| align_chunk(core::pose::Pose &pose) | apps::pilot::AlignChunkMover | inline |
| align_to_ss_only_ | apps::pilot::AlignChunkMover | private |
| align_trial_counter_ | apps::pilot::AlignChunkMover | private |
| AlignChunkMover(numeric::random::RandomGenerator &RG) | apps::pilot::AlignChunkMover | inline |
| apply(core::pose::Pose &pose) | apps::pilot::AlignChunkMover | inline |
| apply_transform(pose::Pose &mod_pose, std::list< Size > const &residue_list, numeric::xyzMatrix< core::Real > const &R, numeric::xyzVector< core::Real > const &preT, numeric::xyzVector< core::Real > const &postT) | apps::pilot::AlignChunkMover | inline |
| atom_map_ | apps::pilot::AlignChunkMover | private |
| copy_ss_torsion_only_ | apps::pilot::AlignChunkMover | private |
| get_local_sequence_mapping(core::pose::Pose const &pose, int registry_shift=0, Size MAX_TRIAL=10) | apps::pilot::AlignChunkMover | inline |
| get_name() const | apps::pilot::AlignChunkMover | inline |
| get_superposition_transformation(pose::Pose const &mod_pose, pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, numeric::xyzMatrix< core::Real > &R, numeric::xyzVector< core::Real > &preT, numeric::xyzVector< core::Real > &postT) | apps::pilot::AlignChunkMover | inline |
| jump_number_ | apps::pilot::AlignChunkMover | private |
| registry_shift_ | apps::pilot::AlignChunkMover | private |
| reset_torsion_unaligned_ | apps::pilot::AlignChunkMover | private |
| RG_ | apps::pilot::AlignChunkMover | private |
| secstruct_ | apps::pilot::AlignChunkMover | private |
| seqpos_start_ | apps::pilot::AlignChunkMover | private |
| seqpos_stop_ | apps::pilot::AlignChunkMover | private |
| sequence_alignment_ | apps::pilot::AlignChunkMover | private |
| sequence_alignment_local_ | apps::pilot::AlignChunkMover | private |
| set_aligned_chunk(core::pose::Pose const &pose, Size const jump_number) | apps::pilot::AlignChunkMover | inline |
| set_registry_shift(int registry_shift) | apps::pilot::AlignChunkMover | inline |
| set_reset_torsion_unaligned(bool reset_torsion_unaligned) | apps::pilot::AlignChunkMover | inline |
| set_template(core::pose::PoseCOP template_pose, std::map< core::Size, core::Size > const &sequence_alignment) | apps::pilot::AlignChunkMover | inline |
| steal_torsion_from_template(core::pose::Pose &pose) | apps::pilot::AlignChunkMover | inline |
| template_pose_ | apps::pilot::AlignChunkMover | private |
| trial_counter(Size ires) | apps::pilot::AlignChunkMover | inline |
