| abort() | BALL::DockingAlgorithm | virtual |
| abort_ | BALL::DockingAlgorithm | protected |
| ALL_INTERMEDIATE_POSES enum value | BALL::DockingAlgorithm | |
| applyBestConformation() | BALL::EvolutionaryDocking | protected |
| BEST_INTERMEDIATE_POSES enum value | BALL::DockingAlgorithm | |
| calculateRMSD(const AtomContainer &S1, const AtomContainer &S2, int *no_matched_atoms=NULL) | BALL::DockingAlgorithm | |
| destroy_() | BALL::EvolutionaryDocking | protected |
| display_mode_ | BALL::DockingAlgorithm | protected |
| DISPLAYMODE enum name | BALL::DockingAlgorithm | |
| DockingAlgorithm() | BALL::DockingAlgorithm | |
| DockingAlgorithm(System &receptor, System &ligand, Options &new_options) | BALL::DockingAlgorithm | |
| DockingAlgorithm(System &receptor, System &ligand) | BALL::DockingAlgorithm | |
| dockLigand(AtomContainer &ligand, bool verbose=0) | BALL::EvolutionaryDocking | virtual |
| dp_ | BALL::EvolutionaryDocking | protected |
| EvolutionaryDocking(System &system1, System &system2, Options &new_options) | BALL::EvolutionaryDocking | |
| EvolutionaryDocking(System &receptor, System &ligand, string config_file) | BALL::EvolutionaryDocking | |
| finish() | BALL::DockingAlgorithm | virtual |
| finished_ | BALL::DockingAlgorithm | protected |
| ga_ | BALL::EvolutionaryDocking | protected |
| getConformationSet(Index total_conformations=0) | BALL::DockingAlgorithm | virtual |
| getDefaultOptions(Options &options) | BALL::EvolutionaryDocking | static |
| getDisplayMode() | BALL::DockingAlgorithm | |
| getLigand() | BALL::DockingAlgorithm | |
| getName() | BALL::DockingAlgorithm | |
| getProgress() const | BALL::EvolutionaryDocking | virtual |
| getReferenceLigand() | BALL::DockingAlgorithm | |
| getReferenceLigandCenter() | BALL::EvolutionaryDocking | |
| getScoringFunction() | BALL::DockingAlgorithm | |
| getVisualizationPose() | BALL::DockingAlgorithm | |
| getVisualizationPoseScore() | BALL::DockingAlgorithm | |
| hasFinished() const | BALL::DockingAlgorithm | virtual |
| ligand_ | BALL::DockingAlgorithm | protected |
| mapCompounds(const AtomContainer &S1, const AtomContainer &S2, Size &no_matched_heavy_atoms, double &rmsd, double upper_bound, double lower_bound, double tolerance) | BALL::DockingAlgorithm | static |
| mapLigandOntoReferenceLigand() | BALL::DockingAlgorithm | protected |
| min_sec_between_visualizations_ | BALL::DockingAlgorithm | protected |
| name_ | BALL::DockingAlgorithm | protected |
| new_pose_to_be_visualized | BALL::DockingAlgorithm | |
| NO_DISPLAY enum value | BALL::DockingAlgorithm | |
| NO_INTERMEDIATE_POSES enum value | BALL::DockingAlgorithm | |
| OPTION_FILE_PARAMETER_NAME | BALL::DockingAlgorithm | static |
| options | BALL::DockingAlgorithm | |
| parameter_filename_ | BALL::DockingAlgorithm | protected |
| pause() | BALL::DockingAlgorithm | virtual |
| pause_ | BALL::DockingAlgorithm | protected |
| proceed() | BALL::DockingAlgorithm | virtual |
| processMultiMoleculeFile(string input_filename, string output_filename, double score_cutoff, vector< double > *min_atoms_in_ref_areas=0, String toolinfo="", String timestamp="") | BALL::DockingAlgorithm | |
| readOptionFile(String filename, Options &output_options, list< Constraint * > &output_constraints, const AtomContainer *ref_ligand=0) | BALL::DockingAlgorithm | static |
| receptor_ | BALL::DockingAlgorithm | protected |
| redraw() | BALL::EvolutionaryDocking | |
| reference_center_ | BALL::EvolutionaryDocking | protected |
| reference_ligand_ | BALL::DockingAlgorithm | protected |
| reset() | BALL::DockingAlgorithm | virtual |
| scoring_function_ | BALL::DockingAlgorithm | protected |
| scoring_type_ | BALL::DockingAlgorithm | protected |
| setDisplayMode(DISPLAYMODE display_mode) | BALL::DockingAlgorithm | |
| setLigand(AtomContainer *ligand) | BALL::DockingAlgorithm | |
| setMaxFps(int no) | BALL::DockingAlgorithm | |
| setScoringFunction(ScoringFunction *scoring) | BALL::DockingAlgorithm | inline |
| setup(System &ligand, BALL::ScoringFunction *sf, Options &new_options) | BALL::EvolutionaryDocking | virtual |
| setup(System &ligand, BALL::ScoringFunction *sf) | BALL::EvolutionaryDocking | virtual |
| setup(System &receptor, System &ligand, Options &new_options) | BALL::EvolutionaryDocking | virtual |
| BALL::DockingAlgorithm::setup(System &receptor, System &ligand) | BALL::DockingAlgorithm | virtual |
| setVisualizationPose(const double &score) | BALL::DockingAlgorithm | |
| start() | BALL::EvolutionaryDocking | virtual |
| system1_ | BALL::DockingAlgorithm | protected |
| system2_ | BALL::DockingAlgorithm | protected |
| visualization_pose_ | BALL::DockingAlgorithm | protected |
| visualization_pose_score_ | BALL::DockingAlgorithm | protected |
| visualization_timer_ | BALL::DockingAlgorithm | protected |
| wasAborted() const | BALL::DockingAlgorithm | inlinevirtual |
| wasPaused() const | BALL::DockingAlgorithm | inlinevirtual |
| writeOptionFile(String filename, Options &input_options, list< Constraint * > &input_constraints) | BALL::DockingAlgorithm | static |
| writeSubcategories_(Options &category, std::ostream &out) | BALL::DockingAlgorithm | protectedstatic |
| ~DockingAlgorithm() | BALL::DockingAlgorithm | virtual |
| ~EvolutionaryDocking() | BALL::EvolutionaryDocking | |
1.8.7