand_radius_ {0.0}
int	ligand_atoms_ {0}
Vector3	ligand_center_ {}
HashGrid3< Atom * > *	hashgrid_ {nullptr}
HashGrid3< Atom * > *	all_residues_hashgrid_ {nullptr}
HashGrid3< Atom * > *	static_residues_hashgrid_ {nullptr}
HashGrid3< Atom * > *	flexible_residues_hashgrid_ {nullptr}
double	resolution_ {0.0}
std::map< Atom *, int >	atoms_to_fragments_ {}
int	reference_neighbors_ {0}
int	neighboring_target_atoms_ {0}
int	misplaced_ligand_atoms_ {0}
int	hashgrid_search_radius_ {0}
double	nonbonded_cutoff_ {0.0}
double	nonbonded_cutoff_2_ {0.0}
bool	ignore_h_clashes_ {false}
int	overlaps_ {0}
int	ligand_intramol_overlaps_ {0}
double	allowed_intermolecular_overlap_ {0.0}
double	allowed_intramolecular_overlap_ {0.0}
double	neighbor_cutoff_2_ {0.0}
vector< StaticLigandFragment * >	static_ligand_fragments_ {}
bool	store_interactions_ {false}
bool	store_interactions_phC_only_ {false}
AtomPairVector *	all_ligand_nonbonded_ {nullptr}
double	conformation_scale_ {0.0}
bool	use_all_lig_nonb_ {false}
bool	use_static_lig_fragments_ {false}
int	burial_depth_scale_ {0}
double	exp_energy_stddev_ {0.0}
double	exp_energy_mean_ {0.0}
std::set< Residue * >	flexible_residues_ {}
Result	result_ {}
double	static_ligand_energy_ {0.0}
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 {}
Static Public Attributes inherited from BALL::ScoringFunction
static const char *	SUBCATEGORY_NAME

Detailed Description

ScoringFunction using a grid-based version of Piecewise Linear Potential

Definition at line 15 of file gridedPLP.h.

Constructor & Destructor Documentation

◆ GridedPLP() [1/2]

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

◆ GridedPLP() [2/2]

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

Member Function Documentation

◆ getAtomTypes()

AtomTypes & BALL::GridedPLP::getAtomTypes ( )

protectedvirtual

Implements BALL::GridBasedScoring.

◆ getES()

double BALL::GridedPLP::getES ( )

protectedvirtual

Reimplemented from BALL::ScoringFunction.

◆ setAtomType()

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.

◆ setLigand()

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

virtual

Reimplemented from BALL::DiffGridBasedScoring.

◆ setup()

void BALL::GridedPLP::setup ( )

protected

Member Data Documentation

◆ atom_types_

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

◆ GridedPLP() [1/2]

◆ GridedPLP() [2/2]

Member Function Documentation

◆ getAtomTypes()

◆ getES()

◆ setAtomType()

◆ setLigand()

◆ setup()

Member Data Documentation

◆ atom_types_