| add_coordinate_constraints(core::pose::Pose &pose, core::pose::Pose const &source_pose, core::Size nearest_to_from, core::Size nearest_to_to, core::Size anchor, std::string atom_type="CA", core::pack::task::PackerTaskOP task=nullptr) | protocols::splice::Splice | |
| add_dihedral_constraints(core::pose::Pose &pose, core::pose::Pose const &source_pose, core::Size nearest_to_from, core::Size nearest_to_to) | protocols::splice::Splice | |
| add_sequence_constraints(core::pose::Pose &pose) | protocols::splice::Splice | |
| add_sequence_constraints_only() const | protocols::splice::Splice | inline |
| add_sequence_constraints_only(bool const a) | protocols::splice::Splice | inline |
| add_sequence_constraints_only_ | protocols::splice::Splice | private |
| allow_all_aa() const | protocols::splice::Splice | inline |
| allow_all_aa(bool const d) | protocols::splice::Splice | inline |
| allow_all_aa_ | protocols::splice::Splice | private |
| allowed_cuts_ | protocols::splice::Splice | private |
| apply(Pose &pose) override | protocols::splice::Splice | virtual |
| bb_comp_db_ | protocols::splice::Splice | private |
| ccd(bool const c) | protocols::splice::Splice | inline |
| ccd() const | protocols::splice::Splice | inline |
| ccd_ | protocols::splice::Splice | private |
| CG_const_ | protocols::splice::Splice | private |
| chain_num() const | protocols::splice::Splice | inline |
| chain_num(core::Size const c) | protocols::splice::Splice | inline |
| chain_num_ | protocols::splice::Splice | private |
| chainbreak_check(core::pose::Pose const &pose, core::Real const tolerance, bool fail_retry_if_found, bool crash_if_found) | protocols::splice::Splice | private |
| checkpointing_file() const | protocols::splice::Splice | |
| checkpointing_file(std::string const &cf) | protocols::splice::Splice | |
| checkpointing_file_ | protocols::splice::Splice | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::splice::Splice | virtual |
| coor_const() const | protocols::splice::Splice | inline |
| coor_const_ | protocols::splice::Splice | private |
| copy_stretch(core::pose::Pose &target, core::pose::Pose const &source, core::Size const from_res, core::Size const to_res) | protocols::splice::Splice | private |
| correct_bb_O_placements(core::pose::Pose Pose, core::Size cut_site) | protocols::splice::Splice | private |
| create() | protocols::moves::Mover | virtual |
| current_dbase_entry_ | protocols::splice::Splice | private |
| current_segment_pos | protocols::splice::Splice | private |
| cut_secondarystruc(bool const r) | protocols::splice::Splice | inline |
| cut_secondarystruc() const | protocols::splice::Splice | inline |
| cut_secondarystruc_ | protocols::splice::Splice | private |
| database_entry() const | protocols::splice::Splice | inline |
| database_entry(core::Size const d) | protocols::splice::Splice | inline |
| database_entry_ | protocols::splice::Splice | private |
| database_pdb_entry(std::string const &s) | protocols::splice::Splice | inline |
| database_pdb_entry() const | protocols::splice::Splice | inline |
| database_pdb_entry_ | protocols::splice::Splice | private |
| database_segment_map_ | protocols::splice::Splice | private |
| DataccacheBoolDataOP typedef | protocols::splice::Splice | |
| dbase_begin() const | protocols::splice::Splice | |
| dbase_const_iterator typedef | protocols::splice::Splice | |
| dbase_end() const | protocols::splice::Splice | |
| dbase_iterate() const | protocols::splice::Splice | inline |
| dbase_iterate(bool const d) | protocols::splice::Splice | inline |
| dbase_iterate_ | protocols::splice::Splice | private |
| dbase_subset_ | protocols::splice::Splice | private |
| debug_ | protocols::splice::Splice | private |
| delete_hairpin(bool const b) | protocols::splice::Splice | inline |
| delete_hairpin() const | protocols::splice::Splice | inline |
| delete_hairpin_ | protocols::splice::Splice | private |
| delete_hairpin_c() const | protocols::splice::Splice | inline |
| delete_hairpin_c(core::Size const c) | protocols::splice::Splice | inline |
| delete_hairpin_c_ | protocols::splice::Splice | private |
