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scoringFunction.h
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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#ifndef BALL_SCORING_COMMON_SCORINGFUNCTION_H
#define BALL_SCORING_COMMON_SCORINGFUNCTION_H
#include <set>
#include <BALL/KERNEL/system.h>
#include <BALL/DATATYPE/options.h>
#include <BALL/DATATYPE/string.h>
#include <BALL/DATATYPE/hashGrid.h>
#include <BALL/KERNEL/atomContainer.h>
#include <BALL/DOCKING/COMMON/staticLigandFragment.h>
#include <BALL/DOCKING/COMMON/constraints.h>
#include <BALL/SCORING/COMMON/baseFunction.h>
#include <BALL/SCORING/COMMON/scoringComponent.h>
#include <BALL/STRUCTURE/residueRotamerSet.h>
namespace BALL
{
typedef std::list<std::pair<Atom*, Atom*> > AtomPairList;
typedef std::vector<std::pair<Atom*, Atom*> > AtomPairVector;
class ScoringComponent;
class BALL_EXPORT ScoringFunction
{
friend class PharmacophoreConstraint;
friend class SideChainOptimizer;
public:
static const char* SUBCATEGORY_NAME;
struct Option
{
static const char* VERBOSITY;
static const char* BASE_FUNCTION_TYPE;
static const char* HASHGRID_RESOLUTION;
static const char* HASHGRID_SIZE;
static const char* NONBONDED_CUTOFF;
static const char* CONFORMATION_SCALE;
static const char* ALL_LIG_NONB_PAIRS;
static const char* USE_STATIC_LIG_FRAGMENTS;
static const char* IGNORE_H_CLASHES;
static const char* ALLOWED_INTERMOL_OVERLAP;
static const char* ALLOWED_INTRAMOL_OVERLAP;
static const char* BURIAL_DEPTH_SCALE;
};
struct Default
{
static const Size VERBOSITY;
static const Size BASE_FUNCTION_TYPE;
static double HASHGRID_RESOLUTION;
static int HASHGRID_SIZE;
static double NONBONDED_CUTOFF;
static double CONFORMATION_SCALE;
static bool ALL_LIG_NONB_PAIRS;
static bool USE_STATIC_LIG_FRAGMENTS;
static bool IGNORE_H_CLASHES;
static double ALLOWED_INTERMOL_OVERLAP;
static double ALLOWED_INTRAMOL_OVERLAP;
static int BURIAL_DEPTH_SCALE;
};
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);
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();
static HashGrid3<Atom*>* initializeHashGrid(AtomContainer* sys,
Vector3& center,
double& resolution,
int hashgrid_size);
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);
static void getDefaultOptions(Options& options);
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();
list<Constraint*> constraints {};
protected:
/* @name Protected structs */
struct Result
{
double ligand_conformation;
double interaction_score;
vector<double> refArea_penalties;
};
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;
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_ {};
};
} // namespace BALL
#endif // BALL_SCORING_COMMON_SCORINGFUNCTION_H
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
system.h
atomContainer.h
baseFunction.h
BALL::AtomContainer
Definition atomContainer.h:32
BALL::Atom
Definition atom.h:90
BALL::Bond
Definition bond.h:57
BALL::HashGrid3
Three-dimensional Hash Grid Class.
