BALL  1.5.0
Classes | List of all members
BALL::SLICKEnergy Class Reference

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

Inheritance diagram for BALL::SLICKEnergy:
BALL::ScoringFunction

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 SLICKEnergyoperator= (const SLICKEnergy &slick)
 
virtual void clear ()
 
Setup Methods
bool setup ()
 
- 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 ()
 
ScoringFunctionoperator= (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)
 
AtomContainergetFirstMolecule () const
 
void setSecondMolecule (AtomContainer &molecule2)
 
AtomContainergetSecondMolecule () const
 
void setReceptor (AtomContainer &receptor)
 
AtomContainergetReceptor () const
 
void setLigand (AtomContainer &ligand)
 
AtomContainergetLigand () const
 
void setIntercept (double intercept)
 
double getIntercept () const
 
void setBaseFunction (ScoringBaseFunction &base_function)
 Set the instance of BaseFunction for the scoring function. More...
 
ScoringBaseFunctiongetBaseFunction () 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
 
ScoringComponentgetComponent (const String &name) const
 
ScoringComponentgetComponent (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 Vector3getLigandCenter () const
 
double getLigandRadius () const
 
bool storeInteractionsEnabled ()
 
virtual int getNoNeighboringReceptorAtoms ()
 
int getNoLigandAtoms ()
 
Options getOptions ()
 
OptionsgetOptionsToModify ()
 
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 ()
 

Accessors specific to the SLICKEnergy scoring function

double getCHPIScore () const
 
double getHydrogenBondScore () const
 
double getVDWScore () const
 
double getPolarSolvationScore () const
 
double getNonpolarSolvationScore () const
 

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)
 
AtomPairVectorcreateNonbondedPairVector (HashGrid3< Atom * > *hashgrid, int &overlaps, bool rec_lig, bool check_fragments=0, bool intra_fragment=0)
 
AtomPairVectorcreateLigandNonbondedPairVector (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_ {}
 
AtomContainerreceptor_ {nullptr}
 
AtomContainerligand_ {nullptr}
 
double score_ {0.0}
 
double intercept_ {0.0}
 
ScoringBaseFunctionbase_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}
 
AtomPairVectorall_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

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

Definition at line 27 of file slickEnergy.h.

Constructor & Destructor Documentation

◆ SLICKEnergy() [1/4]

BALL::SLICKEnergy::SLICKEnergy ( )

Default constructor.

◆ SLICKEnergy() [2/4]

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

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

◆ SLICKEnergy() [3/4]

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

Construct a SLICKEnergy with a system and options.

◆ SLICKEnergy() [4/4]

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

Copy constructor

◆ ~SLICKEnergy()

virtual BALL::SLICKEnergy::~SLICKEnergy ( )
virtual

Destructor

Member Function Documentation

◆ clear()

virtual void BALL::SLICKEnergy::clear ( )
virtual

Clear method.

Reimplemented from BALL::ScoringFunction.

◆ getCHPIScore()

double BALL::SLICKEnergy::getCHPIScore ( ) const

◆ getHydrogenBondScore()

double BALL::SLICKEnergy::getHydrogenBondScore ( ) const

◆ getNonpolarSolvationScore()

double BALL::SLICKEnergy::getNonpolarSolvationScore ( ) const

◆ getPolarSolvationScore()

double BALL::SLICKEnergy::getPolarSolvationScore ( ) const

◆ getVDWScore()

double BALL::SLICKEnergy::getVDWScore ( ) const

◆ operator=()

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

Assignment operator.

◆ setup()

bool BALL::SLICKEnergy::setup ( )

Setup of scoring function