Module _protocols_stepwise_modeler_rna_

Convert_rebuild_residue_string_to_list( (str)rebuild_residue_string) -> object :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:42

    C++ signature :
        utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> > Convert_rebuild_residue_string_to_list(std::string)

add_fade_chain_break_constraint_across_gap( (Pose)pose, (int)five_prime_res, (int)three_prime_res, (int)gap_size) -> None :
    protocols/stepwise/modeler/rna/util.hh:293

    C++ signature :
        void add_fade_chain_break_constraint_across_gap(core::pose::Pose {lvalue},unsigned long,unsigned long,unsigned long)

add_harmonic_chain_break_constraint( (Pose)pose, (int)five_prime_res) -> None :
    protocols/stepwise/modeler/rna/util.hh:296

    C++ signature :
        void add_harmonic_chain_break_constraint(core::pose::Pose {lvalue},unsigned long)

add_virtual_O2Prime_hydrogen( (Pose)pose) -> None :
    protocols/stepwise/modeler/rna/util.hh:154

    C++ signature :
        void add_virtual_O2Prime_hydrogen(core::pose::Pose {lvalue})

align_poses( (Pose)moving_pose, (str)moving_tag, (Pose)static_pose, (str)static_tag, (vector1_Size)working_best_alignment [, (bool)base_only=True]) -> None :
    protocols/stepwise/modeler/rna/util.hh:105

    C++ signature :
        void align_poses(core::pose::Pose {lvalue},std::string,core::pose::Pose,std::string,utility::vector1<unsigned long, std::allocator<unsigned long> > [,bool=True])

apply_full_to_sub_mapping( (vector1_Size)res_vector, (object)working_parameters) -> vector1_Size :
    protocols/stepwise/modeler/rna/util.hh:111

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > apply_full_to_sub_mapping(utility::vector1<unsigned long, std::allocator<unsigned long> >,boost::shared_ptr<protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters const>)

apply_full_to_sub_mapping( (vector1_Size)res_vector, (vector1_Size)is_working_res, (map_Size_Size)full_to_sub) -> vector1_Size :
    protocols/stepwise/modeler/rna/util.hh:108

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > apply_full_to_sub_mapping(utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >)

apply_protonated_H1_adenosine_variant_type( (Pose)pose, (int)seq_num [, (bool)apply_check=True]) -> None :
    protocols/stepwise/modeler/rna/util.hh:55

    C++ signature :
        void apply_protonated_H1_adenosine_variant_type(core::pose::Pose {lvalue},unsigned long [,bool=True])

apply_sub_to_full_mapping( (vector1_Size)working_res_vector, (object)working_parameters) -> vector1_Size :
    protocols/stepwise/modeler/rna/util.hh:123

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > apply_sub_to_full_mapping(utility::vector1<unsigned long, std::allocator<unsigned long> >,boost::shared_ptr<protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters const>)

atom_square_deviation( (Residue)rsd_1, (Residue)rsd_2, (int)atomno_1, (int)atomno_2, (bool)verbose) -> float :
    protocols/stepwise/modeler/rna/util.hh:193

    C++ signature :
        double atom_square_deviation(core::conformation::Residue,core::conformation::Residue,unsigned long,unsigned long,bool)

base_atoms_square_deviation( (Pose)pose1, (Pose)pose2, (int)moving_res_1, (int)moving_res_2, (int)atom_count, (float)sum_sd, (bool)verbose, (bool)ignore_virtual_atom) -> None :
    protocols/stepwise/modeler/rna/util.hh:185

    C++ signature :
        void base_atoms_square_deviation(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long,unsigned long {lvalue},double {lvalue},bool,bool)

check_for_messed_up_structure( (Pose)pose, (str)tag) -> bool :
    protocols/stepwise/modeler/rna/util.hh:233

    C++ signature :
        bool check_for_messed_up_structure(core::pose::Pose,std::string)

check_instantiated_O2Prime_hydrogen( (Pose)pose) -> None :
    protocols/stepwise/modeler/rna/util.hh:157

    C++ signature :
        void check_instantiated_O2Prime_hydrogen(core::pose::Pose)

check_is_working_res( (int)full_seq_num, (object)working_parameters) -> bool :
    protocols/stepwise/modeler/rna/util.hh:117

    C++ signature :
        bool check_is_working_res(unsigned long,boost::shared_ptr<protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters const>)

check_validity_and_get_working_res( (int)full_seq_num, (object)working_parameters) -> int :
    protocols/stepwise/modeler/rna/util.hh:120

