| AbstractArchiveBase(BaseArchiveManagerAP ptr) | protocols::jd2::archive::AbstractArchiveBase | inline |
| AbstractArchiveBase() | protocols::jd2::archive::AbstractArchiveBase | inline |
| accepts_since_last_batch() | protocols::jd2::archive::ArchiveBase | inline |
| accepts_since_last_batch() const | protocols::jd2::archive::ArchiveBase | inline |
| add_evaluated_structure(core::io::silent::SilentStructOP from_batch, core::io::silent::SilentStructOP alternative_decoy, Batch const &) override | protocols::jd2::archive::NormalizedEvaluatedArchive | virtual |
| add_evaluation(evaluation::PoseEvaluatorCOP, core::Real weight=0.0) | protocols::jd2::archive::EvaluatedArchive | |
| add_fullatom_flags(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | protected |
| add_structure(core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy, jd2::archive::Batch const &) override | protocols::abinitio::IterativeBase | virtual |
| add_structure_at_position(SilentStructs::iterator iss, core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy) override | protocols::abinitio::IterativeCentroid | protectedvirtual |
| ArchiveBase(ArchiveManagerAP ptr=nullptr) | protocols::jd2::archive::ArchiveBase | |
| CEN2FULLATOM enum value | protocols::abinitio::IterativeBase | |
| cen_score() const | protocols::abinitio::IterativeBase | inlineprotected |
| cen_score_patch() const | protocols::abinitio::IterativeBase | inlineprotected |
| chemshift_column() const | protocols::abinitio::IterativeBase | inlineprotected |
| cluster() | protocols::abinitio::IterativeBase | protected |
| collect_alternative_decoys(SilentStructs primary_decoys, std::string alternative_decoy_file, SilentStructVector &output_decoys) override | protocols::abinitio::IterativeCentroid | protectedvirtual |
| collect_hedgeing_decoys_from_batches(jd2::archive::Batch const &batch, core::io::silent::SilentStructOPs &start_decoys, core::Real score_cut_per_batch) | protocols::abinitio::IterativeBase | protected |
| compute_beta_topology() | protocols::abinitio::IterativeBase | protected |
| compute_cores() | protocols::abinitio::IterativeBase | protected |
| const_decoy_iterator typedef | protocols::jd2::archive::ArchiveBase | protected |
| core(core::Size i) | protocols::abinitio::IterativeBase | inlineprotected |
| count_removed_structures(core::Size n_removed) | protocols::jd2::archive::ArchiveBase | protected |
| count_structure(Batch const &batch, bool accepted) | protocols::jd2::archive::ArchiveBase | protectedvirtual |
| current_acceptance_ratio() const | protocols::jd2::archive::ArchiveBase | inline |
| decoy_iterator typedef | protocols::jd2::archive::ArchiveBase | protected |
| decoys() const | protocols::jd2::archive::ArchiveBase | inline |
| decoys() | protocols::jd2::archive::ArchiveBase | inline |
| determine_score_variations() const | protocols::jd2::archive::NormalizedEvaluatedArchive | |
| ENUMERATION enum value | protocols::abinitio::IterativeBase | |
| erase_decoy(std::string const &tag) override | protocols::abinitio::IterativeCentroid | protectedvirtual |
| evaluate_local() const | protocols::jd2::archive::EvaluatedArchive | inline |
| evaluate_silent_struct(core::io::silent::SilentStructOP from_batch) const | protocols::jd2::archive::EvaluatedArchive | |
| EvaluatedArchive(ArchiveManagerAP ptr) | protocols::jd2::archive::EvaluatedArchive | |
| EvaluatedArchive() | protocols::jd2::archive::EvaluatedArchive | |
| EvaluatorMap typedef | protocols::jd2::archive::EvaluatedArchive | |
| evaluators() const | protocols::jd2::archive::EvaluatedArchive | inline |
| fa_score() const | protocols::abinitio::IterativeBase | inlineprotected |
| fa_score_patch() const | protocols::abinitio::IterativeBase | inlineprotected |
| FINISHED enum value | protocols::abinitio::IterativeBase | |
| finished() const override | protocols::abinitio::IterativeBase | inlinevirtual |
| fullatom_pool_ptr_ | protocols::abinitio::IterativeCentroid | private |
| gen_cen2fullatom(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | protected |
| gen_cen2fullatom_non_pool_decoys(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | protected |
| gen_diversity_pool(jd2::archive::Batch &batch, bool fullatom=false) override | protocols::abinitio::IterativeCentroid | virtual |
