| already_listed_in_obligate_pair(utility::vector1< core::Size > const &new_pair, utility::vector1< core::Size > const &obligate_pair) const | core::import_pose::RNA_DeNovoSetup | 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 | core::import_pose::RNA_DeNovoSetup | private |
| de_novo_setup_from_command_line() | core::import_pose::RNA_DeNovoSetup | private |
| de_novo_setup_from_command_line_legacy() | core::import_pose::RNA_DeNovoSetup | private |
| de_novo_setup_from_options(utility::options::OptionCollection const &opts) | core::import_pose::RNA_DeNovoSetup | private |
| dock_chunks_ | core::import_pose::RNA_DeNovoSetup | private |
| fasta_files_ | core::import_pose::RNA_DeNovoSetup | private |
| get_refine_pose_list(std::string const &input_silent_file, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &output_res_and_chain_segid, core::chemical::ResidueTypeSetCOP rsd_set) const | core::import_pose::RNA_DeNovoSetup | private |
| 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 | core::import_pose::RNA_DeNovoSetup | private |
| get_silent_resnum(std::string const &silent_file) const | core::import_pose::RNA_DeNovoSetup | private |
| get_silent_seq(std::string const &silent_file) const | core::import_pose::RNA_DeNovoSetup | private |
| helical_substructs_ | core::import_pose::RNA_DeNovoSetup | private |
| initialize_from_command_line() | core::import_pose::RNA_DeNovoSetup | |
| initialize_from_options(utility::options::OptionCollection const &opts) | core::import_pose::RNA_DeNovoSetup | |
| initialize_inputs_from_options(utility::options::OptionCollection const &opts) | core::import_pose::RNA_DeNovoSetup | |
| input_initialization_pdbs_ | core::import_pose::RNA_DeNovoSetup | private |
| input_pdbs_ | core::import_pose::RNA_DeNovoSetup | private |
| input_silent_files_ | core::import_pose::RNA_DeNovoSetup | private |
| list_options_read(utility::options::OptionKeyList &opts) | core::import_pose::RNA_DeNovoSetup | static |
| minimize_rna_ | core::import_pose::RNA_DeNovoSetup | private |
| minimize_rna_has_been_specified_ | core::import_pose::RNA_DeNovoSetup | private |
| native_pose() | core::import_pose::RNA_DeNovoSetup | inline |
| native_pose_ | core::import_pose::RNA_DeNovoSetup | private |
| options() const | core::import_pose::RNA_DeNovoSetup | inline |
| options_ | core::import_pose::RNA_DeNovoSetup | private |
| pose() | core::import_pose::RNA_DeNovoSetup | inline |
| pose_ | core::import_pose::RNA_DeNovoSetup | private |
| refine_pose_list() const | core::import_pose::RNA_DeNovoSetup | inline |
| refine_pose_list_ | core::import_pose::RNA_DeNovoSetup | private |
| RNA_DeNovoSetup() | core::import_pose::RNA_DeNovoSetup | |
| rna_params() const | core::import_pose::RNA_DeNovoSetup | inline |
| rna_params_ | core::import_pose::RNA_DeNovoSetup | private |
| rsd_set_ | core::import_pose::RNA_DeNovoSetup | private |
| sequence_strings_ | core::import_pose::RNA_DeNovoSetup | private |
| set_align_pdb(std::string const &align_pdb) | core::import_pose::RNA_DeNovoSetup | |
| set_fasta_files(utility::vector1< std::string > const &fasta_files) | core::import_pose::RNA_DeNovoSetup | inline |
| set_input_pdbs(utility::vector1< std::string > const &input_pdbs) | core::import_pose::RNA_DeNovoSetup | |
| set_input_silent_files(utility::vector1< std::string > const &input_silent_files) | core::import_pose::RNA_DeNovoSetup | |
| set_minimize_rna(bool const minimize_rna) | core::import_pose::RNA_DeNovoSetup | inline |
| set_native_pose(core::pose::PoseOP native_pose) | core::import_pose::RNA_DeNovoSetup | inline |
| set_nstruct(Size const nstruct) | core::import_pose::RNA_DeNovoSetup | |
| set_sequence_strings(utility::vector1< std::string > const &sequence_strings) | core::import_pose::RNA_DeNovoSetup | inline |
| set_silent_file(std::string const &silent_file) | core::import_pose::RNA_DeNovoSetup | |
| setup_refine_pose_list(utility::options::OptionCollection const &opts) | core::import_pose::RNA_DeNovoSetup | private |
| 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 | core::import_pose::RNA_DeNovoSetup | 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 | core::import_pose::RNA_DeNovoSetup | private |
| working_res_map(std::string const &seq, utility::vector1< core::Size > const &working_res, bool const annotations_in_brackets=true) const | core::import_pose::RNA_DeNovoSetup | private |
| working_res_map(core::pose::rna::RNA_SecStruct const &seq, utility::vector1< core::Size > const &working_res) const | core::import_pose::RNA_DeNovoSetup | private |
| ~RNA_DeNovoSetup() override | core::import_pose::RNA_DeNovoSetup | |
1.8.7