    C++ signature :
        unsigned long check_validity_and_get_working_res(unsigned long,boost::shared_ptr<protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters const>)

choose_random_if_unspecified_nucleotide( (str)newrestype) -> None :
    protocols/stepwise/modeler/rna/util.hh:272

    C++ signature :
        void choose_random_if_unspecified_nucleotide(char {lvalue})

contain_residue_at_seq_num( (int)seq_num, (object)copy_dofs) -> bool :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:69

    C++ signature :
        bool contain_residue_at_seq_num(unsigned long,utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> >)

copy_all_o2prime_torsions( (Pose)mod_pose, (Pose)template_pose) -> None :
    protocols/stepwise/modeler/rna/util.hh:263

    C++ signature :
        void copy_all_o2prime_torsions(core::pose::Pose {lvalue},core::pose::Pose)

copy_dofs_sort_criterion( (Residue_info)residue_info_1, (Residue_info)residue_info_2) -> bool :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:81

    C++ signature :
        bool copy_dofs_sort_criterion(protocols::stepwise::modeler::rna::Residue_info,protocols::stepwise::modeler::rna::Residue_info)

create_full_to_input_res_map( (vector1_Size)input_res_vector) -> map_Size_Size :
    protocols/stepwise/modeler/rna/util.hh:126

    C++ signature :
        std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > > create_full_to_input_res_map(utility::vector1<unsigned long, std::allocator<unsigned long> >)

create_rotamer_string( (Pose)pose, (int)moving_res, (int)reference_res) -> str :
    protocols/stepwise/modeler/rna/util.hh:287

    C++ signature :
        std::string create_rotamer_string(core::pose::Pose,unsigned long,unsigned long)

create_rotamer_string( (Pose)pose, (int)moving_res, (bool)is_prepend) -> str :
    protocols/stepwise/modeler/rna/util.hh:284

    C++ signature :
        std::string create_rotamer_string(core::pose::Pose,unsigned long,bool)

create_standard_o2prime_pack_task( (Pose)pose, (vector1_Size)O2prime_pack_seq_num [, (bool)pack_virtual_o2prime_hydrogen=False]) -> PackerTask :
    protocols/stepwise/modeler/rna/util.hh:218

    C++ signature :
        boost::shared_ptr<core::pack::task::PackerTask> create_standard_o2prime_pack_task(core::pose::Pose,utility::vector1<unsigned long, std::allocator<unsigned long> > [,bool=False])

create_strand_list( (object)copy_dofs) -> object :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:72

    C++ signature :
        utility::vector1<utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> >, std::allocator<utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> > > > create_strand_list(utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> >)

create_tag( (str)prestring, (int)i) -> str :
    protocols/stepwise/modeler/rna/util.hh:278

    C++ signature :
        std::string create_tag(std::string,unsigned long)

create_torsion_value_string( (float)torsion_value) -> str :
    protocols/stepwise/modeler/rna/util.hh:281

    C++ signature :
        std::string create_torsion_value_string(double)

ensure_valid_full_seq_num( (int)full_seq_num, (object)working_parameters) -> None :
    protocols/stepwise/modeler/rna/util.hh:114

    C++ signature :
        void ensure_valid_full_seq_num(unsigned long,boost::shared_ptr<protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters const>)

figure_out_moving_rna_chain_breaks( (Pose)pose, (vector1_Size)moving_partition_res, (vector1_Size)rna_cutpoints_closed, (vector1_Size)rna_five_prime_chain_breaks, (vector1_Size)rna_three_prime_chain_breaks, (vector1_Size)rna_chain_break_gap_sizes) -> None :
    protocols/stepwise/modeler/rna/util.hh:313

    C++ signature :
        void figure_out_moving_rna_chain_breaks(core::pose::Pose,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue})

file_exists( (str)file_name) -> bool :
    protocols/stepwise/modeler/rna/util.hh:145

    C++ signature :
        bool file_exists(std::string)

freeze_sugar_torsions( (MoveMap)mm, (int)total_residue) -> None :
    protocols/stepwise/modeler/rna/util.hh:203

    C++ signature :
        void freeze_sugar_torsions(core::kinematics::MoveMap {lvalue},unsigned long)

get_anchor_res( (int)rebuild_res, (Pose)pose) -> int :
    protocols/stepwise/modeler/rna/util.hh:230

    C++ signature :
        unsigned long get_anchor_res(unsigned long,core::pose::Pose)

get_binary_rna_silent_struct_safe( (Pose)const_pose, (str)tag, (str)silent_file) -> BinarySilentStruct :
    protocols/stepwise/modeler/rna/StepWiseRNA_OutputData.hh:56