Definition hashGrid.h:755
BALL::HashSet
Definition hashSet.h:46
BALL::Options
Definition options.h:48
BALL::ResidueRotamerSet
Definition residueRotamerSet.h:88
BALL::Residue
Definition residue.h:38
BALL::Rotamer
Definition residueRotamerSet.h:38
BALL::ScoringBaseFunction
Definition baseFunction.h:15
BALL::ScoringComponent
Definition scoringComponent.h:21
BALL::ScoringFunction::getUnassignedAtoms
HashSet< const Atom * > & getUnassignedAtoms()
BALL::ScoringFunction::hasPharmacophoreConstraints_
bool hasPharmacophoreConstraints_()
BALL::ScoringFunction::static_residues_hashgrid_
HashGrid3< Atom * > * static_residues_hashgrid_
Definition scoringFunction.h:670
BALL::ScoringFunction::hashgrid_search_radius_
int hashgrid_search_radius_
Definition scoringFunction.h:704
BALL::ScoringFunction::flexible_residues_hashgrid_
HashGrid3< Atom * > * flexible_residues_hashgrid_
Definition scoringFunction.h:671
BALL::ScoringFunction::ligand_center_
Vector3 ligand_center_
Definition scoringFunction.h:662
BALL::ScoringFunction::setup
bool setup()
BALL::ScoringFunction::setReceptor
void setReceptor(AtomContainer &receptor)
BALL::ScoringFunction::valueToString
String valueToString(double value)
BALL::ScoringFunction::hashgrid_
HashGrid3< Atom * > * hashgrid_
Definition scoringFunction.h:667
BALL::ScoringFunction::result_
Result result_
Definition scoringFunction.h:804
BALL::ScoringFunction::updateComponent
void updateComponent(int id, AtomPairList *)
BALL::ScoringFunction::static_ligand_energy_
double static_ligand_energy_
Definition scoringFunction.h:809
BALL::ScoringFunction::enableInteractionComponents_
void enableInteractionComponents_(const list< String > &type_names)
BALL::ScoringFunction::flexres_org_positions_
list< list< Vector3 > > flexres_org_positions_
Definition scoringFunction.h:821
BALL::ScoringFunction::calculateGeometricalCenter
Vector3 calculateGeometricalCenter(AtomContainer *s, int *no_ligand_atoms=NULL)
BALL::ScoringFunction::getCoefficient
bool getCoefficient(const ScoringComponent *component, float &coefficient) const
BALL::ScoringFunction::setCoefficient
void setCoefficient(const String &name, float coefficient)
BALL::ScoringFunction::nonbonded_cutoff_
double nonbonded_cutoff_
Definition scoringFunction.h:709
BALL::ScoringFunction::reference_neighbors_
int reference_neighbors_
Definition scoringFunction.h:687
BALL::ScoringFunction::SUBCATEGORY_NAME
static const char * SUBCATEGORY_NAME
Definition scoringFunction.h:36
BALL::ScoringFunction::getRotatableLigandBonds
const vector< Bond * > * getRotatableLigandBonds() const
BALL::ScoringFunction::allowed_intermolecular_overlap_
double allowed_intermolecular_overlap_
Definition scoringFunction.h:735
BALL::ScoringFunction::resolution_
double resolution_
Definition scoringFunction.h:676
BALL::ScoringFunction::insertComponent
void insertComponent(ScoringComponent *component)
BALL::ScoringFunction::scoring_components_
vector< ScoringComponent * > scoring_components_
Definition scoringFunction.h:631
BALL::ScoringFunction::getOptionsToModify
Options * getOptionsToModify()
BALL::ScoringFunction::use_static_lig_fragments_
bool use_static_lig_fragments_
Definition scoringFunction.h:785
BALL::ScoringFunction::ligand_intramol_overlaps_
int ligand_intramol_overlaps_
Definition scoringFunction.h:729
BALL::ScoringFunction::conformation_scale_
double conformation_scale_
Definition scoringFunction.h:775
BALL::ScoringFunction::unsetTrainingParameters
void unsetTrainingParameters()
BALL::ScoringFunction::getSecondMolecule
AtomContainer * getSecondMolecule() const
BALL::ScoringFunction::constraints
list< Constraint * > constraints
Definition scoringFunction.h:460
BALL::ScoringFunction::getReceptor
AtomContainer * getReceptor() const
BALL::ScoringFunction::base_function_
ScoringBaseFunction * base_function_
Definition scoringFunction.h:626
BALL::ScoringFunction::createStaticLigandFragments
void createStaticLigandFragments()
BALL::ScoringFunction::setBaseFunction
void setBaseFunction(ScoringBaseFunction &base_function)
Set the instance of BaseFunction for the scoring function.
