| abinitio_stage(Pose &pose, Size const fragmentSize, MoveMap const movemap, ScoreFunctionOP sfxOP, Size const max_outer_cycles, Size const max_inner_cycles, std::set< Size > const &disallowedPos, bool const recover_low, std::string stage_name, bool const smoothMoves, Real const fragScoreThreshold) | protocols::forge::remodel::RemodelLoopMover | protected |
| add_fragments(FragSetCOP fragset) | protocols::forge::remodel::RemodelLoopMover | |
| add_loop(Loop const loop) | protocols::forge::remodel::RemodelLoopMover | inline |
| allowed_closure_attempts() const | protocols::forge::remodel::RemodelLoopMover | inline |
| allowed_closure_attempts(Size const attempts) | protocols::forge::remodel::RemodelLoopMover | inline |
| allowed_closure_attempts_ | protocols::forge::remodel::RemodelLoopMover | private |
| apply(Pose &pose) | protocols::forge::remodel::RemodelLoopMover | virtual |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| boost_closure_cycles() const | protocols::forge::remodel::RemodelLoopMover | inline |
| boost_closure_cycles(Size const cycles) | protocols::forge::remodel::RemodelLoopMover | inline |
| boost_closure_cycles_ | protocols::forge::remodel::RemodelLoopMover | private |
| boost_closure_stage(Pose &pose, MonteCarlo &mc, Real const cbreak_increment) | protocols::forge::remodel::RemodelLoopMover | protected |
| check_closure_criteria(Pose &pose, bool const show_in_tracer=false) | protocols::forge::remodel::RemodelLoopMover | protected |
| ClassicFragmentMoverOP typedef | protocols::forge::remodel::RemodelLoopMover | |
| clear_fragments() | protocols::forge::remodel::RemodelLoopMover | |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::forge::remodel::RemodelLoopMover | virtual |
| count_moveable_residues(MoveMap const &movemap, Size const left, Size const right) | protocols::forge::remodel::RemodelLoopMover | protected |
| create() | protocols::moves::Mover | virtual |
| create_fragment_movers(MoveMap const &movemap, Size const largest_frag_size=0) | protocols::forge::remodel::RemodelLoopMover | protected |
| create_fragment_movers(MoveMap const &movemap, FragmentMoverOPs &frag_movers, Size const largest_frag_size=0) | protocols::forge::remodel::RemodelLoopMover | protected |
| create_fragment_movers_limit_size(MoveMap const &movemap, Size const frag_size, std::set< Size > const &disallowedPos, bool const smoothMoves, Real const fragScoreThreshold=999.0) | protocols::forge::remodel::RemodelLoopMover | protected |
| create_per_loop_fragment_movers(loops::LoopsOP const loops, Size const largest_frag_size=0) | protocols::forge::remodel::RemodelLoopMover | protected |
| DataMap typedef | protocols::forge::remodel::RemodelLoopMover | |
| determine_loops_to_model(Pose &pose) | protocols::forge::remodel::RemodelLoopMover | protected |
| enforce_false_movemap(MoveMap &movemap) | protocols::forge::remodel::RemodelLoopMover | protected |
| fa_relax_stage(Pose &pose) | protocols::forge::remodel::RemodelLoopMover | protected |
| false_movemap() const | protocols::forge::remodel::RemodelLoopMover | inline |
| false_movemap(MoveMap const &movemap) | protocols::forge::remodel::RemodelLoopMover | inline |
| false_movemap_ | protocols::forge::remodel::RemodelLoopMover | private |
| Filters_map typedef | protocols::forge::remodel::RemodelLoopMover | |
| FragmentMoverOP typedef | protocols::forge::remodel::RemodelLoopMover | |
| FragmentMoverOPs typedef | protocols::forge::remodel::RemodelLoopMover | |
| FragSetCOP typedef | protocols::forge::remodel::RemodelLoopMover | |
| FragSetOP typedef | protocols::forge::remodel::RemodelLoopMover | |
| FragSetOPs typedef | protocols::forge::remodel::RemodelLoopMover | |
| fragsets_ | protocols::forge::remodel::RemodelLoopMover | private |
| fresh_instance() const | protocols::forge::remodel::RemodelLoopMover | virtual |
| generate_ncs_csts(Pose &pose) | protocols::forge::remodel::RemodelLoopMover | protected |
| generate_residues_to_sample(bool chooseSubsetResidues, Pose &pose, Size fragmentSize) | protocols::forge::remodel::RemodelLoopMover | private |
