| add_flexible_region(core::Size start, core::Size end, core::pose::Pose const &pose, bool clear_existing) | protocols::enzdes::EnzdesFlexBBProtocol | |
| add_pregenerated_enzdes_constraints(core::pose::Pose &pose) const | protocols::enzdes::EnzdesBaseProtocol | |
| apply(core::pose::Pose &pose) override | protocols::enzdes::EnzdesFlexBBProtocol | virtual |
| assemble_next_best_loop_combination(core::pose::Pose &pose) | protocols::enzdes::EnzdesFlexBBProtocol | protected |
| bb_interface_cutoff_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| brub_max_atoms_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| brub_min_atoms_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| brub_mover_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| brub_pivot_atoms_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| catalytic_res(core::pose::Pose const &pose) const | protocols::enzdes::EnzdesBaseProtocol | |
| catmin_movemap_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| catmin_mover_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| catmin_sfxn_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| choose_desired_centroid(core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >) | protocols::ligand_docking::LigandBaseProtocol | protected |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| create() | protocols::moves::Mover | virtual |
| create_enzdes_movemap(core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool min_all_jumps=false) const | protocols::enzdes::EnzdesBaseProtocol | |
| create_enzdes_pack_task(core::pose::Pose &pose, bool design=true) | protocols::enzdes::EnzdesBaseProtocol | |
| cst_minimize(core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool cst_opt=false) const | protocols::enzdes::EnzdesBaseProtocol | |
| design_targets(core::pose::Pose const &pose) const | protocols::enzdes::EnzdesBaseProtocol | |
| design_targets_ | protocols::enzdes::EnzdesBaseProtocol | mutableprotected |
| design_targets_score(core::pose::Pose const &pose) const | protocols::enzdes::EnzdesBaseProtocol | |
| determine_flexible_regions(core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task) | protocols::enzdes::EnzdesFlexBBProtocol | |
| disable_constraint_scoreterms() | protocols::enzdes::EnzdesBaseProtocol | protected |
| enable_constraint_scoreterms() | protocols::enzdes::EnzdesBaseProtocol | protected |
| enz_flexible_region(core::Size region) const | protocols::enzdes::EnzdesFlexBBProtocol | inline |
| enz_loops_file() const | protocols::enzdes::EnzdesFlexBBProtocol | inline |
| enz_loops_file_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| enzdes_pack(core::pose::Pose &pose, core::pack::task::PackerTaskCOP, core::scoring::ScoreFunctionCOP scorefxn, core::Size cycles, bool minimize_after_packing, bool pack_unconstrained, bool favor_native) const | protocols::enzdes::EnzdesBaseProtocol | |
| EnzdesBaseProtocol() | protocols::enzdes::EnzdesBaseProtocol | |
| EnzdesFlexBBProtocol() | protocols::enzdes::EnzdesFlexBBProtocol | |
| exchange_ligands_in_pose(core::pose::Pose &pose, bool check_bb_clashes, core::scoring::ScoreFunctionCOP scofx) | protocols::enzdes::EnzdesBaseProtocol | protected |
| find_interface_backbone(core::pose::Pose const &pose, int jump_id, core::Real cutoff_dist, utility::vector1< bool > &is_interface, utility::vector1< bool > &is_around_interface) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| find_interface_rsds(core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| flex_regions_ | protocols::enzdes::EnzdesFlexBBProtocol | protected |
| fragment_counters_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| fresh_instance() const | protocols::moves::Mover | virtual |
| generate_alc_ensemble_for_region(core::pose::Pose &pose, core::Size region) | protocols::enzdes::EnzdesFlexBBProtocol | |
| generate_backrub_ensemble_for_region(core::pose::Pose &pose, core::Size region) | protocols::enzdes::EnzdesFlexBBProtocol | |
| generate_ensemble_for_region(core::pose::Pose &pose, core::Size region) | protocols::enzdes::EnzdesFlexBBProtocol | |
| generate_explicit_ligand_rotamer_poses(core::pose::Pose const &orig_pose, utility::vector1< core::pose::PoseOP > &ligrot_poses, core::scoring::ScoreFunctionCOP scofx) | protocols::enzdes::EnzdesBaseProtocol | |
| 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_last_move_status() const | protocols::moves::Mover | |
| get_ligand_id(core::pose::Pose const &pose) | protocols::ligand_docking::LigandBaseProtocol | static |
| get_ligand_id(core::pose::Pose const &pose, core::Size jump_id) | protocols::ligand_docking::LigandBaseProtocol | static |
| get_ligand_jump_id(core::pose::Pose const &pose) | protocols::ligand_docking::LigandBaseProtocol | static |
| get_name() const override | protocols::enzdes::EnzdesFlexBBProtocol | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_non_bb_clashing_rotamers(core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const | protocols::ligand_docking::LigandBaseProtocol | |
| get_scorefxn() | protocols::ligand_docking::LigandBaseProtocol | |
| get_scorefxn() const | protocols::ligand_docking::LigandBaseProtocol | |
| 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_tenA_neighbor_residues(core::pose::Pose const &pose, utility::vector1< bool > &residue_positions) const | protocols::enzdes::EnzdesFlexBBProtocol | |
| get_type() const | protocols::moves::Mover | inline |
| hack_assemble_next_loop_combination(core::pose::Pose &pose) | protocols::enzdes::EnzdesFlexBBProtocol | protected |
| hard_scorefxn_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| include_all_design_targets_in_design_interface_ | protocols::enzdes::EnzdesBaseProtocol | protected |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| is_catalytic_position(core::pose::Pose const &pose, core::Size const seqpos) const | protocols::enzdes::EnzdesBaseProtocol | |
| is_flexible(core::Size seqpos) const | protocols::enzdes::EnzdesFlexBBProtocol | |
| is_remodelable(core::Size seqpos) const | protocols::enzdes::EnzdesFlexBBProtocol | |
| kinematic_mover_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| LigandBaseProtocol() | protocols::ligand_docking::LigandBaseProtocol | |