| gen_dynamic_patches(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | virtual |
| gen_enumerate_pairings(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | protected |
| gen_evaluation_output(jd2::archive::Batch &batch, bool fullatom=false) | protocols::abinitio::IterativeBase | virtual |
| gen_noe_assignments(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | protected |
| gen_resample_fragments(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | protected |
| gen_resample_stage2(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | protected |
| gen_resample_topologies(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | protected |
| gen_start_structures(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | protected |
| generate_batch() override | protocols::abinitio::IterativeBase | virtual |
| generate_batch(jd2::archive::Batch &, core::Size repeat_id) override | protocols::abinitio::IterativeBase | virtual |
| get_weight(std::string const &column) const | protocols::jd2::archive::EvaluatedArchive | |
| guess_pairings_from_secondary_structure(core::fragment::FragSet const &frags, std::string const &out_pairings_file, std::string const &out_frag_ss_file) const | protocols::abinitio::IterativeBase | protected |
| has_evaluator(std::string const &column) | protocols::jd2::archive::EvaluatedArchive | |
| idle() override | protocols::abinitio::IterativeBase | virtual |
| init_from_decoy_set(core::io::silent::SilentFileData const &sfd) override | protocols::abinitio::IterativeBase | virtual |
| init_from_options() | protocols::jd2::archive::NormalizedEvaluatedArchive | |
| initialize() override | protocols::abinitio::IterativeBase | virtual |
| invalidate_score_variations() override | protocols::jd2::archive::NormalizedEvaluatedArchive | inlineprotectedvirtual |
| IterationStage enum name | protocols::abinitio::IterativeBase | |
| IterativeBase(std::string name) | protocols::abinitio::IterativeBase | |
| IterativeCentroid(IterativeFullatom *fullatom_pool_ptr) | protocols::abinitio::IterativeCentroid | inline |
| LAST_CENTROID_START enum value | protocols::abinitio::IterativeBase | |
| load_decoys(std::string const &filename, SilentStructs &decoys) | protocols::jd2::archive::ArchiveBase | |
| manager() | protocols::jd2::archive::AbstractArchiveBase | inline |
| manager_ptr() | protocols::jd2::archive::AbstractArchiveBase | inlineprotected |
| max_nstruct() | protocols::jd2::archive::ArchiveBase | inlineprotected |
| name() const | protocols::jd2::archive::AbstractArchiveBase | inline |
| never_switched_noe_filter_ | protocols::abinitio::IterativeBase | protected |
| NOESY_PHASEII_S2_RESAMPLING enum value | protocols::abinitio::IterativeBase | |
| NOESY_PHASEII_TOPO enum value | protocols::abinitio::IterativeBase | |
| NormalizedEvaluatedArchive(ArchiveManagerAP ptr) | protocols::jd2::archive::NormalizedEvaluatedArchive | |
| NormalizedEvaluatedArchive() | protocols::jd2::archive::NormalizedEvaluatedArchive | |
| nstruct() const | protocols::jd2::archive::ArchiveBase | inline |
| overall_cstfilter_weight() const | protocols::abinitio::IterativeBase | inlineprotected |
| Parent typedef | protocols::abinitio::IterativeCentroid | private |
| proposed_since_last_batch() const | protocols::jd2::archive::ArchiveBase | inline |
| PURE_TOPO_RESAMPLING enum value | protocols::abinitio::IterativeBase | |
| read_structures(core::io::silent::SilentFileData &sfd, core::io::silent::SilentFileData &alternative_decoys, jd2::archive::Batch const &batch) override | protocols::abinitio::IterativeBase | virtual |
| ready_for_batch() const | protocols::abinitio::IterativeBase | inlinevirtual |
| reassign_noesy_data(jd2::archive::Batch &batch) | protocols::abinitio::IterativeBase | protected |
| register_options() | protocols::abinitio::IterativeBase | static |
| remove_evaluation(std::string const &column) | protocols::jd2::archive::EvaluatedArchive | |
| rescore() override | protocols::abinitio::IterativeBase | virtual |
| reset_accept_counter() | protocols::jd2::archive::ArchiveBase | inline |
| restore_from_file() override | protocols::abinitio::IterativeCentroid | virtual |
| restore_status(std::istream &) override | protocols::abinitio::IterativeBase | virtual |
| RIGID_CORE_RESAMPLING enum value | protocols::abinitio::IterativeBase | |