BALL::ScoringFunction::enableAllComponents_
void enableAllComponents_()
BALL::ScoringFunction::getNoLigandAtoms
int getNoLigandAtoms()
BALL::ScoringFunction::clear
virtual void clear()
BALL::ScoringFunction::neighbor_cutoff_2_
double neighbor_cutoff_2_
Definition scoringFunction.h:747
BALL::ScoringFunction::getNoNeighboringReceptorAtoms
virtual int getNoNeighboringReceptorAtoms()
BALL::ScoringFunction::setName
void setName(String name)
BALL::ScoringFunction::getComponent
ScoringComponent * getComponent(const Size index) const
BALL::ScoringFunction::setFlexibleResidues
void setFlexibleResidues(const std::set< Residue * > &flexible_residues)
BALL::ScoringFunction::getCoefficient
bool getCoefficient(const String &name, float &coefficient) const
BALL::ScoringFunction::name_
String name_
Definition scoringFunction.h:596
BALL::ScoringFunction::ligand_atoms_
int ligand_atoms_
Definition scoringFunction.h:657
BALL::ScoringFunction::setupFlexibleResidues_
void setupFlexibleResidues_()
BALL::ScoringFunction::ScoringFunction
ScoringFunction(AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options)
BALL::ScoringFunction::static_ligand_fragments_
vector< StaticLigandFragment * > static_ligand_fragments_
Definition scoringFunction.h:756
BALL::ScoringFunction::intercept_
double intercept_
Definition scoringFunction.h:621
BALL::ScoringFunction::receptor_
AtomContainer * receptor_
Definition scoringFunction.h:606
BALL::ScoringFunction::createAllLigandNonBondedPairs
virtual void createAllLigandNonBondedPairs()
BALL::ScoringFunction::getLigandCenter
const Vector3 & getLigandCenter() const
BALL::ScoringFunction::rotatable_ligand_bonds_
vector< Bond * > rotatable_ligand_bonds_
Definition scoringFunction.h:815
BALL::ScoringFunction::countNeighboringReceptorAtoms
Size countNeighboringReceptorAtoms(const Atom *atom, double distance_threshold, bool onePerCell=0, int *number_of_overlaps=0) const
BALL::ScoringFunction::createNonbondedPairVector
AtomPairVector * createNonbondedPairVector(HashGrid3< Atom * > *hashgrid, int &overlaps, bool rec_lig, bool check_fragments=0, bool intra_fragment=0)
BALL::ScoringFunction::max_number_of_errors_
Size max_number_of_errors_
Definition scoringFunction.h:641
BALL::ScoringFunction::enableStoreInteractions
void enableStoreInteractions(bool b=true)
BALL::ScoringFunction::updateScore
virtual double updateScore()
BALL::ScoringFunction::getLigandRadius
double getLigandRadius() const
BALL::ScoringFunction::removeComponent
void removeComponent(const ScoringComponent *component)
BALL::ScoringFunction::store_interactions_phC_only_
bool store_interactions_phC_only_
Definition scoringFunction.h:765
BALL::ScoringFunction::setCoefficient
void setCoefficient(const ScoringComponent *component, float coefficient)
BALL::ScoringFunction::exp_energy_mean_
double exp_energy_mean_
Definition scoringFunction.h:797
BALL::ScoringFunction::storeInteractionsEnabled
bool storeInteractionsEnabled()
BALL::ScoringFunction::neighboring_target_atoms_
int neighboring_target_atoms_
Definition scoringFunction.h:693
BALL::ScoringFunction::getFirstMolecule
AtomContainer * getFirstMolecule() const
BALL::ScoringFunction::initializeHashGrid
static HashGrid3< Atom * > * initializeHashGrid(AtomContainer *sys, Vector3 &center, double &resolution, int hashgrid_size)
BALL::ScoringFunction::setLigand
void setLigand(AtomContainer &ligand)
BALL::ScoringFunction::getDefaultOptions
static void getDefaultOptions(Options &options)
BALL::ScoringFunction::ScoringFunction
ScoringFunction()
BALL::ScoringFunction::hasFlexibleResidues
bool hasFlexibleResidues()
BALL::ScoringFunction::setMaximumNumberOfErrors
void setMaximumNumberOfErrors(Size nr)
BALL::ScoringFunction::ScoringFunction
ScoringFunction(AtomContainer &receptor, AtomContainer &ligand, Options &options)
BALL::ScoringFunction::store_interactions_
bool store_interactions_
Definition scoringFunction.h:763
BALL::ScoringFunction::getES
virtual double getES()
BALL::ScoringFunction::setup
bool setup(AtomContainer &receptor, AtomContainer &ligand)
BALL::ScoringFunction::SideChainOptimizer
friend class SideChainOptimizer
Definition scoringFunction.h:32
BALL::ScoringFunction::calculateStaticLigandFragmentEnergy
virtual double calculateStaticLigandFragmentEnergy()
BALL::ScoringFunction::PharmacophoreConstraint
friend class PharmacophoreConstraint
Definition scoringFunction.h:31
BALL::ScoringFunction::unassigned_atoms_
HashSet< const Atom * > unassigned_atoms_
Definition scoringFunction.h:636
BALL::ScoringFunction::ScoringFunction
