| add_gap_constraints_to_pose(core::pose::Pose &pose, Loops const &chunks, int gap_edge_shift=0, Real stdev=0.1) | protocols::hybridization::FoldTreeHybridize | |
| add_hetatm_ | protocols::hybridization::FoldTreeHybridize | private |
| add_non_init_chunks_ | protocols::hybridization::FoldTreeHybridize | private |
| add_strand_pairing(core::scoring::dssp::Pairing const &pairing) | protocols::hybridization::FoldTreeHybridize | private |
| add_strand_pairings() | protocols::hybridization::FoldTreeHybridize | private |
| apply(core::pose::Pose &pose) | protocols::hybridization::FoldTreeHybridize | virtual |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| auto_frag_insertion_weight(WeightedFragmentTrialMoverOP &frag_1mer_trial_mover, WeightedFragmentTrialMoverOP &small_frag_trial_mover, WeightedFragmentTrialMoverOP &big_frag_trial_mover) | protocols::hybridization::FoldTreeHybridize | private |
| auto_frag_insertion_weight_ | protocols::hybridization::FoldTreeHybridize | private |
| big_frag_insertion_weight_ | protocols::hybridization::FoldTreeHybridize | private |
| center_of_mass(core::pose::Pose const &pose) | protocols::hybridization::FoldTreeHybridize | |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| create() | protocols::moves::Mover | virtual |
| cst_file_ | protocols::hybridization::FoldTreeHybridize | private |
| domain_assembly_ | protocols::hybridization::FoldTreeHybridize | private |
| filter_templates(std::set< core::Size > const &templates_to_remove) | protocols::hybridization::FoldTreeHybridize | private |
| filter_templates_ | protocols::hybridization::FoldTreeHybridize | private |
| Filters_map typedef | protocols::moves::Mover | |
| floating_pairs_ | protocols::hybridization::FoldTreeHybridize | private |
| foldtree_mover_ | protocols::hybridization::FoldTreeHybridize | private |
| FoldTreeHybridize() | protocols::hybridization::FoldTreeHybridize | |
| FoldTreeHybridize(core::Size const initial_template_index, utility::vector1< core::pose::PoseOP > const &template_poses, utility::vector1< core::Real > const &template_weights, utility::vector1< protocols::loops::Loops > const &template_chunks, utility::vector1< protocols::loops::Loops > const &template_contigs, core::fragment::FragSetOP fragments_small_in, core::fragment::FragSetOP fragments_big_in) | protocols::hybridization::FoldTreeHybridize | |
| frag_1mer_insertion_weight_ | protocols::hybridization::FoldTreeHybridize | private |
| frag_libs_1mer_ | protocols::hybridization::FoldTreeHybridize | private |
| frag_libs_big_ | protocols::hybridization::FoldTreeHybridize | private |
| frag_libs_small_ | protocols::hybridization::FoldTreeHybridize | private |
| frag_weight_aligned_ | protocols::hybridization::FoldTreeHybridize | private |
| fresh_instance() const | protocols::moves::Mover | virtual |
| gap_distance(Size Seq_gap) | protocols::hybridization::FoldTreeHybridize | |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_jump_anchors() | protocols::hybridization::FoldTreeHybridize | private |
| get_last_move_status() const | protocols::moves::Mover | |
| get_name() const | protocols::hybridization::FoldTreeHybridize | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_pairings_jump_mover() | protocols::hybridization::FoldTreeHybridize | private |
| get_pairings_residues() | protocols::hybridization::FoldTreeHybridize | |
| get_residue_weights_for_1mers(core::pose::Pose &pose) | protocols::hybridization::FoldTreeHybridize | |
| get_residue_weights_for_big_frags(core::pose::Pose &pose) | protocols::hybridization::FoldTreeHybridize | |
| get_residue_weights_for_small_frags(core::pose::Pose &pose) | protocols::hybridization::FoldTreeHybridize | |
| get_strand_pairs() | protocols::hybridization::FoldTreeHybridize | inline |
| get_type() const | protocols::moves::Mover | inline |
| hetatm_cst_weight_ | protocols::hybridization::FoldTreeHybridize | private |
| increase_cycles_ | protocols::hybridization::FoldTreeHybridize | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| init() | protocols::hybridization::FoldTreeHybridize | |
| initial_template_index_ | protocols::hybridization::FoldTreeHybridize | private |
| jump_frags_ | protocols::hybridization::FoldTreeHybridize | private |
| jump_sample_ | protocols::hybridization::FoldTreeHybridize | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| map_pdb_info_number(const core::pose::Pose &pose, core::Size pdb_res) | protocols::hybridization::FoldTreeHybridize | private |
| max_registry_shift_ | protocols::hybridization::FoldTreeHybridize | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| Mover(Mover const &other) | protocols::moves::Mover | |
| name() | protocols::moves::Mover | inlinestatic |
| native_ | protocols::hybridization::FoldTreeHybridize | private |
| normalize_template_wts() | protocols::hybridization::FoldTreeHybridize | private |
| operator=(Mover const &other) | protocols::moves::Mover | |
| overlap_chainbreaks_ | protocols::hybridization::FoldTreeHybridize | private |
| pairings_file_ | protocols::hybridization::FoldTreeHybridize | private |
| parse_def(utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) | protocols::moves::Mover | virtual |
| parse_my_tag(TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) | protocols::moves::Mover | virtual |