    C++ signature :
        core::io::silent::BinarySilentStruct get_binary_rna_silent_struct_safe(core::pose::Pose,std::string,std::string)

get_binary_rna_silent_struct_safe_wrapper( (Pose)const_pose, (str)tag, (str)silent_file, (bool)write_score_only) -> BinarySilentStruct :
    protocols/stepwise/modeler/rna/StepWiseRNA_OutputData.hh:59

    C++ signature :
        core::io::silent::BinarySilentStruct get_binary_rna_silent_struct_safe_wrapper(core::pose::Pose,std::string,std::string,bool)

get_copy_dofs_from_fasta( (str)full_fasta_sequence) -> object :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:63

    C++ signature :
        utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> > get_copy_dofs_from_fasta(std::string)

get_max_seq_num_from_res_map( (map_Size_Size)my_map) -> int :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:54

    C++ signature :
        unsigned long get_max_seq_num_from_res_map(std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >)

get_modeler_scorefxn( (__CPP_ScoreFunction__)scorefxn_) -> ScoreFunction :
    protocols/stepwise/modeler/rna/util.hh:260

    C++ signature :
        boost::shared_ptr<core::scoring::ScoreFunction> get_modeler_scorefxn(boost::shared_ptr<core::scoring::ScoreFunction const>)

get_one_letter_name( (str)three_letter_name) -> str :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:48

    C++ signature :
        std::string get_one_letter_name(std::string)

get_partition_definition_floating_base( (Pose)pose, (int)moving_res) -> vector1_bool :
    protocols/stepwise/modeler/rna/util.hh:227

    C++ signature :
        utility::vector1<bool, std::allocator<bool> > get_partition_definition_floating_base(core::pose::Pose,unsigned long)

get_possible_O3prime_C5prime_distance_range( (int)gap_size_, (float)min_dist, (float)max_dist) -> None :
    protocols/stepwise/modeler/rna/util.hh:299

    C++ signature :
        void get_possible_O3prime_C5prime_distance_range(unsigned long,double {lvalue},double {lvalue})

get_residue_from_seq_num( (int)seq_num, (object)copy_dofs) -> Residue_info :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:66

    C++ signature :
        protocols::stepwise::modeler::rna::Residue_info get_residue_from_seq_num(unsigned long,utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> >)

get_surrounding_O2prime_hydrogen( (Pose)pose, (vector1_Size)moving_res [, (bool)verbose=False]) -> vector1_Size :
    protocols/stepwise/modeler/rna/util.hh:206

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > get_surrounding_O2prime_hydrogen(core::pose::Pose,utility::vector1<unsigned long, std::allocator<unsigned long> > [,bool=False])

get_three_letter_name( (str)one_letter_name) -> str :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:51

    C++ signature :
        std::string get_three_letter_name(std::string)

is_residues_in_contact( (int)res_ONE, (Pose)pose_ONE, (int)res_TWO, (Pose)pose_TWO, (float)atom_atom_overlap_dist_cutoff, (int)num_atom_contacts_cutoff [, (bool)verbose=False]) -> bool :
    protocols/stepwise/modeler/rna/util.hh:246

    C++ signature :
        bool is_residues_in_contact(unsigned long,core::pose::Pose,unsigned long,core::pose::Pose,double,unsigned long [,bool=False])

is_virtual_base( (Residue)rsd) -> bool :
    protocols/stepwise/modeler/rna/util.hh:138

    C++ signature :
        bool is_virtual_base(core::conformation::Residue)

just_modeling_RNA( (str)sequence) -> bool :
    protocols/stepwise/modeler/rna/util.hh:318

    C++ signature :
        bool just_modeling_RNA(std::string)

just_rna( (vector1_Size)res_list, (Pose)pose) -> vector1_Size :
    protocols/stepwise/modeler/rna/util.hh:305

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > just_rna(utility::vector1<unsigned long, std::allocator<unsigned long> >,core::pose::Pose)

minimize_with_constraints( (Pose)pose, (MoveMap)mm, (__CPP_ScoreFunction__)scorefxn, (MinimizerOptions)options) -> None :
    protocols/stepwise/modeler/rna/util.hh:52

    C++ signature :
        void minimize_with_constraints(core::pose::Pose {lvalue},core::kinematics::MoveMap,boost::shared_ptr<core::scoring::ScoreFunction>,core::optimization::MinimizerOptions)

mutate_res_if_allowed( (Pose)pose, (int)mutate_res [, (float)mutation_frequency=0.5]) -> bool :
    protocols/stepwise/modeler/rna/util.hh:275

