| add_evaluation(evaluation::PoseEvaluatorOP ev) | protocols::abinitio::Protocol | |
| ALL_STAGES enum value | protocols::abinitio::ClassicAbinitio | |
| apply(core::pose::Pose &pose) | protocols::abinitio::KinematicAbinitio | virtual |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| BaseClass typedef | protocols::abinitio::Protocol | |
| bIgnoreSequenceSeparation(bool setting) | protocols::abinitio::FoldConstraints | inlineprotected |
| bIgnoreSequenceSeparation() | protocols::abinitio::FoldConstraints | inlineprotected |
| bOverlapChainbreaks_ | protocols::abinitio::KinematicAbinitio | private |
| bQuickTest() const | protocols::abinitio::ClassicAbinitio | inline |
| bRampChainbreaks_ | protocols::abinitio::KinematicAbinitio | private |
| brute_move_large() | protocols::abinitio::ClassicAbinitio | |
| brute_move_small() | protocols::abinitio::ClassicAbinitio | |
| bSkipStage1_ | protocols::abinitio::ClassicAbinitio | |
| bSkipStage2_ | protocols::abinitio::ClassicAbinitio | |
| bSkipStage3_ | protocols::abinitio::ClassicAbinitio | |
| bSkipStage4_ | protocols::abinitio::ClassicAbinitio | |
| bSkipStage5_ | protocols::abinitio::ClassicAbinitio | |
| centroid_scorefxn() | protocols::abinitio::Protocol | inline |
| ClassicAbinitio(simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int) | protocols::abinitio::ClassicAbinitio | |
| ClassicAbinitio(core::fragment::FragSetCOP fragset_small, core::fragment::FragSetCOP fragset_large, core::kinematics::MoveMapCOP movemap) | protocols::abinitio::ClassicAbinitio | |
| ClassicAbinitio(ClassicAbinitio const &src) | protocols::abinitio::ClassicAbinitio | |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::abinitio::KinematicAbinitio | inlinevirtual |
| closure_protocol(loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol) | protocols::abinitio::KinematicAbinitio | inline |
| closure_protocol_ | protocols::abinitio::KinematicAbinitio | private |
| constraints() | protocols::abinitio::FoldConstraints | inlineprotected |
| create() | protocols::moves::Mover | virtual |
| create_bb_moves(core::pose::Pose &pose, moves::MoverOP std_moves, bool bLargeWobble, core::Real crank_up_angle) | protocols::abinitio::KinematicAbinitio | private |
| create_jump_moves(moves::MoverOP stdmove) | protocols::abinitio::KinematicAbinitio | private |
| current_scorefxn() const | protocols::abinitio::ClassicAbinitio | protected |
| current_scorefxn(core::scoring::ScoreFunction const &scorefxn) | protocols::abinitio::ClassicAbinitio | protected |
| do_stage1_cycles(core::pose::Pose &pose) | protocols::abinitio::FoldConstraints | protectedvirtual |
| do_stage2_cycles(core::pose::Pose &pose) | protocols::abinitio::FoldConstraints | protectedvirtual |
| do_stage3_cycles(core::pose::Pose &pose) | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| do_stage4_cycles(core::pose::Pose &pose) | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| do_stage5_cycles(core::pose::Pose &pose) | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| dump_jump_log(core::pose::Pose &pose, std::string const &file_name) | protocols::abinitio::KinematicAbinitio | private |
| evaluate_pose(core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const | protocols::abinitio::Protocol | |
| evaluator() | protocols::abinitio::Protocol | inline |
| Filters_map typedef | protocols::moves::Mover | |
| FoldConstraints(simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy) | protocols::abinitio::FoldConstraints | |
| FoldConstraints(core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap) | protocols::abinitio::FoldConstraints | |
| FoldConstraints(FoldConstraints const &src) | protocols::abinitio::FoldConstraints | |
| fresh_instance() const | protocols::moves::Mover | virtual |
| full_constraint_set_ | protocols::abinitio::KinematicAbinitio | private |
| fullatom_scorefxn() | protocols::abinitio::Protocol | inline |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_checkpoints() | protocols::abinitio::Protocol | 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 | protocols::abinitio::KinematicAbinitio | 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) | protocols::abinitio::ClassicAbinitio | virtual |
| just_smooth_cycles() const | protocols::abinitio::ClassicAbinitio | inline |
| KinematicAbinitio(simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy) | protocols::abinitio::KinematicAbinitio | |