| save_decoys(std::string const &dirname, std::string const &name, SilentStructs const &decoys) | protocols::jd2::archive::ArchiveBase | |
| save_status(std::ostream &) const override | protocols::abinitio::IterativeBase | virtual |
| save_to_file(std::string suffix="") override | protocols::abinitio::IterativeCentroid | virtual |
| score_variation(std::string const &col) const override | protocols::jd2::archive::NormalizedEvaluatedArchive | virtual |
| score_variations() const override | protocols::jd2::archive::NormalizedEvaluatedArchive | virtual |
| scored_core_ | protocols::abinitio::IterativeBase | protected |
| scorefxn() const | protocols::jd2::archive::EvaluatedArchive | |
| scorefxn_non_const() | protocols::jd2::archive::EvaluatedArchive | protected |
| select_score(core::io::silent::SilentStructOP evaluated_decoy) | protocols::jd2::archive::EvaluatedArchive | |
| set_evaluate_local(bool setting) | protocols::jd2::archive::EvaluatedArchive | inline |
| set_evaluators(EvaluatorMap const &, WeightMap const &) | protocols::jd2::archive::EvaluatedArchive | |
| set_finish_stage(IterationStage setting) | protocols::abinitio::IterativeBase | inline |
| set_manager(BaseArchiveManagerAP manager) | protocols::jd2::archive::AbstractArchiveBase | inlinevirtual |
| set_max_nstruct(core::Size setting) | protocols::jd2::archive::ArchiveBase | inlineprotected |
| set_name(std::string const &set) | protocols::jd2::archive::AbstractArchiveBase | inline |
| set_noesy_assign_float_cycle(core::Real setting) | protocols::abinitio::IterativeBase | inlineprotected |
| set_nstruct(core::Size set) | protocols::jd2::archive::ArchiveBase | inline |
| set_overall_cstfilter_weight(core::Real setting) | protocols::abinitio::IterativeBase | inlineprotected |
| set_scorefxn(core::scoring::ScoreFunctionOP scorefxn_) | protocols::jd2::archive::EvaluatedArchive | |
| set_stage(IterationStage setting) | protocols::abinitio::IterativeBase | inlineprotected |
| set_weight(std::string const &column, core::Real weight) | protocols::jd2::archive::EvaluatedArchive | |
| set_weights(WeightMap const &setting) | protocols::jd2::archive::EvaluatedArchive | |
| setup_default_evaluators() | protocols::abinitio::IterativeBase | |
| setup_filter_cst(core::Real weight) | protocols::abinitio::IterativeBase | protected |
| SilentStructs typedef | protocols::jd2::archive::ArchiveBase | protected |
| SilentStructVector typedef | protocols::abinitio::IterativeBase | protected |
| SOURCE_FILE | protocols::jd2::archive::ArchiveBase | protectedstatic |
| stage() const | protocols::abinitio::IterativeBase | inlineprotected |
| stage2_decoys_ | protocols::abinitio::IterativeCentroid | private |
| STAGE2_RESAMPLING enum value | protocols::abinitio::IterativeBase | |
| start_evaluation_timer() const | protocols::jd2::archive::EvaluatedArchive | |
| statistics_valid() | protocols::jd2::archive::ArchiveBase | inline |
| still_interested(jd2::archive::Batch const &batch) const override | protocols::abinitio::IterativeBase | virtual |
| super_quick_relax_of_centroids() const | protocols::abinitio::IterativeBase | inlineprotected |
| TAG_IN_FILE | protocols::jd2::archive::ArchiveBase | protectedstatic |
| target_sequence() const | protocols::abinitio::IterativeBase | inlineprotected |
| test_broker_settings(jd2::archive::Batch const &batch) | protocols::abinitio::IterativeBase | protected |
| test_for_stage_end() | protocols::abinitio::IterativeBase | |
| TOPO_RESAMPLING enum value | protocols::abinitio::IterativeBase | |
| total_accepts() | protocols::jd2::archive::ArchiveBase | inline |
| total_proposed() | protocols::jd2::archive::ArchiveBase | inline |
| update_noesy_filter_files(std::string const ¤t, bool fullatom) override | protocols::abinitio::IterativeCentroid | virtual |
| WeightMap typedef | protocols::jd2::archive::EvaluatedArchive | |
| weights() const | protocols::jd2::archive::EvaluatedArchive | inline |
| ~AbstractArchiveBase() override | protocols::jd2::archive::AbstractArchiveBase | |
| ~ArchiveBase() override | protocols::jd2::archive::ArchiveBase | |
| ~EvaluatedArchive() override | protocols::jd2::archive::EvaluatedArchive | |
| ~IterativeBase() override | protocols::abinitio::IterativeBase | |
| ~NormalizedEvaluatedArchive() override | protocols::jd2::archive::NormalizedEvaluatedArchive | |
1.8.7