    C++ signature :
        bool mutate_res_if_allowed(core::pose::Pose {lvalue},unsigned long [,double=0.5])

o2prime_trials( (Pose)pose, (__CPP_ScoreFunction__)packer_scorefxn, (vector1_Size)O2prime_seq_num_list [, (bool)pack_virtual_o2prime_hydrogen=False]) -> None :
    protocols/stepwise/modeler/rna/util.hh:214

    C++ signature :
        void o2prime_trials(core::pose::Pose {lvalue},boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<unsigned long, std::allocator<unsigned long> > [,bool=False])

o2prime_trials( (Pose)pose, (__CPP_ScoreFunction__)packer_scorefxn [, (bool)pack_virtual_o2prime_hydrogen=False]) -> None :
    protocols/stepwise/modeler/rna/util.hh:210

    C++ signature :
        void o2prime_trials(core::pose::Pose {lvalue},boost::shared_ptr<core::scoring::ScoreFunction const> [,bool=False])

output_copy_dofs( (object)copy_dofs) -> None :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:60

    C++ signature :
        void output_copy_dofs(utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> >)

output_data( (SilentFileData)silent_file_data, (str)silent_file, (str)tag, (bool)write_score_only, (Pose)pose, (Pose)native_poseCOP, (object)working_parameters_) -> None :
    protocols/stepwise/modeler/rna/StepWiseRNA_OutputData.hh:65

    C++ signature :
        void output_data(core::io::silent::SilentFileData {lvalue},std::string,std::string,bool,core::pose::Pose,boost::shared_ptr<core::pose::Pose const>,boost::shared_ptr<protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters const>)

output_data( (str)silent_file, (str)tag, (bool)write_score_only, (Pose)pose, (Pose)native_poseCOP, (object)working_parameters_) -> None :
    protocols/stepwise/modeler/rna/StepWiseRNA_OutputData.hh:62

    C++ signature :
        void output_data(std::string,std::string,bool,core::pose::Pose,boost::shared_ptr<core::pose::Pose const>,boost::shared_ptr<protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters const>)

output_res_map( (map_Size_Size)my_map, (int)max_seq_num) -> None :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:57

    C++ signature :
        void output_res_map(std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >,unsigned long)

output_residue_struct( (Residue_info)residue) -> None :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:45

    C++ signature :
        void output_residue_struct(protocols::stepwise::modeler::rna::Residue_info)

output_seq_num_list( (str)tag, (vector1_Size)seq_num_list, (OStream)outstream [, (int)spacing=40]) -> None :
    protocols/stepwise/modeler/rna/util.hh:142

    C++ signature :
        void output_seq_num_list(std::string,utility::vector1<unsigned long, std::allocator<unsigned long> >,std::ostream {lvalue} [,unsigned long=40])

output_title_text( (str)title, (OStream)outstream) -> None :
    protocols/stepwise/modeler/rna/util.hh:200

    C++ signature :
        void output_title_text(std::string,std::ostream {lvalue})

phosphate_base_phosphate_rmsd( (Pose)pose1, (Pose)pose2, (int)moving_res_num, (bool)ignore_virtual_atom) -> float :
    protocols/stepwise/modeler/rna/util.hh:179

    C++ signature :
        double phosphate_base_phosphate_rmsd(core::pose::Pose,core::pose::Pose,unsigned long,bool)

phosphate_base_phosphate_square_deviation( (Pose)pose1, (Pose)pose2, (int)moving_res_1, (int)moving_res_2, (int)atom_count, (float)sum_sd, (bool)verbose, (bool)ignore_virtual_atom) -> None :
    protocols/stepwise/modeler/rna/util.hh:182

    C++ signature :
        void phosphate_base_phosphate_square_deviation(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long,unsigned long {lvalue},double {lvalue},bool,bool)

phosphate_square_deviation( (Pose)pose1, (Pose)pose2, (int)moving_res_1, (int)moving_res_2, (int)atom_count, (float)sum_sd, (bool)verbose, (bool)ignore_virtual_atom) -> None :
    protocols/stepwise/modeler/rna/util.hh:189

    C++ signature :
        void phosphate_square_deviation(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long,unsigned long {lvalue},double {lvalue},bool,bool)

print_base_state( (str)tag, (int)base_state, (OStream)outstream) -> None :
    protocols/stepwise/modeler/rna/util.hh:254

    C++ signature :
        void print_base_state(std::string,unsigned long,std::ostream {lvalue})

print_sugar_pucker_state( (str)tag, (int)pucker_state, (OStream)outstream) -> None :
    protocols/stepwise/modeler/rna/util.hh:257

