, including all inherited members.
| add_pregenerated_enzdes_constraints(core::pose::Pose &pose) const | protocols::enzdes::EnzdesBaseProtocol | |
| apply(core::pose::Pose &pose) | protocols::enzdes::EnzdesFixBBProtocol | [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 | [inline, virtual] |
| clone() const | 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 | [mutable, protected] |
| design_targets_score(core::pose::Pose const &pose) const | protocols::enzdes::EnzdesBaseProtocol | |
| disable_constraint_scoreterms() | protocols::enzdes::EnzdesBaseProtocol | [protected] |
| 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 | |
| EnzdesFixBBProtocol() | protocols::enzdes::EnzdesFixBBProtocol | |
| exchange_ligands_in_pose(core::pose::Pose &pose, bool check_bb_clashes, core::scoring::ScoreFunctionCOP scofx) | protocols::enzdes::EnzdesBaseProtocol | [protected] |
| Filters_map typedef | protocols::moves::Mover | |
| 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] |
| fresh_instance() const | protocols::moves::Mover | [virtual] |
| 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) const | protocols::ligand_docking::LigandBaseProtocol | |
| get_ligand_id(core::pose::Pose const &pose, core::Size jump_id) const | protocols::ligand_docking::LigandBaseProtocol | |
| get_ligand_jump_id(core::pose::Pose const &pose) const | protocols::ligand_docking::LigandBaseProtocol | |
| get_name() const | protocols::enzdes::EnzdesFixBBProtocol | [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_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 | [inline, virtual] |
| info() const | protocols::moves::Mover | [inline, virtual] |
| is_catalytic_position(core::pose::Pose const &pose, core::Size const seqpos) const | protocols::enzdes::EnzdesBaseProtocol | |
| last_proposal_density_ratio() | protocols::moves::Mover | [inline, virtual] |
| 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] |
| 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 | |
| Mover(Mover const &other) | protocols::moves::Mover | |
| operator=(Mover const &other) | protocols::moves::Mover | |
| parse_my_tag(TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) | protocols::moves::Mover | [virtual] |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| reduced_scorefxn() const | protocols::enzdes::EnzdesBaseProtocol | |
| reduced_scorefxn() | protocols::enzdes::EnzdesBaseProtocol | |
| reduced_sfxn_ | protocols::enzdes::EnzdesBaseProtocol | [protected] |
| register_options() | protocols::enzdes::EnzdesFixBBProtocol | [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 | |
| 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::constraints::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 | [inline] |
| 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 | |
| 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 | |
| soft_scorefxn_ | protocols::ligand_docking::LigandBaseProtocol | [protected] |
| start_from_random_rb_conf_ | protocols::enzdes::EnzdesFixBBProtocol | [protected] |
| Strings typedef | protocols::moves::Mover | |
| TagPtr typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | [inline, virtual] |
| type() const | protocols::moves::Mover | [inline] |
| type(const std::string &type_in) | protocols::moves::Mover | [inline] |
| unboundrot_ | protocols::ligand_docking::LigandBaseProtocol | [protected] |
| use_soft_rep_ | protocols::ligand_docking::LigandBaseProtocol | [protected] |
| ~EnzdesFixBBProtocol() | protocols::enzdes::EnzdesFixBBProtocol | |
| ~LigandBaseProtocol() | protocols::ligand_docking::LigandBaseProtocol | [virtual] |
| ~Mover() | protocols::moves::Mover | [virtual] |
1.7.4