| KinematicAbinitio(core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap) | protocols::abinitio::KinematicAbinitio | |
| kinematics() | protocols::abinitio::Protocol | inline |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| max_seq_sep_fudge() const | protocols::abinitio::FoldConstraints | inlineprotected |
| max_seq_sep_fudge(core::Real setting) | protocols::abinitio::FoldConstraints | inlineprotected |
| mc() | protocols::abinitio::ClassicAbinitio | inline |
| mc() const | protocols::abinitio::ClassicAbinitio | inline |
| mc_ptr() | protocols::abinitio::ClassicAbinitio | protected |
| min_move() | protocols::abinitio::FoldConstraints | inlineprotected |
| min_trial(core::pose::Pose &pose) | protocols::abinitio::FoldConstraints | protected |
| movemap() | protocols::abinitio::ClassicAbinitio | |
| 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 |
| protocols::abinitio::Protocol::operator=(Mover const &other) | protocols::moves::Mover | |
| output_debug_structure(core::pose::Pose &pose, std::string prefix) | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| Parent typedef | protocols::abinitio::KinematicAbinitio | 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(TagCOP tag, basic::datacache::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 | |
| prepare_loop_in_stage3(core::pose::Pose &, Size, Size) | protocols::abinitio::KinematicAbinitio | virtual |
| prepare_loop_in_stage4(core::pose::Pose &, Size, Size) | protocols::abinitio::KinematicAbinitio | virtual |
| prepare_stage1(core::pose::Pose &pose) | protocols::abinitio::KinematicAbinitio | virtual |
| prepare_stage2(core::pose::Pose &pose) | protocols::abinitio::KinematicAbinitio | virtual |
| prepare_stage3(core::pose::Pose &pose) | protocols::abinitio::KinematicAbinitio | virtual |
| prepare_stage4(core::pose::Pose &pose) | protocols::abinitio::FoldConstraints | protectedvirtual |
| prepare_stage5(core::pose::Pose &pose) | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| Protocol() | protocols::abinitio::Protocol | |
| recover_low(core::pose::Pose &pose, StageID stage) | protocols::abinitio::ClassicAbinitio | protected |
| recover_low_stages_ | protocols::abinitio::ClassicAbinitio | |
| register_options() | protocols::abinitio::KinematicAbinitio | static |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| replace_scorefxn(core::pose::Pose &pose, StageID, core::Real intra_stage_progress) | protocols::abinitio::KinematicAbinitio | protectedvirtual |
| reset_status() | protocols::moves::Mover | |
| return_centroid() const | protocols::abinitio::Protocol | inlinevirtual |
| return_centroid(bool setting) | protocols::abinitio::Protocol | inlinevirtual |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| set_centroid_scorefxn(core::scoring::ScoreFunctionOP sfxn) | protocols::abinitio::Protocol | inline |
| set_constraint_weight(core::Real setting) | protocols::abinitio::FoldConstraints | inline |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_current_weight(core::scoring::ScoreType type, core::Real setting) | protocols::abinitio::ClassicAbinitio | protected |
| set_cycles(core::Real increase_cycles=1.0) | protocols::abinitio::ClassicAbinitio | virtual |
| set_default_mc(core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn) | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| set_default_options() | protocols::abinitio::KinematicAbinitio | protectedvirtual |
| set_default_scores() | protocols::abinitio::KinematicAbinitio | protectedvirtual |
| set_defaults(core::pose::Pose const &pose) | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| set_evaluation(evaluation::MetaPoseEvaluatorOP ev) | protocols::abinitio::Protocol | |
| set_fullatom_scorefxn(core::scoring::ScoreFunctionOP sfxn) | protocols::abinitio::Protocol | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_kinematics(abinitio::KinematicControlOP kc) | protocols::abinitio::Protocol | inline |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_max_seq_sep(core::pose::Pose &pose, Size setting) | protocols::abinitio::KinematicAbinitio | virtual |
| set_mc(moves::MonteCarloOP) | protocols::abinitio::ClassicAbinitio | |
| set_min_move(protocols::simple_moves::MinMoverOP mm) | protocols::abinitio::FoldConstraints | protected |
| set_movemap(core::kinematics::MoveMapCOP mm) | protocols::abinitio::FoldConstraints | protectedvirtual |