| parse_state(SerializableState const &state) | protocols::moves::Mover | virtual |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| random_sheets_ | protocols::hybridization::FoldTreeHybridize | private |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| reset_status() | protocols::moves::Mover | |
| restore_original_foldtree(core::pose::Pose &pose) | protocols::hybridization::FoldTreeHybridize | |
| revert_loops_to_original(core::pose::Pose &pose, Loops loops) | protocols::hybridization::FoldTreeHybridize | |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| scorefxn_ | protocols::hybridization::FoldTreeHybridize | private |
| set_add_hetatm(bool add_hetatm_in, core::Real hetatm_cst_weight_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_add_non_init_chunks(bool add_non_init_chunks_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_auto_frag_insertion_weight(bool auto_frag_insertion_weight_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_big_frag_insertion_weight(core::Real big_frag_insertion_weight_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_constraint_file(std::string cst_file_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inline |
| set_domain_assembly(bool domain_assembly_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_filter_templates(bool filter_templates_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_frag_1mer_insertion_weight(core::Real frag_1mer_insertion_weight_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_frag_weight_aligned(core::Real frag_weight_aligned_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_increase_cycles(core::Real increase_cycles_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_loops_to_virt_ala(core::pose::Pose &pose, Loops loops) | protocols::hybridization::FoldTreeHybridize | |
| set_max_registry_shift(core::Size max_registry_shift_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_pairings_file(std::string pairings_file_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_random_sheets(utility::vector1< core::Size > random_sheets_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_scorefunction(core::scoring::ScoreFunctionOP const scorefxn) | protocols::hybridization::FoldTreeHybridize | inline |
| set_sheets(utility::vector1< core::Size > sheets_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_small_frag_insertion_weight(core::Real small_frag_insertion_weight_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_stage1_1_cycles(core::Size stage1_1_cycles_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_stage1_2_cycles(core::Size stage1_2_cycles_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_stage1_3_cycles(core::Size stage1_3_cycles_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_stage1_4_cycles(core::Size stage1_4_cycles_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_top_n_big_frag(core::Size top_n_big_frag_in) | protocols::hybridization::FoldTreeHybridize | inline |
| set_top_n_small_frag(core::Size top_n_small_frag_in) | protocols::hybridization::FoldTreeHybridize | inline |
| setup_foldtree(core::pose::Pose &pose) | protocols::hybridization::FoldTreeHybridize | |
| setup_scorefunctions(core::scoring::ScoreFunctionOP score0, core::scoring::ScoreFunctionOP score1, core::scoring::ScoreFunctionOP score2, core::scoring::ScoreFunctionOP score5, core::scoring::ScoreFunctionOP score3) | protocols::hybridization::FoldTreeHybridize | |
| sheets_ | protocols::hybridization::FoldTreeHybridize | private |
| small_frag_insertion_weight_ | protocols::hybridization::FoldTreeHybridize | private |
| ss_chunks_pose_ | protocols::hybridization::FoldTreeHybridize | private |
| stage1_1_cycles_ | protocols::hybridization::FoldTreeHybridize | private |
| stage1_2_cycles_ | protocols::hybridization::FoldTreeHybridize | private |
| stage1_3_cycles_ | protocols::hybridization::FoldTreeHybridize | private |
| stage1_4_cycles_ | protocols::hybridization::FoldTreeHybridize | private |
| strand_pairings_template_indices_ | protocols::hybridization::FoldTreeHybridize | private |
| strand_pairs_ | protocols::hybridization::FoldTreeHybridize | private |
| Strings typedef | protocols::moves::Mover | |
| superimpose_strand_pairings_to_templates(core::pose::Pose &pose) | protocols::hybridization::FoldTreeHybridize | private |
| TagPtr typedef | protocols::moves::Mover | |
| target_sequence_ | protocols::hybridization::FoldTreeHybridize | private |
| template_chunks_ | protocols::hybridization::FoldTreeHybridize | private |
| template_contigs_ | protocols::hybridization::FoldTreeHybridize | private |
| template_poses_ | protocols::hybridization::FoldTreeHybridize | private |
| template_wts_ | protocols::hybridization::FoldTreeHybridize | private |
| templates_with_incorrect_strand_pairings_ | protocols::hybridization::FoldTreeHybridize | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| top_n_big_frag_ | protocols::hybridization::FoldTreeHybridize | private |
| top_n_small_frag_ | protocols::hybridization::FoldTreeHybridize | private |
| translate_virt_to_CoM(core::pose::Pose &pose) | protocols::hybridization::FoldTreeHybridize | |
| type() const | protocols::moves::Mover | inline |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| ~Mover() | protocols::moves::Mover | virtual |
1.8.4