|
| | SLICKScore () |
| | SLICKScore (Molecule &protein, Molecule &ligand, Options &options) |
| | SLICKScore (const SLICKScore &slick) |
| virtual | ~SLICKScore () |
| const SLICKScore & | operator= (const SLICKScore &slick) |
| virtual void | clear () |
| bool | setup () |
| | 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 () |
| 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 () |
|
| static HashGrid3< Atom * > * | initializeHashGrid (AtomContainer *sys, Vector3 ¢er, double &resolution, int hashgrid_size) |
| static void | getDefaultOptions (Options &options) |
| list< Constraint * > | constraints {} |
| static const char * | SUBCATEGORY_NAME |
| void | setName (String name) |
| void | updateComponent (int id, AtomPairList *) |
| Vector3 | calculateGeometricalCenter (AtomContainer *s, int *no_ligand_atoms=NULL) |
| double | calculateMoleculeRadius (AtomContainer *sys, Vector3 ¢er) |
| 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_ {} |
SLICKEnergy scoring function {\bf Definition:} \URL{BALL/SCORING/FUNCTIONS/slickScore.h}
Definition at line 27 of file slickScore.h.
1.15.0