| delete_hairpin_n() const | protocols::splice::Splice | inline |
| delete_hairpin_n(core::Size const c) | protocols::splice::Splice | inline |
| delete_hairpin_n_ | protocols::splice::Splice | private |
| delta_lengths(utility::vector1< int > const &dl) | protocols::splice::Splice | inline |
| delta_lengths() | protocols::splice::Splice | inline |
| delta_lengths_ | protocols::splice::Splice | private |
| design() const | protocols::splice::Splice | inline |
| design(bool const d) | protocols::splice::Splice | inline |
| design_ | protocols::splice::Splice | private |
| design_shell(core::Real const c) | protocols::splice::Splice | inline |
| design_shell() const | protocols::splice::Splice | inline |
| design_shell_ | protocols::splice::Splice | private |
| design_task_factory() const | protocols::splice::Splice | |
| design_task_factory(core::pack::task::TaskFactoryOP tf) | protocols::splice::Splice | |
| design_task_factory_ | protocols::splice::Splice | private |
| dihedral_const() const | protocols::splice::Splice | inline |
| dihedral_const_ | protocols::splice::Splice | private |
| dofs_pdb_name | protocols::splice::Splice | private |
| end_dbase_subset_ | protocols::splice::Splice | private |
| enzdes_ | protocols::splice::Splice | private |
| equal_length(bool const e) | protocols::splice::Splice | inline |
| equal_length() const | protocols::splice::Splice | inline |
| equal_length_ | protocols::splice::Splice | private |
| find_dbase_entry(core::pose::Pose const &pose) | protocols::splice::Splice | |
| find_non_active_site_cut_site(core::pose::Pose const &pose) | protocols::splice::Splice | private |
| first_pass_ | protocols::splice::Splice | private |
| fold_tree(core::pose::Pose &pose, core::Size const start, core::Size const stop, core::Size const cut) const | protocols::splice::Splice | |
| fresh_instance() const override | protocols::splice::Splice | inlinevirtual |
| from_res(core::Size const f) | protocols::splice::Splice | |
| from_res(core::pose::Pose const &pose) const | protocols::splice::Splice | |
| from_res_ | protocols::splice::Splice | private |
| generate_sequence_profile(core::pose::Pose &pose) | protocols::splice::Splice | |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_current_job() const | protocols::moves::Mover | |
| get_current_seg() | protocols::splice::Splice | inline |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_dofs_pdb_name() const | protocols::splice::Splice | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_name() const override | protocols::splice::Splice | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_segment_names_ordered() const | protocols::splice::Splice | inline |
| get_self_ptr() const | protocols::moves::Mover | inline |
| get_self_ptr() | protocols::moves::Mover | inline |
| get_self_weak_ptr() const | protocols::moves::Mover | inline |
| get_self_weak_ptr() | protocols::moves::Mover | inline |
| get_type() const | protocols::moves::Mover | inline |
| ignore_chain_break_ | protocols::splice::Splice | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| load_from_checkpoint() | protocols::splice::Splice | |
| load_pdb_segments_from_pose_comments(core::pose::Pose const &p) | protocols::splice::Splice | |
| locked_res() const | protocols::splice::Splice | |
| locked_res(core::Size const r) | protocols::splice::Splice | |
| locked_res_ | protocols::splice::Splice | private |
| locked_res_id(char const c) | protocols::splice::Splice | |
| locked_res_id() const | protocols::splice::Splice | |
| locked_res_id_ | protocols::splice::Splice | private |
| loop_dbase_file_name() const | protocols::splice::Splice | |
| loop_dbase_file_name(std::string const &f) | protocols::splice::Splice | |
| loop_dbase_file_name_ | protocols::splice::Splice | private |
| loop_pdb_source(std::string const &l) | protocols::splice::Splice | |
| loop_pdb_source() const | protocols::splice::Splice | |
| loop_pdb_source_ | protocols::splice::Splice | private |
| min_seg_ | protocols::splice::Splice | private |
| modify_pdb_segments_with_current_segment(std::string const &pdb_name) | protocols::splice::Splice | |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::splice::Splice | static |
