| AmberNonBonded() | BALL::AmberNonBonded | |
| AmberNonBonded(ForceField &force_field) | BALL::AmberNonBonded | |
| AmberNonBonded(const AmberNonBonded &amber_non_bonded) | BALL::AmberNonBonded | |
| atom_pairwise_ | BALL::ScoringComponent | protected |
| base_function_ | BALL::ScoringComponent | protected |
| buildVectorOfNonBondedAtomPairs(const std::vector< std::pair< Atom *, Atom * > > &atom_vector, const LennardJones &lennard_jones, const Potential1210 &hydrogen_bond) | BALL::AmberNonBonded | virtual |
| clear() | BALL::AmberNonBonded | virtual |
| coefficient_ | BALL::ScoringComponent | protected |
| determineMethodOfAtomPairGeneration() | BALL::AmberNonBonded | virtual |
| disable() | BALL::ScoringComponent | |
| electrostatic_energy_ | BALL::AmberNonBonded | protected |
| ELECTROSTATIC_FACTOR | BALL::AmberNonBonded | static |
| enable() | BALL::ScoringComponent | |
| enableStoreInteractions(bool b=true) | BALL::AmberNonBonded | |
| energy_ | BALL::ForceFieldComponent | protected |
| force_field_ | BALL::ForceFieldComponent | protected |
| ForceFieldComponent() | BALL::ForceFieldComponent | |
| ForceFieldComponent(ForceField &force_field) | BALL::ForceFieldComponent | |
| ForceFieldComponent(const ForceFieldComponent &force_field_component) | BALL::ForceFieldComponent | |
| getCoefficient() | BALL::ScoringComponent | |
| getElectrostaticEnergy() const | BALL::AmberNonBonded | virtual |
| getEnergy() const | BALL::ForceFieldComponent | virtual |
| getForceField() const | BALL::ForceFieldComponent | |
| getName() const | BALL::ForceFieldComponent | |
| getNormalizationParameters(double &stddev, double &mean) | BALL::ScoringComponent | |
| getRawScore() const | BALL::ScoringComponent | |
| getScaledScore() const | BALL::ScoringComponent | |
| getScoringFunction() const | BALL::ScoringComponent | |
| getTypeName() | BALL::ScoringComponent | |
| getVdwEnergy() const | BALL::AmberNonBonded | virtual |
| gridable_ | BALL::ScoringComponent | protected |
| isAtomPairwise() | BALL::ScoringComponent | |
| isEnabled() const | BALL::ForceFieldComponent | inline |
| BALL::ScoringComponent::isEnabled() | BALL::ScoringComponent | |
| isGridable() | BALL::ScoringComponent | |
| isLigandIntraMolecular() | BALL::ScoringComponent | |
| ligand_intra_molecular_ | BALL::ScoringComponent | protected |
| mean_ | BALL::ScoringComponent | protected |
| operator=(const AmberNonBonded &anb) | BALL::AmberNonBonded | |
| operator==(const AmberNonBonded &anb) | BALL::AmberNonBonded | |
| scaleScore(double score) const | BALL::ScoringComponent | protected |
| score_ | BALL::ScoringComponent | protected |
| scoring_function_ | BALL::ScoringComponent | protected |
| ScoringComponent() | BALL::ScoringComponent | |
| ScoringComponent(const ScoringComponent &sc) | BALL::ScoringComponent | |
| ScoringComponent(ScoringFunction &sf) | BALL::ScoringComponent | |
| selectBaseFunction(String function) | BALL::ScoringComponent | |
| setAdvancedElectrostatic(AdvancedElectrostatic *advES) | BALL::AmberNonBonded | |
| setCoefficient(const double &coeff) | BALL::ScoringComponent | |
| setEnabled(bool state) | BALL::ForceFieldComponent | inline |
| setForceField(ForceField &force_field) | BALL::ForceFieldComponent | |
| setLigandIntraMolecular(bool b) | BALL::ScoringComponent | virtual |
| setName(const String &name) | BALL::ForceFieldComponent | |
| setNormalizationParameters(double stddev, double mean) | BALL::ScoringComponent | |
| setScoringFunction(ScoringFunction &sf) | BALL::ScoringComponent | |
| setup() | BALL::AmberNonBonded | virtual |
| setup(Options &options, ForceFieldParameters &par) | BALL::AmberNonBonded | |
| setupLigand() | BALL::ScoringComponent | virtual |
| stddev_ | BALL::ScoringComponent | protected |
| type_name_ | BALL::ScoringComponent | protected |
| update() | BALL::AmberNonBonded | virtual |
| update(const std::vector< std::pair< Atom *, Atom * > > &atom_vector) | BALL::AmberNonBonded | virtual |
| updateEnergy() | BALL::AmberNonBonded | virtual |
| updateForces() | BALL::AmberNonBonded | virtual |
| updateScore() | BALL::ForceFieldComponent | virtual |
| vdw_energy_ | BALL::AmberNonBonded | protected |
| ~AmberNonBonded() | BALL::AmberNonBonded | virtual |
| ~ForceFieldComponent() | BALL::ForceFieldComponent | virtual |
| ~ScoringComponent() | BALL::ScoringComponent | virtual |
1.8.7