| align_chunk_ | protocols::hybridization::ChunkTrialMover | private |
| align_option_ | protocols::hybridization::ChunkTrialMover | private |
| apply(core::pose::Pose &pose) | protocols::hybridization::ChunkTrialMover | virtual |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| ChunkTrialMover(utility::vector1< core::pose::PoseCOP > const &template_poses, utility::vector1< protocols::loops::Loops > const &template_chunks, Loops ss_chunks_pose, bool random_template=true, AlignOption align_option=all_chunks, Size max_registry_shift=0) | protocols::hybridization::ChunkTrialMover | |
| ChunkTrialMover(utility::vector1< core::pose::PoseCOP > const &template_poses, utility::vector1< protocols::loops::Loops > const &template_chunks, Loops ss_chunks_pose, bool random_template, AlignOption align_option, utility::vector1< bool > residue_sample_template, utility::vector1< Size > residue_max_registry_shift) | protocols::hybridization::ChunkTrialMover | |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| create() | protocols::moves::Mover | virtual |
| Filters_map typedef | protocols::moves::Mover | |
| fresh_instance() const | protocols::moves::Mover | virtual |
| get_additional_output() | protocols::moves::Mover | virtual |
| 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) | protocols::hybridization::ChunkTrialMover | |
| get_alignment_from_template(core::pose::PoseCOP template_pose, std::map< core::Size, core::Size > &seqpos_alignment) | protocols::hybridization::ChunkTrialMover | |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_name() const | protocols::hybridization::ChunkTrialMover | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_type() const | protocols::moves::Mover | inline |
| highest_tmpl_resnum_ | protocols::hybridization::ChunkTrialMover | private |
| ignore_template_indices_ | protocols::hybridization::ChunkTrialMover | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| jump_number_ | protocols::hybridization::ChunkTrialMover | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| max_registry_shift_global_ | protocols::hybridization::ChunkTrialMover | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| Mover(Mover const &other) | protocols::moves::Mover | |
| name() | protocols::moves::Mover | inlinestatic |
| operator=(Mover const &other) | protocols::moves::Mover | |
| parse_def(utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) | protocols::moves::Mover | virtual |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) | protocols::moves::Mover | virtual |
| parse_state(SerializableState const &state) | protocols::moves::Mover | virtual |
| pick_random_chunk(core::pose::Pose &pose) | protocols::hybridization::ChunkTrialMover | |
| pick_random_template() | protocols::hybridization::ChunkTrialMover | |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| random_template_ | protocols::hybridization::ChunkTrialMover | private |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| reset_status() | protocols::moves::Mover | |
| residue_covered_by_template_ | protocols::hybridization::ChunkTrialMover | private |
| residue_max_registry_shift_ | protocols::hybridization::ChunkTrialMover | private |
| sampling_chunk_ | protocols::hybridization::ChunkTrialMover | private |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| sequence_alignments_ | protocols::hybridization::ChunkTrialMover | private |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_template(core::Size const template_number) | protocols::hybridization::ChunkTrialMover | |
| set_templates_to_ignore(std::set< core::Size > template_indices_in) | protocols::hybridization::ChunkTrialMover | inline |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| Strings typedef | protocols::moves::Mover | |
| TagCOP typedef | protocols::moves::Mover | |
| template_chunks_ | protocols::hybridization::ChunkTrialMover | private |
| template_number() | protocols::hybridization::ChunkTrialMover | |
| template_number_ | protocols::hybridization::ChunkTrialMover | private |
| template_poses_ | protocols::hybridization::ChunkTrialMover | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| trial_counter(Size ires) | protocols::hybridization::ChunkTrialMover | |
| type() const | protocols::moves::Mover | inline |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| ~Mover() | protocols::moves::Mover | virtual |
1.8.7