ScoringFunction(AtomContainer &receptor, AtomContainer &ligand)
BALL::ScoringFunction::all_residues_hashgrid_
HashGrid3< Atom * > * all_residues_hashgrid_
Definition scoringFunction.h:669
BALL::ScoringFunction::setNormalizationParameters
void setNormalizationParameters(double stddev, double mean)
BALL::ScoringFunction::setFirstMolecule
void setFirstMolecule(AtomContainer &molecule1)
BALL::ScoringFunction::getLigand
AtomContainer * getLigand() const
BALL::ScoringFunction::allowed_intramolecular_overlap_
double allowed_intramolecular_overlap_
Definition scoringFunction.h:741
BALL::ScoringFunction::atoms_to_fragments_
std::map< Atom *, int > atoms_to_fragments_
Definition scoringFunction.h:681
BALL::ScoringFunction::checkForAtomOverlaps
int checkForAtomOverlaps(const AtomPairVector *pair_vector)
BALL::ScoringFunction::convertTime
String convertTime(double seconds)
BALL::ScoringFunction::calculateMoleculeRadius
double calculateMoleculeRadius(AtomContainer *sys, Vector3 &center)
BALL::ScoringFunction::countCovalentBonds
int countCovalentBonds(const Atom *atom, int threshold=-1)
BALL::ScoringFunction::ligand_radius_
double ligand_radius_
Definition scoringFunction.h:651
BALL::ScoringFunction::getComponent
ScoringComponent * getComponent(const String &name) const
BALL::ScoringFunction::insertComponent
void insertComponent(ScoringComponent *component, float coefficient)
BALL::ScoringFunction::flexible_residues_
std::set< Residue * > flexible_residues_
Definition scoringFunction.h:799
BALL::ScoringFunction::getEquation
String getEquation()
BALL::ScoringFunction::getName
String getName()
BALL::ScoringFunction::getHashGrid
const HashGrid3< Atom * > * getHashGrid()
BALL::ScoringFunction::getIntercept
double getIntercept() const
BALL::ScoringFunction::calculateConstraintsScore
double calculateConstraintsScore()
BALL::ScoringFunction::all_ligand_nonbonded_
AtomPairVector * all_ligand_nonbonded_
Definition scoringFunction.h:770
BALL::ScoringFunction::getOptions
Options getOptions()
BALL::ScoringFunction::getMaximumNumberOfErrors
Size getMaximumNumberOfErrors() const
BALL::ScoringFunction::ScoringFunction
ScoringFunction(const ScoringFunction &sf)
BALL::ScoringFunction::assignRotamer
bool assignRotamer(Residue *residue, ResidueRotamerSet *rotamer_set, const Rotamer *rotamer)
BALL::ScoringFunction::clearStoredInteractions_
void clearStoredInteractions_()
BALL::ScoringFunction::resetFlexibleResidues
void resetFlexibleResidues()
BALL::ScoringFunction::getScoreContributions
void getScoreContributions(vector< double > &score_contributions, vector< String > &names)
BALL::ScoringFunction::isPeptideBond
bool isPeptideBond(const Bond *bond) const
BALL::ScoringFunction::getAtomFragmentMap
const std::map< Atom *, int > * getAtomFragmentMap()
BALL::ScoringFunction::getBurialDepthScale
int getBurialDepthScale()
BALL::ScoringFunction::options_
Options options_
Definition scoringFunction.h:601
BALL::ScoringFunction::setup
bool setup(AtomContainer &receptor, AtomContainer &ligand, const Options &options)
BALL::ScoringFunction::number_of_errors_
Size number_of_errors_
Definition scoringFunction.h:646
BALL::ScoringFunction::setSecondMolecule
void setSecondMolecule(AtomContainer &molecule2)
BALL::ScoringFunction::~ScoringFunction
virtual ~ScoringFunction()
BALL::ScoringFunction::printResult
virtual void printResult(bool detail=0)
BALL::ScoringFunction::exp_energy_stddev_
double exp_energy_stddev_
Definition scoringFunction.h:792
BALL::ScoringFunction::resetResiduePositions
void resetResiduePositions(Residue *residue, list< Vector3 > &old_positions)
BALL::ScoringFunction::createLigandNonbondedPairVector
AtomPairVector * createLigandNonbondedPairVector(bool intra_fragment, int &overlaps)
BALL::ScoringFunction::ligand_
AtomContainer * ligand_
Definition scoringFunction.h:611
BALL::ScoringFunction::use_all_lig_nonb_
bool use_all_lig_nonb_
Definition scoringFunction.h:780
BALL::ScoringFunction::enableStoreInteractionsOnlyForPhContraints
void enableStoreInteractionsOnlyForPhContraints()
BALL::ScoringFunction::overlaps_
int overlaps_
Definition scoringFunction.h:724
BALL::ScoringFunction::getUnassignedAtoms
const HashSet< const Atom * > & getUnassignedAtoms() const
BALL::ScoringFunction::getExpEnergyStddev
double getExpEnergyStddev()
BALL::ScoringFunction::calculateScore
double calculateScore()
BALL::ScoringFunction::getStaticLigandFragments
const vector< StaticLigandFragment * > * getStaticLigandFragments() const
BALL::ScoringFunction::nonbonded_cutoff_2_
double nonbonded_cutoff_2_
Definition scoringFunction.h:714
