| all_ligand_nonbonded_ | BALL::ScoringFunction | protected |
| all_residues_hashgrid_ | BALL::ScoringFunction | protected |
| allowed_intermolecular_overlap_ | BALL::ScoringFunction | protected |
| allowed_intramolecular_overlap_ | BALL::ScoringFunction | protected |
| assignRotamer(Residue *residue, ResidueRotamerSet *rotamer_set, const Rotamer *rotamer) | BALL::ScoringFunction | |
| atoms_to_fragments_ | BALL::ScoringFunction | protected |
| base_function_ | BALL::ScoringFunction | protected |
| burial_depth_scale_ | BALL::ScoringFunction | protected |
| calculateConstraintsScore() | BALL::ScoringFunction | protected |
| calculateGeometricalCenter(AtomContainer *s, int *no_ligand_atoms=NULL) | BALL::ScoringFunction | protected |
| calculateMoleculeRadius(AtomContainer *sys, Vector3 ¢er) | BALL::ScoringFunction | protected |
| calculateScore() | BALL::ScoringFunction | |
| calculateStaticLigandFragmentEnergy() | BALL::ScoringFunction | protectedvirtual |
| checkForAtomOverlaps(const AtomPairVector *pair_vector) | BALL::ScoringFunction | protected |
| clear() | BALL::SLICKScore | virtual |
| clearStoredInteractions_() | BALL::ScoringFunction | protected |
| conformation_scale_ | BALL::ScoringFunction | protected |
| constraints | BALL::ScoringFunction | |
| convertTime(double seconds) | BALL::ScoringFunction | |
| countCovalentBonds(const Atom *atom, int threshold=-1) | BALL::ScoringFunction | protected |
| countNeighboringReceptorAtoms(const Atom *atom, double distance_threshold, bool onePerCell=0, int *number_of_overlaps=0) const | BALL::ScoringFunction | |
| createAllLigandNonBondedPairs() | BALL::ScoringFunction | protectedvirtual |
| createLigandNonbondedPairVector(bool intra_fragment, int &overlaps) | BALL::ScoringFunction | protected |
| createNonbondedPairVector(HashGrid3< Atom * > *hashgrid, int &overlaps, bool rec_lig, bool check_fragments=0, bool intra_fragment=0) | BALL::ScoringFunction | protected |
| createStaticLigandFragments() | BALL::ScoringFunction | |
| enableAllComponents_() | BALL::ScoringFunction | protected |
| enableInteractionComponents_(const list< String > &type_names) | BALL::ScoringFunction | protected |
| enableStoreInteractions(bool b=true) | BALL::ScoringFunction | |
| enableStoreInteractionsOnlyForPhContraints() | BALL::ScoringFunction | |
| exp_energy_mean_ | BALL::ScoringFunction | protected |
| exp_energy_stddev_ | BALL::ScoringFunction | protected |
| fetchStaticLigandFragment(Atom *a1, int index) | BALL::ScoringFunction | protected |
| flexible_residues_ | BALL::ScoringFunction | protected |
| flexible_residues_hashgrid_ | BALL::ScoringFunction | protected |
| flexres_org_positions_ | BALL::ScoringFunction | protected |
| getAtomFragmentMap() | BALL::ScoringFunction | |
| getBaseFunction() const | BALL::ScoringFunction | |
| getBurialDepthScale() | BALL::ScoringFunction | |
| getCHPIScore() const | BALL::SLICKScore | |
| getCoefficient(const ScoringComponent *component, float &coefficient) const | BALL::ScoringFunction | |
| getCoefficient(const String &name, float &coefficient) const | BALL::ScoringFunction | |
| getComponent(const String &name) const | BALL::ScoringFunction | |
| getComponent(const Size index) const | BALL::ScoringFunction | |
| getDefaultOptions(Options &options) | BALL::ScoringFunction | static |
| getEquation() | BALL::ScoringFunction | |
| getES() | BALL::ScoringFunction | protectedvirtual |
