| add_all_restraints() | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| add_states_and_filters() (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| align() (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| all_rs_filt_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| asmb_data_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| cg_sorted_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| clear_caches() | IMP::Object | virtual |
| conn_rs_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| conn_rs_with_filter_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| dmap_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| do_destroy() | IMP::Object | protectedvirtual |
| dummy_rs_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| em_rs_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| ev_rs_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| ev_thr_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| fast_scoring_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| filters_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| filters_set_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| fit_state_key_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| get_alignment_restraints() const (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| get_check_level() const (defined in IMP::Object) | IMP::Object | |
| get_combinations(bool uniques=false) const (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| get_log_level() const (defined in IMP::Object) | IMP::Object | |
| get_model() (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| get_molecules() const (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| get_name() const (defined in IMP::Object) | IMP::Object | |
| get_restraint_set() | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| get_rigid_bodies() const (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| get_type_name() const (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | virtual |
| get_version_info() const | IMP::multifit::ProteomicsEMAlignmentAtomic | virtual |
| jt_rs_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| load_atomic_molecules() (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| load_combination_of_states(const Ints &state4particles) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| mapping_data_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| mdl_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| mhs_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| NonCopyable() (defined in IMP::NonCopyable) | IMP::NonCopyable | protected |
| Object(std::string name) | IMP::Object | protected |
| order_key_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| params_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| post_sampling_ev_pairs_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| prot_data_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| ProteomicsEMAlignmentAtomic(const ProteinsAnchorsSamplingSpace &mapping_data, multifit::SettingsData *asmb_data, const AlignmentParams &align_param) (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| pst_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| rbs_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| rc_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| restraint_set_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| sampled_assignments_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| sampled_solutions_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| set_check_level(CheckLevel l) | IMP::Object | |
| set_density_map(em::DensityMap *dmap, float threshold) (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| set_fast_scoring(bool state) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| set_log_level(LogLevel l) | IMP::Object | |
| set_name(std::string name) (defined in IMP::Object) | IMP::Object | |
| set_particle_states_table(domino::SubsetFilterTables &filters) (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| set_was_used(bool tf) const | IMP::Object | |
| show(std::ostream &out=std::cout) const (defined in IMP::Object) | IMP::Object | |
| show_domino_merge_tree() const (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| show_scores_header(std::ostream &ous=std::cout) const (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | |
| states_set_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| threshold_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| xlink_rs_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| xlink_rs_with_filter_ (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protected |
| ~Object() (defined in IMP::Object) | IMP::Object | virtual |
| ~ProteomicsEMAlignmentAtomic() (defined in IMP::multifit::ProteomicsEMAlignmentAtomic) | IMP::multifit::ProteomicsEMAlignmentAtomic | protectedvirtual |
