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Rosetta
2021.16
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Rosetta
2021.16
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This is the complete list of members for protocols::rna::denovo::movers::RNA_DeNovoProtocolMover, including all inherited members.
| add_chem_shift_info(core::pose::Pose ¬_very_const_pose) const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| all_lores_score_final_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| already_listed_in_obligate_pair(utility::vector1< core::Size > const &new_pair, utility::vector1< core::Size > const &obligate_pair) const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| already_listed_in_obligate_pair(utility::vector1< Size > const &new_pair, utility::vector1< Size > const &obligate_pair, utility::vector1< Size > const &obligate_pair_explicit) const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| apply(core::pose::Pose &pose) override | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | virtual |
| check_secstructs(bool const modeling_with_density, bool const rna_protein_docking, std::string const &sequence, core::pose::rna::RNA_SecStruct const &secstruct, core::pose::rna::RNA_SecStruct const &secstruct_general) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | virtual |
| constraint_setup(bool const constraint_file_provided, std::string const &constraint_file, utility::vector1< core::Size > const &working_res, core::pose::Pose &full_pose) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| create() | protocols::moves::Mover | virtual |
| de_novo_setup_from_command_line() | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | |
| de_novo_setup_from_options(utility::options::OptionCollection const &opts) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | |
| de_novo_setup_from_tag(utility::tag::TagCOP const &tag) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | |
| denovo_scorefxn_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| dock_chunks_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| fasta_files_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| fresh_instance() const override | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | virtual |
| get_additional_output() | protocols::moves::Mover | virtual |
| 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::rna::denovo::movers::RNA_DeNovoProtocolMover | virtual |
| get_native_pose() | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | inlineprivate |
| protocols::moves::Mover::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_seq_and_resnum(std::string const &pdb, std::string &seq, utility::vector1< int > &resnum, utility::vector1< char > &chain, utility::vector1< std::string > &segid) const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| get_silent_resnum(std::string const &silent_file) const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| get_silent_seq(std::string const &silent_file) const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| get_type() const | protocols::moves::Mover | inline |
| helical_substructs_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| hires_scorefxn_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| initial_pose_setup(std::string const &in_path, bool const lores_sfxn_provided, bool const native_provided, bool const edensity_mapfile_provided, bool const working_native_provided, std::string const &working_native, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &working_res, core::pose::Pose &full_pose, bool &is_rna_and_protein) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| initialize_scorefxn(core::pose::Pose &pose) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| initialize_sequence_information(int const offset, bool const edensity_mapfile_provided, bool const rna_protein_docking, bool const virtual_anchor_provided, bool const cutpoint_open_provided, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &possible_cutpoint_open_numbering, core::pose::full_model_info::FullModelParametersOP &full_model_parameters, utility::vector1< core::Size > &cutpoint_open_in_full_model) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| input_initialization_pdb_numbering_setup(std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > &input_initialization_res) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| input_initialization_pdbs_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| input_numbering_setup(std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &input_res_resnum_and_chain, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &input_silent_res_resnum_and_chain, std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > &input_res, utility::vector1< utility::vector1< int > > &resnum_list, utility::vector1< core::Size > &input_res_initialize, utility::vector1< utility::vector1< core::Size > > &helical_substruct_res, utility::vector1< core::Size > &dock_chunks_res) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| input_pdb_numbering_setup(std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > &input_res, utility::vector1< utility::vector1< core::Size > > &helical_substruct_res, utility::vector1< core::Size > &dock_chunks_res, utility::vector1< utility::vector1< int > > &resnum_list, utility::vector1< core::Size > &input_res_user_defined, Size &input_res_user_defined_count) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| input_pdbs_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| input_silent_files_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| input_silent_numbering_setup(std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &input_silent_res_resnum_and_chain, std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &input_res_user_defined, core::Size const &input_res_user_defined_count, utility::vector1< core::Size > &input_res, utility::vector1< utility::vector1< core::Size > > &helical_substruct_res, utility::vector1< core::Size > &dock_chunks_res, utility::vector1< utility::vector1< int > > &resnum_list) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| list_options_read(utility::options::OptionKeyList &opts) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | static |
| minimize_rna_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| minimize_rna_has_been_specified_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | static |
| name() | protocols::moves::Mover | inlinestatic |