| getExpEnergyStddev() | BALL::ScoringFunction | |
| getFirstMolecule() const | BALL::ScoringFunction | |
| getHashGrid() | BALL::ScoringFunction | |
| getHydrogenBondScore() const | BALL::SLICKScore | |
| getIntercept() const | BALL::ScoringFunction | |
| getLigand() const | BALL::ScoringFunction | |
| getLigandCenter() const | BALL::ScoringFunction | |
| getLigandRadius() const | BALL::ScoringFunction | |
| getMaximumNumberOfErrors() const | BALL::ScoringFunction | |
| getName() | BALL::ScoringFunction | |
| getNoLigandAtoms() | BALL::ScoringFunction | |
| getNoNeighboringReceptorAtoms() | BALL::ScoringFunction | virtual |
| getNonpolarSolvationScore() const | BALL::SLICKScore | |
| getOptions() | BALL::ScoringFunction | |
| getOptionsToModify() | BALL::ScoringFunction | |
| getPolarSolvationScore() const | BALL::SLICKScore | |
| getReceptor() const | BALL::ScoringFunction | |
| getRotatableLigandBonds() const | BALL::ScoringFunction | |
| getScore() | BALL::ScoringFunction | |
| getScoreContributions(vector< double > &score_contributions, vector< String > &names) | BALL::ScoringFunction | |
| getSecondMolecule() const | BALL::ScoringFunction | |
| getStaticLigandFragments() const | BALL::ScoringFunction | |
| getUnassignedAtoms() const | BALL::ScoringFunction | |
| getUnassignedAtoms() | BALL::ScoringFunction | |
| getVDWScore() const | BALL::SLICKScore | |
| hasFlexibleResidues() | BALL::ScoringFunction | |
| hashgrid_ | BALL::ScoringFunction | protected |
| hashgrid_search_radius_ | BALL::ScoringFunction | protected |
| hasPharmacophoreConstraints_() | BALL::ScoringFunction | protected |
| ignore_h_clashes_ | BALL::ScoringFunction | protected |
| initializeHashGrid(AtomContainer *sys, Vector3 ¢er, double &resolution, int hashgrid_size) | BALL::ScoringFunction | static |
| insertComponent(ScoringComponent *component) | BALL::ScoringFunction | |
| insertComponent(ScoringComponent *component, float coefficient) | BALL::ScoringFunction | |
| intercept_ | BALL::ScoringFunction | protected |
| isPeptideBond(const Bond *bond) const | BALL::ScoringFunction | protected |
| ligand_ | BALL::ScoringFunction | protected |
| ligand_atoms_ | BALL::ScoringFunction | protected |
| ligand_center_ | BALL::ScoringFunction | protected |
| ligand_intramol_overlaps_ | BALL::ScoringFunction | protected |
| ligand_radius_ | BALL::ScoringFunction | protected |
| max_number_of_errors_ | BALL::ScoringFunction | protected |
| misplaced_ligand_atoms_ | BALL::ScoringFunction | protected |
| name_ | BALL::ScoringFunction | protected |
| neighbor_cutoff_2_ | BALL::ScoringFunction | protected |
| neighboring_target_atoms_ | BALL::ScoringFunction | protected |
| nonbonded_cutoff_ | BALL::ScoringFunction | protected |
| nonbonded_cutoff_2_ | BALL::ScoringFunction | protected |
| number_of_errors_ | BALL::ScoringFunction | protected |
| operator=(const SLICKScore &slick) | BALL::SLICKScore | |
| BALL::ScoringFunction::operator=(const ScoringFunction &sf) | BALL::ScoringFunction | |
| options_ | BALL::ScoringFunction | protected |
| overlaps_ | BALL::ScoringFunction | protected |
| printResult(bool detail=0) | BALL::ScoringFunction | virtual |
| receptor_ | BALL::ScoringFunction | protected |
| reference_neighbors_ | BALL::ScoringFunction | protected |
| removeComponent(const ScoringComponent *component) | BALL::ScoringFunction | |
| removeComponent(const String &name) | BALL::ScoringFunction | |
