| align_chunk_ | apps::pilot::MultiTemplateAlignChunkMover | private |
| align_option_ | apps::pilot::MultiTemplateAlignChunkMover | private |
| apply(core::pose::Pose &pose) | apps::pilot::MultiTemplateAlignChunkMover | inline |
| get_alignment_from_chunk_mapping(std::map< core::Size, core::Size > const &chunk_mapping, Loops const template_ss_chunks, Loops const target_ss_chunks, std::map< core::Size, core::Size > &sequence_alignment) | apps::pilot::MultiTemplateAlignChunkMover | inline |
| get_alignment_from_template(core::pose::PoseCOP const template_pose, std::map< core::Size, core::Size > &seqpos_alignment) | apps::pilot::MultiTemplateAlignChunkMover | inline |
| get_name() const | apps::pilot::MultiTemplateAlignChunkMover | inline |
| jump_number_ | apps::pilot::MultiTemplateAlignChunkMover | private |
| max_registry_shift_ | apps::pilot::MultiTemplateAlignChunkMover | private |
| max_registry_shift_input_ | apps::pilot::MultiTemplateAlignChunkMover | private |
| MultiTemplateAlignChunkMover(numeric::random::RandomGenerator &RG, utility::vector1< core::pose::PoseOP > const &template_poses, Loops ss_chunks_pose, AlignOption align_option=all_chunks, Size max_registry_shift=0) | apps::pilot::MultiTemplateAlignChunkMover | inline |
| pick_random_chunk(core::pose::Pose &pose) | apps::pilot::MultiTemplateAlignChunkMover | inline |
| pick_random_template() | apps::pilot::MultiTemplateAlignChunkMover | inline |
| RG_ | apps::pilot::MultiTemplateAlignChunkMover | private |
| sequence_alignments_ | apps::pilot::MultiTemplateAlignChunkMover | private |
| template_number_ | apps::pilot::MultiTemplateAlignChunkMover | private |
| template_poses_ | apps::pilot::MultiTemplateAlignChunkMover | private |
| template_ss_chunks_ | apps::pilot::MultiTemplateAlignChunkMover | private |
| trial_counter(Size ires) | apps::pilot::MultiTemplateAlignChunkMover | inline |
