| add_coord_cst(loops::Loops const &loops, core::pose::Pose &pose) | protocols::abinitio::LoopJumpFoldCst | protectedvirtual |
| add_evaluation(evaluation::PoseEvaluatorOP ev) | protocols::abinitio::Protocol | |
| add_rigidity_jumps(loops::Loops const &rigid, KinematicControlOP current_kinematics) | protocols::abinitio::LoopJumpFoldCst | protectedvirtual |
| apply(core::pose::Pose &pose) override | protocols::abinitio::KinematicTaskControl | virtual |
| BaseClass typedef | protocols::abinitio::Protocol | |
| centroid_scorefxn() | protocols::abinitio::Protocol | inline |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| coordinate_constraint_weight_ | protocols::abinitio::LoopJumpFoldCst | protected |
| coordinate_constraint_weights_ | protocols::abinitio::LoopJumpFoldCst | protected |
| create() | protocols::moves::Mover | virtual |
| current_kinematics() | protocols::abinitio::KinematicTaskControl | inline |
| current_kinematics_ | protocols::abinitio::KinematicTaskControl | mutableprotected |
| DoubleLayerKinematicAbinitio(jumping::BaseJumpSetupOP jump_def, loops::Loops extended_loops, loops::Loops rigid_core, ProtocolOP sampler, ProtocolOP extended_chain_sampler, core::fragment::SecondaryStructureOP ss_def, core::Real coord_cst_weight, bool bCstAllAtom=false) | protocols::abinitio::DoubleLayerKinematicAbinitio | inline |
| evaluate_pose(core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const | protocols::abinitio::Protocol | |
| evaluator() | protocols::abinitio::Protocol | inline |
| extended_loops_ | protocols::abinitio::DoubleLayerKinematicAbinitio | private |
| fresh_instance() const | protocols::moves::Mover | virtual |
| fullatom_scorefxn() | protocols::abinitio::Protocol | inline |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_checkpoints() override | protocols::abinitio::KinematicTaskControl | inlinevirtual |
| 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_name() const override | protocols::abinitio::DoubleLayerKinematicAbinitio | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| 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 |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| init(core::pose::Pose const &pose) override | protocols::abinitio::KinematicTaskControl | virtual |
| inner_loop(core::pose::Pose &pose) override | protocols::abinitio::DoubleLayerKinematicAbinitio | protectedvirtual |
| kinematics() | protocols::abinitio::Protocol | inline |
| KinematicTaskControl() | protocols::abinitio::KinematicTaskControl | inline |
| KinematicTaskControl(ProtocolOP sampler) | protocols::abinitio::KinematicTaskControl | inline |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| LoopJumpFoldCst(jumping::BaseJumpSetupOP jump_def, loops::Loops loops, ProtocolOP sampler, core::fragment::SecondaryStructureOP ss_def, core::Real coord_cst_weight, bool bCstAllAtom=false) | protocols::abinitio::LoopJumpFoldCst | inline |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| name() | protocols::moves::Mover | inlinestatic |
| new_kinematics(core::pose::Pose &pose) override | protocols::abinitio::DoubleLayerKinematicAbinitio | virtual |
| output_debug_structure(core::pose::Pose &pose, std::string prefix) | protocols::abinitio::Protocol | virtual |
| parse_jump_def(KinematicControlOP current_kinematics, core::kinematics::MoveMapOP) | protocols::abinitio::LoopJumpFoldCst | protectedvirtual |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data) | protocols::moves::Mover | virtual |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| Protocol() | protocols::abinitio::Protocol | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| register_options() | protocols::abinitio::Protocol | static |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| res_switch() | protocols::abinitio::KinematicTaskControl | inlineprotected |
| reset_status() | protocols::moves::Mover | |
| return_centroid() const | protocols::abinitio::Protocol | inlinevirtual |
| return_centroid(bool setting) | protocols::abinitio::Protocol | inlinevirtual |
| rigid_loops_ | protocols::abinitio::DoubleLayerKinematicAbinitio | private |
| sampling_protocol() | protocols::abinitio::KinematicTaskControl | inline |
| select_core_loops(loops::Loops &loops_select) const | protocols::abinitio::DoubleLayerKinematicAbinitio | protectedvirtual |
| select_loops(loops::Loops &loops_select) const | protocols::abinitio::LoopJumpFoldCst | protectedvirtual |
| set_centroid_scorefxn(core::scoring::ScoreFunctionOP sfxn) | protocols::abinitio::Protocol | inline |
| set_coord_cst_weight_array(utility::vector1< core::Real > const &vec) | protocols::abinitio::LoopJumpFoldCst | inline |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_dump_weights_file(std::string const &str) | protocols::abinitio::LoopJumpFoldCst | inline |
| set_evaluation(evaluation::MetaPoseEvaluatorOP ev) | protocols::abinitio::Protocol | |
| set_extended_torsions_and_idealize_loops(core::pose::Pose &pose, loops::Loops loops) const | protocols::abinitio::KinematicTaskControl | protected |
| set_fullatom_scorefxn(core::scoring::ScoreFunctionOP sfxn) | protocols::abinitio::Protocol | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_input_pose_is_fa(bool setting=true) | protocols::abinitio::KinematicTaskControl | inline |
| set_kinematics(abinitio::KinematicControlOP kc) | protocols::abinitio::Protocol | inline |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_silentout_file_name(std::string str) | protocols::abinitio::Protocol | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_use_trRosetta_constraints(bool const setting) | protocols::abinitio::Protocol | |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| stage1_sampler_ | protocols::abinitio::DoubleLayerKinematicAbinitio | private |
| start_from_centroid() const | protocols::abinitio::Protocol | inlinevirtual |
| Strings typedef | protocols::moves::Mover | |
| supports_trRosetta_constraints() const | protocols::abinitio::Protocol | virtual |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| use_trRosetta_constraints() const | protocols::abinitio::Protocol | inline |
| ~DoubleLayerKinematicAbinitio() override | protocols::abinitio::DoubleLayerKinematicAbinitio | |
| ~KinematicTaskControl() override | protocols::abinitio::KinematicTaskControl | |
| ~LoopJumpFoldCst() override | protocols::abinitio::LoopJumpFoldCst | |
| ~Protocol() override=default | protocols::abinitio::Protocol | |
1.8.7