| set_moves(simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small) | protocols::abinitio::ClassicAbinitio | |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_score_weight(core::scoring::ScoreType, core::Real setting, StageID stage=ALL_STAGES) | protocols::abinitio::ClassicAbinitio | virtual |
| set_seq_sep_stage1(core::Real setting) | protocols::abinitio::FoldConstraints | inlineprotected |
| set_seq_sep_stage3(core::Real setting) | protocols::abinitio::FoldConstraints | inlineprotected |
| set_show_viol_level(core::Size setting) | protocols::abinitio::FoldConstraints | inline |
| set_silentout_file_name(std::string str) | protocols::abinitio::Protocol | inline |
| set_skip_stage1(bool setting) | protocols::abinitio::ClassicAbinitio | inline |
| set_skip_stage2(bool setting) | protocols::abinitio::ClassicAbinitio | inline |
| set_stage4_cycles(Size stage4_cycles_new) | protocols::abinitio::ClassicAbinitio | inline |
| set_trials() | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| setup_default_min_move() | protocols::abinitio::FoldConstraints | protectedvirtual |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| smooth_move_small() | protocols::abinitio::ClassicAbinitio | |
| stage1_cycles() const | protocols::abinitio::ClassicAbinitio | inline |
| stage1_cycles_ | protocols::abinitio::ClassicAbinitio | protected |
| stage1_mover(core::pose::Pose &pose, moves::TrialMoverOP trials_in) | protocols::abinitio::KinematicAbinitio | virtual |
| stage2_cycles() const | protocols::abinitio::ClassicAbinitio | inline |
| stage2_cycles_ | protocols::abinitio::ClassicAbinitio | protected |
| stage2_mover(core::pose::Pose &pose, moves::TrialMoverOP trials_in) | protocols::abinitio::KinematicAbinitio | virtual |
| stage3_cycles() const | protocols::abinitio::ClassicAbinitio | inline |
| stage3_cycles_ | protocols::abinitio::ClassicAbinitio | protected |
| stage3_mover(core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in) | protocols::abinitio::KinematicAbinitio | virtual |
| stage4_cycles() const | protocols::abinitio::ClassicAbinitio | inline |
| stage4_cycles_ | protocols::abinitio::ClassicAbinitio | protected |
| stage4_cycles_pack_rate_ | protocols::abinitio::ClassicAbinitio | protected |
| stage4_mover(core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in) | protocols::abinitio::KinematicAbinitio | virtual |
| stage4rot_mover(core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in) | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| stage5_cycles() const | protocols::abinitio::ClassicAbinitio | inline |
| stage5_cycles_ | protocols::abinitio::ClassicAbinitio | protected |
| stage5_mover(core::pose::Pose &pose, moves::TrialMoverOP trials_in) | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| STAGE_1 enum value | protocols::abinitio::ClassicAbinitio | |
| STAGE_2 enum value | protocols::abinitio::ClassicAbinitio | |
| STAGE_3a enum value | protocols::abinitio::ClassicAbinitio | |
| STAGE_3b enum value | protocols::abinitio::ClassicAbinitio | |
| STAGE_4 enum value | protocols::abinitio::ClassicAbinitio | |
| STAGE_4rot enum value | protocols::abinitio::ClassicAbinitio | |
| STAGE_5 enum value | protocols::abinitio::ClassicAbinitio | |
| StageID enum name | protocols::abinitio::ClassicAbinitio | |
| start_from_centroid() const | protocols::abinitio::Protocol | inlinevirtual |
| Strings typedef | protocols::moves::Mover | |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| total_res(core::pose::Pose const &pose) const | protocols::abinitio::FoldConstraints | protected |
| total_trials() const | protocols::abinitio::ClassicAbinitio | inline |
| trial_large() | protocols::abinitio::ClassicAbinitio | protected |
| trial_small() | protocols::abinitio::ClassicAbinitio | protected |
| trial_smooth() | protocols::abinitio::ClassicAbinitio | protected |
| type() const | protocols::moves::Mover | inline |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| update_moves() | protocols::abinitio::ClassicAbinitio | protectedvirtual |
| ~ClassicAbinitio() | protocols::abinitio::ClassicAbinitio | |
| ~FoldConstraints() | protocols::abinitio::FoldConstraints | |
| ~KinematicAbinitio() | protocols::abinitio::KinematicAbinitio | |
| ~Mover() | protocols::moves::Mover | virtual |
| ~Protocol() | protocols::abinitio::Protocol | inline |
1.8.7