| add_loop(Loop loop, core::Size minimal_gap=0) | protocols::loops::Loops | |
| add_loop(core::Size const start, core::Size const stop, core::Size const cut=0, core::Real skip_rate=0.0, bool const extended=false) | protocols::loops::Loops | |
| add_loop(const const_iterator &it) | protocols::loops::Loops | |
| add_loop(const iterator &it) | protocols::loops::Loops | |
| add_overlap_loop(Loops loops) | protocols::loops::Loops | |
| add_overlap_loop(const Loop &loop) | protocols::loops::Loops | |
| auto_choose_cutpoints(core::pose::Pose const &pose) | protocols::loops::Loops | |
| begin() const | protocols::loops::Loops | |
| center_of_mass(const core::pose::Pose &pose, numeric::xyzVector< core::Real > *center) const | protocols::loops::Loops | |
| choose_cutpoints(core::pose::Pose const &pose) | protocols::loops::Loops | |
| clear() | protocols::loops::Loops | |
| clone() const | protocols::loops::Loops | |
| const_iterator typedef | protocols::loops::Loops | |
| delete_loop(core::Size const start, core::Size const stop) | protocols::loops::Loops | |
| empty() const | protocols::loops::Loops | |
| end() const | protocols::loops::Loops | |
| file_reading_token() | protocols::loops::Loops | |
| file_reading_token_ | protocols::loops::Loops | private |
| get_loop_file_reader() | protocols::loops::Loops | static |
| get_residues(utility::vector1< core::Size > &selection) const | protocols::loops::Loops | |
| grow_all_loops(core::Size nres, core::Real magnitude) | protocols::loops::Loops | |
| grow_all_loops(core::pose::Pose const &pose, core::Real magnitude) | protocols::loops::Loops | |
| grow_loop(core::pose::Pose const &pose, Loop &loop, core::Real magnitude) | protocols::loops::Loops | |
| grow_loop(core::Size nres, Loop &loop, core::Real magnitude) | protocols::loops::Loops | |
| grow_loop(core::Size nres, Loop &loop, core::Real mag_left, core::Real mag_right) | protocols::loops::Loops | |
| grow_loop_away_from_sheets(core::pose::Pose const &pose, Loop &loop, core::Real magnitude) | protocols::loops::Loops | |
| has(core::Size const seqpos, int const offset=0) const | protocols::loops::Loops | |
| init(LoopList const &loops_in, bool const read_loop_file_from_options=false, std::string const &passed_in_filename="") | protocols::loops::Loops | private |
| invert(core::Size num_residues) const | protocols::loops::Loops | |
| is_loop_residue(core::Size const seqpos, int const offset=0) const | protocols::loops::Loops | |
| iterator typedef | protocols::loops::Loops | |
| loop_file_name() | protocols::loops::Loops | |
| loop_filename_ | protocols::loops::Loops | private |
| loop_index_of_residue(core::Size const seqpos) const | protocols::loops::Loops | |
| loop_of_residue(core::Size const seqpos, Loop &loop) const | protocols::loops::Loops | |
| loop_size(core::Size const loop_num) const | protocols::loops::Loops | |
| loop_size() const | protocols::loops::Loops | |
| LoopList typedef | protocols::loops::Loops | |
| loops() const | protocols::loops::Loops | |
| Loops() | protocols::loops::Loops | |
| Loops(const Loops &src) | protocols::loops::Loops | |
| Loops(SerializedLoopList const &src) | protocols::loops::Loops | |
| Loops(std::string const &loop_file_name) | protocols::loops::Loops | |
| Loops(bool setup_loops_from_options_system) | protocols::loops::Loops | |
| Loops(utility::vector1< bool > const &selection, bool randomize_cutpoint=true) | protocols::loops::Loops | |
| loops_ | protocols::loops::Loops | private |
| make_sequence_shift(int shift) | protocols::loops::Loops | |
| nr_residues() const | protocols::loops::Loops | |
| num_loop() const | protocols::loops::Loops | |
| one_random_loop() const | protocols::loops::Loops | |
| operator!=(Loops const &other) const | protocols::loops::Loops | |
| operator<<(std::ostream &os, const Loops &loops) | protocols::loops::Loops | friend |
| operator=(Loops const &src) | protocols::loops::Loops | |
| operator==(Loops const &other) const | protocols::loops::Loops | |
| operator[](core::Size const i) const | protocols::loops::Loops | |
| operator[](core::Size const i) | protocols::loops::Loops | |
| push_back(Loop loop) | protocols::loops::Loops | |
| push_back(core::Size const start, core::Size const stop, core::Size const cut=0, core::Real skip_rate=0.0, bool const extended=false) | protocols::loops::Loops | |
| read_loop_file() | protocols::loops::Loops | private |
| read_loops_options() | protocols::loops::Loops | |
| remove_terminal_loops(core::pose::Pose const &pose) | protocols::loops::Loops | |
| sequential_order() | protocols::loops::Loops | |
| SerializedLoopList typedef | protocols::loops::Loops | |
| set_extended(bool input) | protocols::loops::Loops | |
| set_file_reading_token(std::string const &token) | protocols::loops::Loops | |
| set_loop_file_name_and_reset(std::string const &loop_filename) | protocols::loops::Loops | |
| set_strict_looprelax_checks(bool const check) | protocols::loops::Loops | |
| setup_loops_from_data(SerializedLoopList const &loop_data) | protocols::loops::Loops | private |
| size() const | protocols::loops::Loops | |
| strict_looprelax_checks() | protocols::loops::Loops | |
| strict_looprelax_checks_on_file_reads_ | protocols::loops::Loops | private |
| switch_movemap(core::kinematics::MoveMap &movemap, core::id::TorsionType, bool allow_moves=true) const | protocols::loops::Loops | |
| transfer_to_residue_vector(utility::vector1< T > &, T val) const | protocols::loops::Loops | |
| v_begin() | protocols::loops::Loops | |
| v_end() | protocols::loops::Loops | |
| verify_against(core::pose::Pose const &pose) const | protocols::loops::Loops | |
| write_loops_to_file(std::string const &filename, std::string token="LOOP") const | protocols::loops::Loops | |
| write_loops_to_stream(std::ostream &data, std::string token) const | protocols::loops::Loops | |
| ~Loops() override | protocols::loops::Loops | |
1.8.7