| aa_order_ | protocols::simple_moves::StructProfileMover | private |
| add_csts_to_pose_ | protocols::simple_moves::StructProfileMover | private |
| add_MSAcst_to_pose(utility::vector1< utility::vector1< core::Real > > profile_score, core::pose::Pose &pose) | protocols::simple_moves::StructProfileMover | |
| allowed_deviation_ | protocols::simple_moves::StructProfileMover | private |
| allowed_deviation_loops_ | protocols::simple_moves::StructProfileMover | private |
| apply(Pose &pose) override | protocols::simple_moves::StructProfileMover | virtual |
| burialWt_ | protocols::simple_moves::StructProfileMover | private |
| calc_cenlist(core::pose::Pose const &pose) | protocols::simple_moves::StructProfileMover | |
| cenType_ | protocols::simple_moves::StructProfileMover | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::simple_moves::StructProfileMover | inlinevirtual |
| consider_topN_frags_ | protocols::simple_moves::StructProfileMover | private |
| create() | protocols::moves::Mover | virtual |
| eliminate_background_ | protocols::simple_moves::StructProfileMover | private |
| fresh_instance() const | protocols::moves::Mover | virtual |
| generate_counts(utility::vector1< utility::vector1< std::string > > top_frag_sequences, core::pose::Pose const &pose) | protocols::simple_moves::StructProfileMover | |
| generate_profile_score(utility::vector1< utility::vector1< core::Size > > res_per_pos, core::pose::Pose const &pose) | protocols::simple_moves::StructProfileMover | |
| generate_profile_score_wo_background(utility::vector1< utility::vector1< core::Size > > res_per_pos, utility::vector1< core::Real > cenList, core::pose::Pose const &pose) | protocols::simple_moves::StructProfileMover | |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_cen_deviation(std::vector< core::Real > cenListFrag, utility::vector1< core::Real > cenListModel) | protocols::simple_moves::StructProfileMover | |
| get_closest_sequence_at_res(core::pose::Pose const &pose, core::Size res, utility::vector1< core::Real > cenList) | protocols::simple_moves::StructProfileMover | |
| get_closest_sequences(core::pose::Pose const &pose, utility::vector1< core::Real > cenList, core::select::residue_selector::ResidueSubset const &subset) | protocols::simple_moves::StructProfileMover | |
| 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 override | protocols::simple_moves::StructProfileMover | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_self_ptr() const | protocols::moves::Mover | inline |
| get_self_ptr() | protocols::moves::Mover | inline |
| get_self_weak_ptr() const | protocols::moves::Mover | inline |
| get_self_weak_ptr() | protocols::moves::Mover | inline |
| get_type() const | protocols::moves::Mover | inline |
| ignore_terminal_res_ | protocols::simple_moves::StructProfileMover | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::simple_moves::StructProfileMover | static |
| name() | protocols::moves::Mover | inlinestatic |
| only_loops_ | protocols::simple_moves::StructProfileMover | private |
| outputProfile_ | protocols::simple_moves::StructProfileMover | private |
| P_AA_SS_burial_ | protocols::simple_moves::StructProfileMover | private |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override | protocols::simple_moves::StructProfileMover | virtual |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| Probability_AA_n_n typedef | protocols::simple_moves::StructProfileMover | private |
| profile_save_filename_ | protocols::simple_moves::StructProfileMover | private |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::simple_moves::StructProfileMover | static |
| read_P_AA_SS_cen6() | protocols::simple_moves::StructProfileMover | |
| 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_selector_ | protocols::simple_moves::StructProfileMover | private |
| rmsThreshold_ | protocols::simple_moves::StructProfileMover | private |
| save_MSAcst_file(utility::vector1< utility::vector1< core::Real > > profile_score, core::pose::Pose const &pose) | protocols::simple_moves::StructProfileMover | |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| 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_profile_save_name(std::string const &name) | protocols::simple_moves::StructProfileMover | inline |
| set_residue_selector(core::select::residue_selector::ResidueSelector const &selector) | protocols::simple_moves::StructProfileMover | |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| ss_type_convert(char ss_type) | protocols::simple_moves::StructProfileMover | |
| SSHashedFragmentStore_ | protocols::simple_moves::StructProfileMover | private |
| Strings typedef | protocols::moves::Mover | |
| StructProfileMover() | protocols::simple_moves::StructProfileMover | |
| StructProfileMover(core::Real rmsThreshold, core::Size consider_topN_frags, core::Real burialWt, bool only_loops, core::Real allowed_deviation, core::Real allowed_deviation_loops, bool eliminate_background, bool outputProfile, bool add_csts_to_pose, bool ignore_terminal_res) | protocols::simple_moves::StructProfileMover | |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
1.8.7