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protocols::jumping::JumpSample Member List

This is the complete list of members for protocols::jumping::JumpSample, including all inherited members.

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::JumpSampleprivate
bValidTree_protocols::jumping::JumpSampleprivate
correct_jump_atoms_for_fragments() const protocols::jumping::JumpSampleprivate
cuts() const protocols::jumping::JumpSampleinline
cuts_protocols::jumping::JumpSampleprivate
downstream_res_nr(core::Size jump_nr) const protocols::jumping::JumpSampleinline
dump_pymol(std::string fn) const protocols::jumping::JumpSample
fold_tree() const protocols::jumping::JumpSampleinline
fold_tree_protocols::jumping::JumpSampleprivate
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::JumpSampleprivate
generate_tree_from_jumps_and_cuts(core::Size root=1)protocols::jumping::JumpSampleprivate
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::JumpSampleinline
jump_atoms() const protocols::jumping::JumpSampleinline
jump_atoms_protocols::jumping::JumpSampleprivate
jump_pairings_protocols::jumping::JumpSampleprivate
jumps() const protocols::jumping::JumpSampleinline
jumps2pairings()protocols::jumping::JumpSampleprivate
jumps_protocols::jumping::JumpSampleprivate
JumpSample()protocols::jumping::JumpSampleinline
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::JumpSampleprivate
operator<<(std::ostream &os, JumpSample const &t)protocols::jumping::JumpSamplefriend
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::JumpSampleinline
set_fold_tree_in_pose(core::pose::Pose &pose) const protocols::jumping::JumpSample
size() const protocols::jumping::JumpSampleinline
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::JumpSampleinline
total_residue_protocols::jumping::JumpSampleprivate
transfer_jumps(core::pose::Pose &pose, core::pose::Pose &native_pose) const protocols::jumping::JumpSample
~JumpSample()=defaultprotocols::jumping::JumpSample