| mover_name_ | protocols::splice::Splice | private |
| mover_tag_ | protocols::splice::Splice | private |
| name() | protocols::moves::Mover | inlinestatic |
| order_segments_ | protocols::splice::Splice | private |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &) override | protocols::splice::Splice | virtual |
| parse_pdb_code(std::string pdb_file_name) | protocols::splice::Splice | private |
| Pdb4LetName_ | protocols::splice::Splice | private |
| pdb_segments_ | protocols::splice::Splice | private |
| pdb_to_H3_seq_map_ | protocols::splice::Splice | private |
| poly_ala(bool const p) | protocols::splice::Splice | inline |
| poly_ala() const | protocols::splice::Splice | inline |
| poly_ala_ | protocols::splice::Splice | private |
| Pose typedef | protocols::splice::Splice | |
| PoseCOP typedef | protocols::moves::Mover | |
| profile_weight_away_from_interface(core::Real const p) | protocols::splice::Splice | |
| profile_weight_away_from_interface() const | protocols::splice::Splice | |
| profile_weight_away_from_interface_ | protocols::splice::Splice | private |
| protein_family(std::string const &s) | protocols::splice::Splice | inline |
| protein_family_ | protocols::splice::Splice | private |
| protein_family_to_database_ | protocols::splice::Splice | private |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::splice::Splice | static |
| randomize_cut(bool const r) | protocols::splice::Splice | inline |
| randomize_cut() const | protocols::splice::Splice | inline |
| randomize_cut_ | protocols::splice::Splice | private |
| rb_adjust_template(core::pose::Pose const &pose) | protocols::splice::Splice | |
| rb_sensitive() const | protocols::splice::Splice | inline |
| rb_sensitive(bool const r) | protocols::splice::Splice | inline |
| rb_sensitive_ | protocols::splice::Splice | private |
| read_splice_segments(std::string const &segment_type, std::string const &segment_name, std::string const &file_name) | protocols::splice::Splice | |
| read_torsion_database() | protocols::splice::Splice | |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| remove_hairpin(core::pose::Pose &pose) const | protocols::splice::Splice | |
| repack_shell(core::Real const c) | protocols::splice::Splice | inline |
| repack_shell() const | protocols::splice::Splice | inline |
| repack_shell_ | protocols::splice::Splice | private |
| res_move(core::Size const r) | protocols::splice::Splice | inline |
| res_move() const | protocols::splice::Splice | inline |
| res_move_ | protocols::splice::Splice | private |
| reset_status() | protocols::moves::Mover | |
| restrict_to_repacking_chain2() const | protocols::splice::Splice | inline |
| restrict_to_repacking_chain2(bool const r) | protocols::splice::Splice | inline |
| restrict_to_repacking_chain2_ | protocols::splice::Splice | private |
| retrieve_values() | protocols::splice::Splice | private |
| rms_cutoff() const | protocols::splice::Splice | inline |
| rms_cutoff(core::Real const r) | protocols::splice::Splice | inline |
| rms_cutoff_ | protocols::splice::Splice | private |
| rms_cutoff_loop() const | protocols::splice::Splice | inline |
| rms_cutoff_loop(core::Real const r) | protocols::splice::Splice | inline |
| rms_cutoff_loop_ | protocols::splice::Splice | private |
| rtmin() const | protocols::splice::Splice | inline |
| rtmin(bool const d) | protocols::splice::Splice | inline |
| rtmin_ | protocols::splice::Splice | private |
| save_to_checkpoint() const | protocols::splice::Splice | |
| save_values(core::pose::Pose const &pose) | protocols::splice::Splice | private |
| saved_fold_tree_ | protocols::splice::Splice | private |
| saved_from_res_ | protocols::splice::Splice | private |
| saved_to_res_ | protocols::splice::Splice | private |
| scorefxn(core::scoring::ScoreFunctionOP sf) | protocols::splice::Splice | |
| scorefxn() const | protocols::splice::Splice | |
| scorefxn_ | protocols::splice::Splice | private |
| segment_names_ordered_ | protocols::splice::Splice | private |
| segment_type_ | protocols::splice::Splice | private |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_cut_res(core::Size const r) | protocols::splice::Splice | inline |
