| 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 |
| activated_ | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| 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_structure(core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy, Batch const &batch) override | protocols::jd2::archive::EvaluatedArchive | virtual |
| add_structure_at_position(SilentStructs::iterator iss, core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy) | protocols::jd2::archive::ArchiveBase | protectedvirtual |
| ArchiveBase(ArchiveManagerAP ptr=nullptr) | protocols::jd2::archive::ArchiveBase | |
| const_decoy_iterator typedef | protocols::jd2::archive::ArchiveBase | protected |
| 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 | |
| erase_decoy(std::string const &tag) | protocols::jd2::archive::ArchiveBase | 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 |
| finished() const override | protocols::jd2::archive::ArchiveBase | inlinevirtual |
| generate_batch() override=0 | protocols::jd2::archive::ArchiveBase | pure virtual |
| protocols::jd2::archive::AbstractArchiveBase::generate_batch(jd2::archive::Batch &, core::Size) | protocols::jd2::archive::AbstractArchiveBase | inlinevirtual |
| get_weight(std::string const &column) const | protocols::jd2::archive::EvaluatedArchive | |
| has_evaluator(std::string const &column) | protocols::jd2::archive::EvaluatedArchive | |
| idle() override | protocols::jd2::archive::ArchiveBase | inlinevirtual |
| init_from_decoy_set(core::io::silent::SilentFileData const &sfd) override=0 | protocols::jd2::archive::EvaluatedArchive | pure virtual |
| init_from_options() | protocols::jd2::archive::NormalizedEvaluatedArchive | |
| initialize() override | protocols::jd2::archive::NormalizedEvaluatedArchive | virtual |
| insertion_prob_ | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| invalidate_score_variations() override | protocols::jd2::archive::NormalizedEvaluatedArchive | inlineprotectedvirtual |
| is_start_zero_score(std::string const &) const | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| keep_adding_to_statistics_ | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| load_decoys(std::string const &filename, SilentStructs &decoys) | protocols::jd2::archive::ArchiveBase | |
| lower_quartile_ | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| manager() | protocols::jd2::archive::AbstractArchiveBase | inline |
| manager_ptr() | protocols::jd2::archive::AbstractArchiveBase | inlineprotected |
| max_nstruct() | protocols::jd2::archive::ArchiveBase | inlineprotected |
| min_decoys_for_statistics_ | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| name() const | protocols::jd2::archive::AbstractArchiveBase | inline |
| NormalizedEvaluatedArchive(ArchiveManagerAP ptr) | protocols::jd2::archive::NormalizedEvaluatedArchive | |
| NormalizedEvaluatedArchive() | protocols::jd2::archive::NormalizedEvaluatedArchive | |
| nstruct() const | protocols::jd2::archive::ArchiveBase | inline |
| nstruct_for_statistics_ | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| options_registered_ | protocols::jd2::archive::NormalizedEvaluatedArchive | privatestatic |
| Parent typedef | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| positive_scores_ | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| proposed_since_last_batch() const | protocols::jd2::archive::ArchiveBase | inline |
| read_structures(core::io::silent::SilentFileData &sfd, core::io::silent::SilentFileData &alternative_decoys, Batch const &batch) override | protocols::jd2::archive::EvaluatedArchive | virtual |
| register_options() | protocols::jd2::archive::NormalizedEvaluatedArchive | static |
| remove_evaluation(std::string const &column) | protocols::jd2::archive::EvaluatedArchive | |
| rescore() override | protocols::jd2::archive::NormalizedEvaluatedArchive | virtual |
| reset_accept_counter() | protocols::jd2::archive::ArchiveBase | inline |
| restore_from_file() override | protocols::jd2::archive::NormalizedEvaluatedArchive | virtual |
| restore_status(std::istream &) | protocols::jd2::archive::ArchiveBase | virtual |
| save_decoys(std::string const &dirname, std::string const &name, SilentStructs const &decoys) | protocols::jd2::archive::ArchiveBase | |
| save_status(std::ostream &) const override | protocols::jd2::archive::ArchiveBase | virtual |
| save_to_file(std::string suffix="") override | protocols::jd2::archive::NormalizedEvaluatedArchive | virtual |
| score(core::pose::Pose &pose) const | protocols::jd2::archive::EvaluatedArchive | protectedvirtual |
| score_variation(std::string const &col) const override | protocols::jd2::archive::NormalizedEvaluatedArchive | virtual |
| score_variations() const override | protocols::jd2::archive::NormalizedEvaluatedArchive | virtual |
| score_variations_ | protocols::jd2::archive::NormalizedEvaluatedArchive | mutableprivate |
| score_variations_are_clean_ | protocols::jd2::archive::NormalizedEvaluatedArchive | mutableprivate |
| 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_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_nstruct(core::Size set) | protocols::jd2::archive::ArchiveBase | inline |
| set_scorefxn(core::scoring::ScoreFunctionOP scorefxn_) | protocols::jd2::archive::EvaluatedArchive | |
| 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::jd2::archive::EvaluatedArchive | |
| SilentStructs typedef | protocols::jd2::archive::ArchiveBase | protected |
| SOURCE_FILE | protocols::jd2::archive::ArchiveBase | protectedstatic |
| start_evaluation_timer() const | protocols::jd2::archive::EvaluatedArchive | |
| statistics_valid() | protocols::jd2::archive::ArchiveBase | inline |
| still_interested(jd2::archive::Batch const &) const | protocols::jd2::archive::AbstractArchiveBase | inlinevirtual |
| TAG_IN_FILE | protocols::jd2::archive::ArchiveBase | protectedstatic |
| total_accepts() | protocols::jd2::archive::ArchiveBase | inline |
| total_proposed() | protocols::jd2::archive::ArchiveBase | inline |
| use_variance_archive_ | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| variance_archive_ | protocols::jd2::archive::NormalizedEvaluatedArchive | private |
| 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 | |
| ~NormalizedEvaluatedArchive() override | protocols::jd2::archive::NormalizedEvaluatedArchive | |
1.8.7