| 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_name() const | protocols::forge::remodel::RemodelLoopMover | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_type() const | protocols::moves::Mover | inline |
| independent_cycles() const | protocols::forge::remodel::RemodelLoopMover | inline |
| independent_cycles(Size const cycles) | protocols::forge::remodel::RemodelLoopMover | inline |
| independent_cycles_ | protocols::forge::remodel::RemodelLoopMover | private |
| independent_stage(Pose &pose, MonteCarlo &mc, Real const cbreak_increment) | protocols::forge::remodel::RemodelLoopMover | protected |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| insert_random_smallestmer_per_loop(Pose &pose, bool const only_broken_loops=true) | protocols::forge::remodel::RemodelLoopMover | protected |
| keep_input_foldtree_ | protocols::forge::remodel::RemodelLoopMover | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| Loop typedef | protocols::forge::remodel::RemodelLoopMover | |
| loophash_cycles() const | protocols::forge::remodel::RemodelLoopMover | inline |
| loophash_cycles(Size const cycles) | protocols::forge::remodel::RemodelLoopMover | inline |
| loophash_cycles_ | protocols::forge::remodel::RemodelLoopMover | private |
| loophash_stage(Pose &pose, MonteCarlo &mc, Real const cbreak_increment) | protocols::forge::remodel::RemodelLoopMover | protected |
| loops() const | protocols::forge::remodel::RemodelLoopMover | inline |
| loops(loops::LoopsOP const loops) | protocols::forge::remodel::RemodelLoopMover | inline |
| Loops typedef | protocols::forge::remodel::RemodelLoopMover | |
| loops_ | protocols::forge::remodel::RemodelLoopMover | private |
| mark_loop_moveable(Loop const &loop, MoveMap &movemap, bool const allow_omega) | protocols::forge::remodel::RemodelLoopMover | protected |
| mark_loops_moveable(loops::LoopsOP const loops, MoveMap &movemap, bool const allow_omega) | protocols::forge::remodel::RemodelLoopMover | protected |
| max_linear_chainbreak() const | protocols::forge::remodel::RemodelLoopMover | inline |
| max_linear_chainbreak(Real const val) | protocols::forge::remodel::RemodelLoopMover | inline |
| max_linear_chainbreak_ | protocols::forge::remodel::RemodelLoopMover | private |
| MonteCarlo typedef | protocols::forge::remodel::RemodelLoopMover | |
| MoveMap typedef | protocols::forge::remodel::RemodelLoopMover | |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| Mover(Mover const &other) | protocols::moves::Mover | |
| MoverOP typedef | protocols::forge::remodel::RemodelLoopMover | |
| Movers_map typedef | protocols::forge::remodel::RemodelLoopMover | |
| name() | protocols::moves::Mover | inlinestatic |
| operator=(RemodelLoopMover const &rval) | protocols::forge::remodel::RemodelLoopMover | private |
| protocols::moves::Mover::operator=(Mover const &other) | protocols::moves::Mover | |
| 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::forge::remodel::RemodelLoopMover | |
| PoseCOP typedef | protocols::moves::Mover | |
| PoseOP typedef | protocols::forge::remodel::RemodelLoopMover | |
| randomize_loops() const | protocols::forge::remodel::RemodelLoopMover | inline |
| randomize_loops(bool const flag) | protocols::forge::remodel::RemodelLoopMover | inline |
| randomize_loops_ | protocols::forge::remodel::RemodelLoopMover | private |
| randomize_stage(Pose &pose) | protocols::forge::remodel::RemodelLoopMover | |
| Real typedef | protocols::forge::remodel::RemodelLoopMover | |
| register_options() | protocols::forge::remodel::RemodelLoopMover | static |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| remodel_data_ | protocols::forge::remodel::RemodelLoopMover | private |
| remodelData(protocols::forge::remodel::RemodelData const remodel_data) | protocols::forge::remodel::RemodelLoopMover | |
| RemodelLoopMover() | protocols::forge::remodel::RemodelLoopMover | |
| RemodelLoopMover(loops::LoopsOP const loops) | protocols::forge::remodel::RemodelLoopMover | |