| set_cut_res() const | protocols::splice::Splice | inline |
| set_cut_res_ | protocols::splice::Splice | private |
| set_dofs_pdb_name(std::string dofsPDBname) | protocols::splice::Splice | inline |
| set_fold_tree(core::pose::Pose &pose, core::Size const vl_vh_cut) | protocols::splice::Splice | |
| set_fold_tree_only_ | protocols::splice::Splice | private |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_segment_names_ordered(utility::vector1< std::string > SegNameOrder) | protocols::splice::Splice | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| skip_alignment() const | protocols::splice::Splice | inline |
| skip_alignment(bool const b) | protocols::splice::Splice | inline |
| skip_alignment_ | protocols::splice::Splice | private |
| source_pdb() const | protocols::splice::Splice | inline |
| source_pdb(std::string const &s) | protocols::splice::Splice | inline |
| source_pdb_ | protocols::splice::Splice | private |
| source_pdb_from_res() const | protocols::splice::Splice | inline |
| source_pdb_from_res(core::Size const s) | protocols::splice::Splice | inline |
| source_pdb_from_res_ | protocols::splice::Splice | private |
| source_pdb_to_res() const | protocols::splice::Splice | inline |
| source_pdb_to_res(core::Size const s) | protocols::splice::Splice | inline |
| source_pdb_to_res_ | protocols::splice::Splice | private |
| source_pose_ | protocols::splice::Splice | private |
| Splice() | protocols::splice::Splice | |
| splice_filter() const | protocols::splice::Splice | |
| splice_filter(protocols::filters::FilterOP f) | protocols::splice::Splice | |
| splice_filter_ | protocols::splice::Splice | private |
| splice_segments_ | protocols::splice::Splice | private |
| start_pose_ | protocols::splice::Splice | private |
| Strings typedef | protocols::moves::Mover | |
| superimpose_source_on_pose(core::pose::Pose const &, core::pose::Pose &) | protocols::splice::Splice | private |
| superimposed() const | protocols::splice::Splice | inline |
| superimposed(bool const b) | protocols::splice::Splice | inline |
| superimposed_ | protocols::splice::Splice | private |
| TagCOP typedef | protocols::moves::Mover | |
| tail_fold_tree(core::pose::Pose &pose, core::Size const vl_vh_cut, core::Size chain_break, std::string segment_name) const | protocols::splice::Splice | |
| tail_segment_ | protocols::splice::Splice | private |
| tail_torsion_database_ | protocols::splice::Splice | private |
| task_factory() const | protocols::splice::Splice | |
| task_factory(core::pack::task::TaskFactoryOP tf) | protocols::splice::Splice | |
| task_factory_ | protocols::splice::Splice | private |
| template_file() const | protocols::splice::Splice | inline |
| template_file(std::string const &s) | protocols::splice::Splice | inline |
| template_file_ | protocols::splice::Splice | private |
| template_pose_ | protocols::splice::Splice | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| thread_original_sequence() const | protocols::splice::Splice | inline |
| thread_original_sequence(bool const s) | protocols::splice::Splice | inline |
| thread_original_sequence_ | protocols::splice::Splice | private |
| to_res(core::Size const t) | protocols::splice::Splice | |
| to_res(core::pose::Pose const &pose) const | protocols::splice::Splice | |
| to_res_ | protocols::splice::Splice | private |
| tolerance_ | protocols::splice::Splice | private |
| torsion_database() const | protocols::splice::Splice | inline |
| torsion_database(utility::vector1< ResidueBBDofs > const &d) | protocols::splice::Splice | inline |
| torsion_database_ | protocols::splice::Splice | private |
| torsion_database_fname() const | protocols::splice::Splice | inline |
| torsion_database_fname(std::string const &d) | protocols::splice::Splice | inline |
| torsion_database_fname_ | protocols::splice::Splice | private |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| use_sequence_profiles_ | protocols::splice::Splice | private |
| vl_vh_cut | protocols::splice::Splice | private |
| ~Splice() override | protocols::splice::Splice | |
1.8.7