BALL::DifferentiableScoringFunction Class Reference

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

Inheritance diagram for BALL::DifferentiableScoringFunction:

Public Member Functions
	DifferentiableScoringFunction (AtomContainer &receptor, AtomContainer &ligand, Options &options)
	DifferentiableScoringFunction (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.
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 {}
Static Public Attributes inherited from BALL::ScoringFunction
static const char *	SUBCATEGORY_NAME
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_ {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_ {}

Detailed Description

Definition at line 15 of file diffScoringFunction.h.

Constructor & Destructor Documentation

DifferentiableScoringFunction() [1/2]

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

DifferentiableScoringFunction() [2/2]

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