| native_pose_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| options() const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | inline |
| options_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data) override | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | virtual |
| Pose typedef | protocols::moves::Mover | |
| pose_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| PoseCOP typedef | protocols::moves::Mover | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | static |
| refine_working_obligate_pairs(std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &remove_obligate_pair_rc, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &obligate_pair, utility::vector1< std::string > &obligate_pair_explicit, utility::vector1< core::Size > const &working_res, utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | 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 | |
| RNA_DeNovoProtocolMover() | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | |
| rna_fragment_monte_carlo_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| rna_params() const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | inline |
| rna_params_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| rsd_set_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| sequence_strings_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| set_align_pdb(std::string const &align_pdb) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_dock_chunks(utility::vector1< std::string > const &dock_chunks) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | inline |
| set_fasta_files(utility::vector1< std::string > const &fasta_files) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | inline |
| set_helical_substructs(utility::vector1< std::string > const &helical_substructs) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | inline |
| set_input_initialization_pdbs(utility::vector1< std::string > const &input_initialization_pdbs) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | |
| set_input_pdbs(utility::vector1< std::string > const &input_pdbs) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_input_silent_files(utility::vector1< std::string > const &input_silent_files) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_minimize_rna(bool const minimize_rna) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | inline |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_nstruct(Size const nstruct) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | |
| set_protocol_options(core::import_pose::options::RNA_DeNovoProtocolOptionsOP const &protocol_options) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | inline |
| set_residue_type_set(core::chemical::ResidueTypeSetCOP const &rts) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | inline |
| set_sequence_strings(utility::vector1< std::string > const &sequence_strings) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | inline |
| set_silent_file(std::string const &silent_file) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| setup_final_res_lists(utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &cutpoint_open_in_full_model, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &extra_minimize_res_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &extra_minimize_chi_res_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &output_jump_res_rc, bool const minimize_rna_specified, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &syn_chi_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &anti_chi_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &block_stack_above_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &block_stack_below_rc, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| setup_ft_from_silent(bool const ft_from_silent_provided, std::string const &ft_silent_file, bool const tag_provided, utility::vector1< std::string > const &tag, bool &use_fold_tree_from_silent_file, core::kinematics::FoldTree &fold_tree_from_silent_file) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| setup_obligate_pair(std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &extra_minimize_res, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< utility::vector1< int > > const &resnum_list, core::pose::rna::RNA_SecStruct const &secstruct, core::pose::rna::RNA_SecStruct const &secstruct_general, utility::vector1< core::Size > const &cutpoint_open_in_full_model, utility::vector1< core::Size > &obligate_pair, utility::vector1< std::string > &obligate_pair_explicit, utility::vector1< core::Size > &domain_map) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| setup_pairing_sets(utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &working_stems, utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs, core::pose::rna::RNA_BasePairList &rna_pairing_list, utility::vector1< utility::vector1< core::Size > > &working_obligate_pair_sets, utility::vector1< utility::vector1< core::Size > > &working_stem_pairing_sets) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| setup_working_chain_connections(utility::vector1< std::string > const &chain_connections, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &working_res, utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > &working_chain_connections) | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| Size typedef | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| Strings typedef | protocols::moves::Mover | |
| 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 |
| update_working_obligate_pairs_with_stems(utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &working_stems, utility::vector1< core::Size > const &working_input_res) const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| vdw_grid_ | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| working_res_map(utility::vector1< core::Size > const &vec, utility::vector1< core::Size > const &working_res, bool const leave_out_last_working_residue=false) const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| working_res_map(std::string const &seq, utility::vector1< core::Size > const &working_res, bool const annotations_in_brackets=true) const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| working_res_map(core::pose::rna::RNA_SecStruct const &seq, utility::vector1< core::Size > const &working_res) const | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover | private |
| ~RNA_DeNovoProtocolMover() override | protocols::rna::denovo::movers::RNA_DeNovoProtocolMover |
1.8.7