| resetFlexibleResidues() | BALL::ScoringFunction | |
| resetResiduePositions(Residue *residue, list< Vector3 > &old_positions) | BALL::ScoringFunction | |
| resolution_ | BALL::ScoringFunction | protected |
| result_ | BALL::ScoringFunction | protected |
| rotatable_ligand_bonds_ | BALL::ScoringFunction | protected |
| score_ | BALL::ScoringFunction | protected |
| scoring_components_ | BALL::ScoringFunction | protected |
| ScoringFunction() | BALL::ScoringFunction | |
| ScoringFunction(const ScoringFunction &sf) | BALL::ScoringFunction | |
| ScoringFunction(AtomContainer &receptor, AtomContainer &ligand) | BALL::ScoringFunction | |
| ScoringFunction(AtomContainer &receptor, AtomContainer &ligand, const Options &options) | BALL::ScoringFunction | |
| ScoringFunction(AtomContainer &receptor, AtomContainer &ligand, Options &options) | BALL::ScoringFunction | |
| ScoringFunction(AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options) | BALL::ScoringFunction | |
| setBaseFunction(ScoringBaseFunction &base_function) | BALL::ScoringFunction | |
| setCoefficient(const ScoringComponent *component, float coefficient) | BALL::ScoringFunction | |
| setCoefficient(const String &name, float coefficient) | BALL::ScoringFunction | |
| setFirstMolecule(AtomContainer &molecule1) | BALL::ScoringFunction | |
| setFlexibleResidues(const std::set< Residue * > &flexible_residues) | BALL::ScoringFunction | |
| setIntercept(double intercept) | BALL::ScoringFunction | |
| setLigand(AtomContainer &ligand) | BALL::ScoringFunction | |
| setMaximumNumberOfErrors(Size nr) | BALL::ScoringFunction | |
| setName(String name) | BALL::ScoringFunction | protected |
| setNormalizationParameters(double stddev, double mean) | BALL::ScoringFunction | |
| setReceptor(AtomContainer &receptor) | BALL::ScoringFunction | |
| setSecondMolecule(AtomContainer &molecule2) | BALL::ScoringFunction | |
| setup() | BALL::SLICKScore | |
| BALL::ScoringFunction::setup(AtomContainer &receptor, AtomContainer &ligand) | BALL::ScoringFunction | |
| BALL::ScoringFunction::setup(AtomContainer &receptor, AtomContainer &ligand, const Options &options) | BALL::ScoringFunction | |
| setupFlexibleResidues_() | BALL::ScoringFunction | protected |
| setupReferenceLigand() | BALL::ScoringFunction | protectedvirtual |
| SLICKScore() | BALL::SLICKScore | |
| SLICKScore(Molecule &protein, Molecule &ligand, Options &options) | BALL::SLICKScore | |
| SLICKScore(const SLICKScore &slick) | BALL::SLICKScore | |
| static_ligand_energy_ | BALL::ScoringFunction | protected |
| static_ligand_fragments_ | BALL::ScoringFunction | protected |
| static_residues_hashgrid_ | BALL::ScoringFunction | protected |
| store_interactions_ | BALL::ScoringFunction | protected |
| store_interactions_phC_only_ | BALL::ScoringFunction | protected |
| storeInteractionsEnabled() | BALL::ScoringFunction | |
| unassigned_atoms_ | BALL::ScoringFunction | protected |
| unsetTrainingParameters() | BALL::ScoringFunction | |
| update() | BALL::ScoringFunction | virtual |
| updateComponent(int id, AtomPairList *) | BALL::ScoringFunction | protected |
| updateScore() | BALL::ScoringFunction | virtual |
| use_all_lig_nonb_ | BALL::ScoringFunction | protected |
| use_static_lig_fragments_ | BALL::ScoringFunction | protected |
| valueToString(double value) | BALL::ScoringFunction | |
| ~ScoringFunction() | BALL::ScoringFunction | virtual |
| ~SLICKScore() | BALL::SLICKScore | virtual |
1.8.7