| loop_ensemble_size_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| loopgen_trials_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| make_movemap(core::pose::Pose const &pose, core::Size jump_id, core::Real sc_padding, bool include_all_rsds, bool include_backbone, bool include_ligands, bool include_water) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| make_packer_task(core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| make_packer_task(core::pose::Pose const &pose, int jump_id, core::Real sc_padding, bool include_all_rsds, bool ligand_protonation) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| make_packer_task_ligand_only(core::pose::Pose const &pose, int jump_id, bool ligand_protonation) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| make_tweaked_scorefxn(std::string const &weights_tag, bool estat_exclude_protein, bool estat_upweight, bool hbonds_downweight) | protocols::ligand_docking::LigandBaseProtocol | protected |
| mc_kt_high_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| mc_kt_low_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| minimize_cats_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| minimize_flexible_region(core::pose::Pose &pose, core::Size region, core::scoring::ScoreFunctionCOP scorefxn, std::set< core::Size > const &chi_to_move, bool const including_CA_angles, core::Real min_tolerance) | protocols::enzdes::EnzdesFlexBBProtocol | |
| modified_task(core::pose::Pose const &pose, core::pack::task::PackerTask const &orig_task) | protocols::enzdes::EnzdesFlexBBProtocol | |
| move_ligand_to_desired_centroid(core::pose::Pose &pose, core::Size jump_id, utility::vector1< core::Vector > start_from_pts) | protocols::ligand_docking::LigandBaseProtocol | protected |
| move_ligand_to_desired_centroid(core::pose::Pose &pose, core::Size jump_id, core::Vector desired_centroid) | protocols::ligand_docking::LigandBaseProtocol | protected |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| name() | protocols::moves::Mover | inlinestatic |
| native_fragment_bb_energies_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| pack_region_ala_pose_ | protocols::enzdes::EnzdesFlexBBProtocol | private |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data) | protocols::moves::Mover | virtual |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| rb_min_jumps() const | protocols::enzdes::EnzdesBaseProtocol | |
| rb_min_jumps(utility::vector1< core::Size > const ) | protocols::enzdes::EnzdesBaseProtocol | |
| recover_loops_from_file(core::pose::Pose const &pose) | protocols::enzdes::EnzdesFlexBBProtocol | protected |
| reduced_scorefxn() const | protocols::enzdes::EnzdesBaseProtocol | |
| reduced_scorefxn() | protocols::enzdes::EnzdesBaseProtocol | |
| reduced_sfxn_ | protocols::enzdes::EnzdesBaseProtocol | protected |
| register_options() | protocols::enzdes::EnzdesFlexBBProtocol | static |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| remap_resid(core::pose::Pose const &pose, core::id::SequenceMapping const &smap) override | protocols::enzdes::EnzdesFlexBBProtocol | virtual |
| remove_enzdes_constraints(core::pose::Pose &pose, bool keep_covalent) const | protocols::enzdes::EnzdesBaseProtocol | |
| reorder_foldtree_around_mobile_regions(core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const | protocols::ligand_docking::LigandBaseProtocol | |
| reset_status() | protocols::moves::Mover | |
| restrain_ligand_nbr_atom(core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| restrain_protein_Calphas(core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::func::FuncOP restr_func) const | protocols::ligand_docking::LigandBaseProtocol | |
| restype_set() const | protocols::enzdes::EnzdesBaseProtocol | inline |
| sc_interface_padding_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| scorefxn_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| set_all_jumps_minimizable(bool const &setting) | protocols::enzdes::EnzdesBaseProtocol | inline |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_fix_cataa(bool const &setting) | protocols::enzdes::EnzdesBaseProtocol | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_minimize_options(bool const &min_sc, bool const &min_bb, bool const &min_rb, bool const &min_lig, bool backrub=false) | protocols::enzdes::EnzdesBaseProtocol | inline |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_scorefxn(core::scoring::ScoreFunctionCOP scorefxn) | protocols::enzdes::EnzdesBaseProtocol | |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| setup_bbmin_foldtree(core::pose::Pose &pose, core::Size const &jump_id, core::Real cutoff_dist, core::Real stddev_Angstroms) | protocols::ligand_docking::LigandBaseProtocol | protected |
| setup_bbmin_ft_and_csts(core::pose::Pose &pose, utility::vector1< bool > allow_move_bb, core::Size jump_id) const | protocols::enzdes::EnzdesBaseProtocol | |
| setup_catalytic_residue_minimization_for_region(core::pose::Pose const &pose, core::Size region) | protocols::enzdes::EnzdesFlexBBProtocol | protected |
| setup_enzdes_constraints(core::pose::Pose &pose, bool allow_missing_remark_blocks) const | protocols::enzdes::EnzdesBaseProtocol | protected |
| setup_sequence_recovery_cache(core::pose::Pose &pose, core::pack::task::PackerTask const &task) const | protocols::enzdes::EnzdesBaseProtocol | |
| shared_from_this() | protocols::ligand_docking::LigandBaseProtocol | inline |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| soft_scorefxn_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| Strings typedef | protocols::moves::Mover | |
| TagCOP typedef | protocols::moves::Mover | |
| test_flexbb_rotamer_sets(core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task) | protocols::enzdes::EnzdesFlexBBProtocol | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| unboundrot_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| use_soft_rep_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| ~EnzdesFlexBBProtocol() override | protocols::enzdes::EnzdesFlexBBProtocol | |
| ~LigandBaseProtocol() override | protocols::ligand_docking::LigandBaseProtocol | |
1.8.7