| add_chainbreaks(core::pose::Pose &pose) const | protocols::jumping::JumpSample | |
| add_chainbreaks(core::pose::Pose &pose, core::Size max_dist, core::kinematics::ShortestPathInFoldTree const &) const | protocols::jumping::JumpSample | |
| add_chainbreaks_as_distance_constraint(core::pose::Pose &pose) const | protocols::jumping::JumpSample | |
| add_chainbreaks_as_distance_constraint(core::pose::Pose &pose, core::Size max_dist, core::kinematics::ShortestPathInFoldTree const &sp) const | protocols::jumping::JumpSample | |
| apply_to(core::kinematics::FoldTreeOP f) | protocols::jumping::JumpSample | private |
| bValidTree_ | protocols::jumping::JumpSample | private |
| correct_jump_atoms_for_fragments() const | protocols::jumping::JumpSample | private |
| cuts() const | protocols::jumping::JumpSample | inline |
| cuts_ | protocols::jumping::JumpSample | private |
| downstream_res_nr(core::Size jump_nr) const | protocols::jumping::JumpSample | inline |
| dump_pymol(std::string fn) const | protocols::jumping::JumpSample | |
| fold_tree() const | protocols::jumping::JumpSample | inline |
| fold_tree_ | protocols::jumping::JumpSample | private |
| generate_jump_frags(PairingLibrary const &pairings, core::kinematics::MoveMap const &, bool bWithTorsion, core::fragment::FrameList &) const | protocols::jumping::JumpSample | |
| generate_jump_frames(core::fragment::FrameList &, core::kinematics::MoveMap const &, bool bWithTorsion=true) const | protocols::jumping::JumpSample | |
| generate_random_tree_from_jumps(ObjexxFCL::FArray1D_float const &prob, core::Size root=1) | protocols::jumping::JumpSample | private |
| generate_tree_from_jumps_and_cuts(core::Size root=1) | protocols::jumping::JumpSample | private |
| get_pairing(core::Size res1, core::Size res2) const | protocols::jumping::JumpSample | |
| has_orientation_and_pleating() const | protocols::jumping::JumpSample | |
| is_valid() const | protocols::jumping::JumpSample | inline |
| jump_atoms() const | protocols::jumping::JumpSample | inline |
| jump_atoms_ | protocols::jumping::JumpSample | private |
| jump_pairings_ | protocols::jumping::JumpSample | private |
| jumps() const | protocols::jumping::JumpSample | inline |
| jumps2pairings() | protocols::jumping::JumpSample | private |
| jumps_ | protocols::jumping::JumpSample | private |
| JumpSample() | protocols::jumping::JumpSample | inline |
| JumpSample(JumpSetup const &) | protocols::jumping::JumpSample | |
| JumpSample(core::Size total_residue, core::Size njump, ObjexxFCL::FArray2D_int jumps, ObjexxFCL::FArray1D_int cuts, core::Size root=1) | protocols::jumping::JumpSample | |
| JumpSample(core::Size total_residue, core::Size njump, ObjexxFCL::FArray2D_int jumps, ObjexxFCL::FArray2D< std::string > jump_atoms, ObjexxFCL::FArray1D_int cuts, core::Size root=1) | protocols::jumping::JumpSample | |
| JumpSample(core::Size total_residue, core::scoring::dssp::PairingsList const &jumps, ObjexxFCL::FArray1D_float const &cut_probability, core::Size root=1) | protocols::jumping::JumpSample | |
| JumpSample(core::Size total_residue, core::scoring::dssp::PairingsList const &jumps, core::fragment::SecondaryStructure const &ss_def, core::Size root=1) | protocols::jumping::JumpSample | |
| JumpSample(core::kinematics::FoldTree const &f) | protocols::jumping::JumpSample | |
| JumpSample(core::kinematics::FoldTreeOP f) | protocols::jumping::JumpSample | |
| njump_ | protocols::jumping::JumpSample | private |
| operator<<(std::ostream &os, JumpSample const &t) | protocols::jumping::JumpSample | friend |
| remove_chainbreaks(core::pose::Pose &pose) const | protocols::jumping::JumpSample | |
| resize(core::Size njump) | protocols::jumping::JumpSample | |
| safe_secstruct(core::pose::Pose &pose) const | protocols::jumping::JumpSample | |
| set_fold_tree_and_chainbreaks(core::pose::Pose &pose) const | protocols::jumping::JumpSample | inline |
| set_fold_tree_in_pose(core::pose::Pose &pose) const | protocols::jumping::JumpSample | |
| size() const | protocols::jumping::JumpSample | inline |
| steal_jumps(core::pose::Pose &native_pose, core::fragment::FrameIterator const &begin, core::fragment::FrameIterator const &end) const | protocols::jumping::JumpSample | |
| steal_orientation_and_pleating(core::pose::Pose &native_pose) | protocols::jumping::JumpSample | |
| total_residue() const | protocols::jumping::JumpSample | inline |
| total_residue_ | protocols::jumping::JumpSample | private |
| transfer_jumps(core::pose::Pose &pose, core::pose::Pose &native_pose) const | protocols::jumping::JumpSample | |
| ~JumpSample()=default | protocols::jumping::JumpSample | |
1.8.7