BALL::ScoringFunction::removeComponent
void removeComponent(const String &name)
BALL::ScoringFunction::fetchStaticLigandFragment
void fetchStaticLigandFragment(Atom *a1, int index)
BALL::ScoringFunction::burial_depth_scale_
int burial_depth_scale_
Definition scoringFunction.h:787
BALL::ScoringFunction::setupReferenceLigand
virtual void setupReferenceLigand()
BALL::ScoringFunction::setIntercept
void setIntercept(double intercept)
BALL::ScoringFunction::score_
double score_
Definition scoringFunction.h:616
BALL::ScoringFunction::getBaseFunction
ScoringBaseFunction * getBaseFunction() const
BALL::ScoringFunction::misplaced_ligand_atoms_
int misplaced_ligand_atoms_
Definition scoringFunction.h:699
BALL::ScoringFunction::ignore_h_clashes_
bool ignore_h_clashes_
Definition scoringFunction.h:719
BALL::ScoringFunction::getScore
double getScore()
BALL::ScoringFunction::ScoringFunction
ScoringFunction(AtomContainer &receptor, AtomContainer &ligand, const Options &options)
BALL::ScoringFunction::update
virtual void update()
BALL::String
Definition string.h:57
constraints.h
hashGrid.h
BALL
Definition constants.h:13
BALL::Size
BALL_SIZE_TYPE Size
Definition COMMON/global.h:114
BALL::AtomPairVector
std::vector< std::pair< Atom *, Atom * > > AtomPairVector
Definition scoringFunction.h:24
BALL::Vector3
TVector3< float > Vector3
Definition vector3.h:1084
BALL::AtomPairList
std::list< std::pair< Atom *, Atom * > > AtomPairList
Definition scoringFunction.h:23
options.h
residueRotamerSet.h
scoringComponent.h
staticLigandFragment.h
string.h
BALL::ScoringFunction::Default
Definition scoringFunction.h:91
BALL::ScoringFunction::Default::ALLOWED_INTERMOL_OVERLAP
static double ALLOWED_INTERMOL_OVERLAP
Definition scoringFunction.h:121
BALL::ScoringFunction::Default::USE_STATIC_LIG_FRAGMENTS
static bool USE_STATIC_LIG_FRAGMENTS
Definition scoringFunction.h:115
BALL::ScoringFunction::Default::HASHGRID_RESOLUTION
static double HASHGRID_RESOLUTION
Definition scoringFunction.h:101
BALL::ScoringFunction::Default::BASE_FUNCTION_TYPE
static const Size BASE_FUNCTION_TYPE
Definition scoringFunction.h:98
BALL::ScoringFunction::Default::BURIAL_DEPTH_SCALE
static int BURIAL_DEPTH_SCALE
Definition scoringFunction.h:126
BALL::ScoringFunction::Default::IGNORE_H_CLASHES
static bool IGNORE_H_CLASHES
Definition scoringFunction.h:118
BALL::ScoringFunction::Default::HASHGRID_SIZE
static int HASHGRID_SIZE
Definition scoringFunction.h:104
BALL::ScoringFunction::Default::NONBONDED_CUTOFF
static double NONBONDED_CUTOFF
Definition scoringFunction.h:106
BALL::ScoringFunction::Default::VERBOSITY
static const Size VERBOSITY
Definition scoringFunction.h:94
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Definition scoringFunction.h:124
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Definition scoringFunction.h:109
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Definition scoringFunction.h:112
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Definition scoringFunction.h:39
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Definition scoringFunction.h:50
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Definition scoringFunction.h:74
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Definition scoringFunction.h:54
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Definition scoringFunction.h:46
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Definition scoringFunction.h:86
BALL::ScoringFunction::Option::CONFORMATION_SCALE
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Definition scoringFunction.h:62
BALL::ScoringFunction::Option::ALLOWED_INTRAMOL_OVERLAP
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Definition scoringFunction.h:82
BALL::ScoringFunction::Option::ALL_LIG_NONB_PAIRS
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Definition scoringFunction.h:66
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Definition scoringFunction.h:70
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Definition scoringFunction.h:78
BALL::ScoringFunction::Option::VERBOSITY
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Definition scoringFunction.h:42
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Definition scoringFunction.h:58
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Definition scoringFunction.h:465
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Definition scoringFunction.h:474
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Definition scoringFunction.h:479
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Definition scoringFunction.h:469