| RemodelLoopMover(RemodelLoopMover const &rval) | protocols::forge::remodel::RemodelLoopMover | |
| repeat_generation_with_additional_residue(Pose &pose, Pose &repeat_pose) | protocols::forge::remodel::RemodelLoopMover | |
| repeat_length_ | protocols::forge::remodel::RemodelLoopMover | private |
| repeat_pose_ | protocols::forge::remodel::RemodelLoopMover | private |
| repeat_propagation(Pose &pose, Pose &repeat_pose, Size repeat_number) | protocols::forge::remodel::RemodelLoopMover | |
| repeat_sync(core::pose::Pose &repeat_pose, core::Size repeat_number) | protocols::forge::remodel::RemodelLoopMover | |
| repeat_tail_length_ | protocols::forge::remodel::RemodelLoopMover | private |
| reset_status() | protocols::moves::Mover | |
| RGF_ | protocols::forge::remodel::RemodelLoopMover | private |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| scorefunction() const | protocols::forge::remodel::RemodelLoopMover | |
| scorefunction(ScoreFunction const &sfx) | protocols::forge::remodel::RemodelLoopMover | |
| ScoreFunction typedef | protocols::forge::remodel::RemodelLoopMover | |
| ScoreFunctionOP typedef | protocols::forge::remodel::RemodelLoopMover | |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inline |
| set_ideal_helices(Pose &pose) | protocols::forge::remodel::RemodelLoopMover | private |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_keep_input_foldtree(bool const setting) | protocols::forge::remodel::RemodelLoopMover | inline |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_param_from_options() | protocols::forge::remodel::RemodelLoopMover | |
| set_repeat_tail_length(Size const length) | protocols::forge::remodel::RemodelLoopMover | inline |
| set_starting_pdb(Pose &pose) | protocols::forge::remodel::RemodelLoopMover | private |
| set_starting_sequence(Pose &pose) | protocols::forge::remodel::RemodelLoopMover | private |
| set_user_provided_movers(utility::vector1< moves::MoverOP > const &movers) | protocols::forge::remodel::RemodelLoopMover | |
| sfx_ | protocols::forge::remodel::RemodelLoopMover | private |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| simultaneous_cycles() const | protocols::forge::remodel::RemodelLoopMover | inline |
| simultaneous_cycles(Size const cycles) | protocols::forge::remodel::RemodelLoopMover | inline |
| simultaneous_cycles_ | protocols::forge::remodel::RemodelLoopMover | private |
| simultaneous_stage(Pose &pose, MonteCarlo &mc, Real const cbreak_increment) | protocols::forge::remodel::RemodelLoopMover | protected |
| Size typedef | protocols::forge::remodel::RemodelLoopMover | |
| small_move_stage(Pose &pose, MoveMap const movemap, ScoreFunctionOP sfxOP, Size const max_outer_cycles, Size const max_inner_cycles, bool const recover_low, Real const h_range, Real const e_range, Real const l_range) | protocols::forge::remodel::RemodelLoopMover | protected |
| String typedef | protocols::forge::remodel::RemodelLoopMover | |
| Strings typedef | protocols::moves::Mover | |
| Super typedef | protocols::forge::remodel::RemodelLoopMover | private |
| TagCOP typedef | protocols::forge::remodel::RemodelLoopMover | |
| temperature() const | protocols::forge::remodel::RemodelLoopMover | inline |
| temperature(Real const temp) | protocols::forge::remodel::RemodelLoopMover | inline |
| temperature_ | protocols::forge::remodel::RemodelLoopMover | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| total_standard_cycles() const | protocols::forge::remodel::RemodelLoopMover | inline |
| type() const | protocols::moves::Mover | inline |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| unit_length_ | protocols::forge::remodel::RemodelLoopMover | private |
| user_provided_movers_ | protocols::forge::remodel::RemodelLoopMover | private |
| user_provided_movers_apply_cycle(Size const cycle) | protocols::forge::remodel::RemodelLoopMover | inline |
| user_provided_movers_apply_cycle_ | protocols::forge::remodel::RemodelLoopMover | private |
| ~Mover() | protocols::moves::Mover | virtual |
| ~RemodelLoopMover() | protocols::forge::remodel::RemodelLoopMover | virtual |
1.8.7