| add_enz_cst_interaction_to_pose(core::pose::Pose &pose, toolbox::match_enzdes_util::EnzConstraintParametersCOP params, toolbox::match_enzdes_util::EnzCstTemplateResCOP missing_template, toolbox::match_enzdes_util::EnzCstTemplateResCOP present_template, toolbox::match_enzdes_util::EnzConstraintIOCOP cstio) | protocols::enzdes::SecondaryMatchProtocol | protected |
| add_pregenerated_enzdes_constraints(core::pose::Pose &pose) const | protocols::enzdes::EnzdesBaseProtocol | |
| apply(core::pose::Pose &start_pose) override | protocols::enzdes::SecondaryMatchProtocol | virtual |
| bb_interface_cutoff_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| catalytic_res(core::pose::Pose const &pose) const | protocols::enzdes::EnzdesBaseProtocol | |
| 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 | |
| cut1_ | protocols::enzdes::SecondaryMatchProtocol | private |
| cut2_ | protocols::enzdes::SecondaryMatchProtocol | private |
| cut3_ | protocols::enzdes::SecondaryMatchProtocol | private |
| cut4_ | protocols::enzdes::SecondaryMatchProtocol | private |
| 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_found_residues_compatibility(core::pose::PoseCOP ref_poseCOP) | protocols::enzdes::SecondaryMatchProtocol | protected |
| disable_constraint_scoreterms() | protocols::enzdes::EnzdesBaseProtocol | protected |
| do_matching(core::pose::Pose &start_pose) | protocols::enzdes::SecondaryMatchProtocol | |
| enable_constraint_scoreterms() | protocols::enzdes::EnzdesBaseProtocol | protected |
| 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 | |
| exchange_ligands_in_pose(core::pose::Pose &pose, bool check_bb_clashes, core::scoring::ScoreFunctionCOP scofx) | protocols::enzdes::EnzdesBaseProtocol | protected |
| find_all_allowed_positions(core::pose::Pose const &pose) | protocols::enzdes::SecondaryMatchProtocol | 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 |
| found_res_compatibility_ | protocols::enzdes::SecondaryMatchProtocol | private |
| found_res_compatibility_determined_ | protocols::enzdes::SecondaryMatchProtocol | private |
| found_resis_ | protocols::enzdes::SecondaryMatchProtocol | private |
| fresh_instance() const | protocols::moves::Mover | virtual |
| generate_and_dump_pose_found_residues_combinations(core::pose::PoseCOP ref_poseCOP) | protocols::enzdes::SecondaryMatchProtocol | protected |
| 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::SecondaryMatchProtocol | 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_type() const | protocols::moves::Mover | inline |
| 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 | |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| LigandBaseProtocol() | protocols::ligand_docking::LigandBaseProtocol | |
| 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 |
| match_params_ | protocols::enzdes::SecondaryMatchProtocol | private |
| 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 |
| 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 | |
| reduced_scofx_ | protocols::enzdes::SecondaryMatchProtocol | private |
| reduced_scorefxn() const | protocols::enzdes::EnzdesBaseProtocol | |
| reduced_scorefxn() | protocols::enzdes::EnzdesBaseProtocol | |
| reduced_sfxn_ | protocols::enzdes::EnzdesBaseProtocol | protected |
| register_options() | protocols::enzdes::EnzdesBaseProtocol | 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) | protocols::enzdes::EnzdesBaseProtocol | 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 | |
| residues_compatible(core::conformation::ResidueCOP res1, core::conformation::ResidueCOP res2) const | protocols::enzdes::SecondaryMatchProtocol | |
| 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_possible_at_position(core::pose::Pose const &pose, core::chemical::ResidueTypeCOP restype, core::conformation::ResidueCOP target_residue, core::Size const trial_pos) | protocols::enzdes::SecondaryMatchProtocol | protected |
| restype_set() const | protocols::enzdes::EnzdesBaseProtocol | inline |
| sc_interface_padding_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| scorefxn_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| SecondaryMatchProtocol() | protocols::enzdes::SecondaryMatchProtocol | |
| 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_trial_positions(utility::vector1< core::Size > const &trial_pos) | protocols::enzdes::SecondaryMatchProtocol | inline |
| 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_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_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| trial_positions_ | protocols::enzdes::SecondaryMatchProtocol | private |
| 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 |
| ~LigandBaseProtocol() override | protocols::ligand_docking::LigandBaseProtocol | |
| ~SecondaryMatchProtocol() override | protocols::enzdes::SecondaryMatchProtocol | |
1.8.7