| add_coordinate_csts_from_lookback(core::Size stub_ss_index_match, core::Size fragment_index, core::Size pose_residue, bool match_stub_alone, core::pose::PoseOP &poseOP) | protocols::pose_length_moves::PossibleLoop | private |
| add_dihedral_csts_from_lookback(core::Size stub_ss_index_match, core::Size fragment_index, core::Size pose_residue, core::pose::PoseOP &poseOP) | protocols::pose_length_moves::PossibleLoop | private |
| assign_phi_psi_omega_from_lookback(core::Size db_index, core::Size fragment_index, core::pose::PoseOP &poseOP) | protocols::pose_length_moves::PossibleLoop | private |
| below_distance_threshold_ | protocols::pose_length_moves::PossibleLoop | private |
| check_loop_abego(core::pose::PoseOP &poseOP, core::Size loopStart, core::Size loopStop, std::string allowed_loop_abegos, core::Real loop_rmsd) | protocols::pose_length_moves::PossibleLoop | private |
| evaluate_distance_closure() | protocols::pose_length_moves::PossibleLoop | |
| extendRegion(bool towardCTerm, core::Size resStart, core::Size numberAddRes, core::pose::PoseOP &poseOP) | protocols::pose_length_moves::PossibleLoop | private |
| final_rmsd_ | protocols::pose_length_moves::PossibleLoop | private |
| finalPoseOP_ | protocols::pose_length_moves::PossibleLoop | private |
| fullLength_resBeforeLoop_ | protocols::pose_length_moves::PossibleLoop | private |
| fullLengthPoseOP_ | protocols::pose_length_moves::PossibleLoop | private |
| generate_output_pose(bool output_closed, bool ideal_loop, core::Real rms_threshold, std::string allowed_loop_abegos, std::string closure_type) | protocols::pose_length_moves::PossibleLoop | |
| generate_stub_rmsd() | protocols::pose_length_moves::PossibleLoop | |
| generate_uncached_stub_rmsd() | protocols::pose_length_moves::PossibleLoop | |
| get_below_distance_threshold() | protocols::pose_length_moves::PossibleLoop | inline |
| get_center_of_mass(const core::Real *coordinates, int number_of_atoms) | protocols::pose_length_moves::PossibleLoop | private |
| get_coordinates_from_pose(core::pose::PoseOP const poseOP, core::Size resid, core::Size length) | protocols::pose_length_moves::PossibleLoop | private |
| get_description() | protocols::pose_length_moves::PossibleLoop | |
| get_final_RMSD() | protocols::pose_length_moves::PossibleLoop | inline |
| get_finalPoseOP() | protocols::pose_length_moves::PossibleLoop | |
| get_stubRMSD() | protocols::pose_length_moves::PossibleLoop | inline |
| get_uncached_stubRMSD() | protocols::pose_length_moves::PossibleLoop | inline |
| get_valid_resid(int resid, core::pose::Pose const pose) | protocols::pose_length_moves::PossibleLoop | private |
| insertedAfterLoopRes_ | protocols::pose_length_moves::PossibleLoop | private |
| insertedBeforeLoopRes_ | protocols::pose_length_moves::PossibleLoop | private |
| kic_closure(core::scoring::ScoreFunctionOP scorefxn_, core::pose::PoseOP &poseOP, core::Size firstLoopRes, core::Size lastLoopRes, core::Size numb_kic_cycles) | protocols::pose_length_moves::PossibleLoop | private |
| loopLength_ | protocols::pose_length_moves::PossibleLoop | private |
| minimize_loop(core::scoring::ScoreFunctionOP scorefxn, bool ideal_loop, core::pose::PoseOP &poseOP) | protocols::pose_length_moves::PossibleLoop | private |
| original_atom_type_fullLengthPoseOP_ | protocols::pose_length_moves::PossibleLoop | private |
| output_fragment_debug(std::vector< numeric::xyzVector< numeric::Real > > coordinates, std::string filename) | protocols::pose_length_moves::PossibleLoop | private |
| outputed() | protocols::pose_length_moves::PossibleLoop | inline |
| outputed(bool outputed) | protocols::pose_length_moves::PossibleLoop | inline |
| outputed_ | protocols::pose_length_moves::PossibleLoop | private |
| PossibleLoop(int resAdjustmentBeforeLoop, int resAdjustmentAfterLoop, core::Size loopLength, core::Size resBeforeLoop, core::Size resAfterLoop, char resTypeBeforeLoop, char resTypeAfterLoop, core::Size insertedBeforeLoopRes, core::Size insertedAfterLoopRes, core::pose::PoseOP fullLengthPoseOP, core::pose::PoseOP orig_atom_type_fullLengthPoseOP) | protocols::pose_length_moves::PossibleLoop | |
| resAdjustmentAfterLoop_ | protocols::pose_length_moves::PossibleLoop | private |
| resAdjustmentBeforeLoop_ | protocols::pose_length_moves::PossibleLoop | private |
| resAfterLoop_ | protocols::pose_length_moves::PossibleLoop | private |
| resBeforeLoop_ | protocols::pose_length_moves::PossibleLoop | private |
| resTypeAfterLoop_ | protocols::pose_length_moves::PossibleLoop | private |
| resTypeBeforeLoop_ | protocols::pose_length_moves::PossibleLoop | private |
| rmsd_between_coordinates(std::vector< numeric::xyzVector< numeric::Real > > fragCoordinates, std::vector< numeric::xyzVector< numeric::Real > > coordinates) | protocols::pose_length_moves::PossibleLoop | private |
| SSHashedFragmentStore_ | protocols::pose_length_moves::PossibleLoop | private |
| stub_index_match_ | protocols::pose_length_moves::PossibleLoop | private |
| stub_rmsd_match_ | protocols::pose_length_moves::PossibleLoop | private |
| stub_ss_index_match_ | protocols::pose_length_moves::PossibleLoop | private |
| trimRegion(core::pose::PoseOP &poseOP, core::Size resStart, core::Size resStop) | protocols::pose_length_moves::PossibleLoop | private |
| uncached_stub_index_ | protocols::pose_length_moves::PossibleLoop | private |
| uncached_stub_rmsd_ | protocols::pose_length_moves::PossibleLoop | private |
| ~PossibleLoop() override | protocols::pose_length_moves::PossibleLoop | |
1.8.7