    C++ signature :
        void print_sugar_pucker_state(std::string,unsigned long,std::ostream {lvalue})

print_torsion_info( (Pose)pose, (int)seq_num, (int)rna_torsion_number, (str)type) -> None :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:39

    C++ signature :
        void print_torsion_info(core::pose::Pose,unsigned long,unsigned long,std::string)

remove_all_variant_types( (Pose)pose) -> None :
    protocols/stepwise/modeler/rna/util.hh:58

    C++ signature :
        void remove_all_variant_types(core::pose::Pose {lvalue})

remove_all_virtual_phosphates( (Pose)pose) -> None :
    protocols/stepwise/modeler/rna/util.hh:302

    C++ signature :
        void remove_all_virtual_phosphates(core::pose::Pose {lvalue})

remove_chain_break_variants( (Pose)pose, (int)cutpoint) -> None :
    protocols/stepwise/modeler/rna/util.hh:224

    C++ signature :
        void remove_chain_break_variants(core::pose::Pose {lvalue},unsigned long)

remove_file( (str)file_name) -> None :
    protocols/stepwise/modeler/rna/util.hh:148

    C++ signature :
        void remove_file(std::string)

remove_virtual_O2Prime_hydrogen( (Pose)pose) -> bool :
    protocols/stepwise/modeler/rna/util.hh:160

    C++ signature :
        bool remove_virtual_O2Prime_hydrogen(core::pose::Pose {lvalue})

rescale_scorefxn( (__CPP_ScoreFunction__)starting_scorefxn, (float)scaling_factor) -> ScoreFunction :
    protocols/stepwise/modeler/rna/util.hh:266

    C++ signature :
        boost::shared_ptr<core::scoring::ScoreFunction> rescale_scorefxn(boost::shared_ptr<core::scoring::ScoreFunction>,double)

rmsd_over_residue_list( (Pose)pose1, (Pose)pose2, (object)working_parameters_ [, (bool)ignore_virtual_atom=False]) -> float :
    protocols/stepwise/modeler/rna/util.hh:169

    C++ signature :
        double rmsd_over_residue_list(core::pose::Pose,core::pose::Pose,boost::shared_ptr<protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters const> [,bool=False])

rmsd_over_residue_list( (Pose)pose1, (Pose)pose2, (vector1_Size)residue_list, (map_Size_Size)full_to_sub, (object)is_prepend_map, (bool)verbose [, (bool)ignore_virtual_atom=False]) -> float :
    protocols/stepwise/modeler/rna/util.hh:166

    C++ signature :
        double rmsd_over_residue_list(core::pose::Pose,core::pose::Pose,utility::vector1<unsigned long, std::allocator<unsigned long> >,std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >,std::map<unsigned long, bool, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, bool> > >,bool [,bool=False])

set_CCD_torsions_to_zero( (Pose)pose, (int)five_prime_res) -> None :
    protocols/stepwise/modeler/rna/util.hh:251

    C++ signature :
        void set_CCD_torsions_to_zero(core::pose::Pose {lvalue},unsigned long)

set_difference( (object)copy_dofs_1, (object)copy_dofs_2) -> object :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:75

    C++ signature :
        utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> > set_difference(utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> >,utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> >)

set_union( (object)copy_dofs_1, (object)copy_dofs_2) -> object :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:78

    C++ signature :
        utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> > set_union(utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> >,utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> >)

setup_chain_break_variants( (Pose)pose, (int)cutpoint) -> None :
    protocols/stepwise/modeler/rna/util.hh:221

    C++ signature :
        void setup_chain_break_variants(core::pose::Pose {lvalue},unsigned long)

setup_suite_atom_id_map( (Pose)pose_1, (Pose)pose_2, (int)base_res_1, (int)base_res_2, (AtomID_Map_T_core_id_AtomID_T)atom_ID_map [, (bool)base_only=True]) -> None :
    protocols/stepwise/modeler/rna/util.hh:95

    C++ signature :
        void setup_suite_atom_id_map(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long,core::id::AtomID_Map<core::id::AtomID> {lvalue} [,bool=True])

setup_suite_atom_id_map( (Pose)pose_1, (Pose)pose_2, (int)base_res, (AtomID_Map_T_core_id_AtomID_T)atom_ID_map [, (bool)base_only=True]) -> None :
    protocols/stepwise/modeler/rna/util.hh:85

    C++ signature :
        void setup_suite_atom_id_map(core::pose::Pose,core::pose::Pose,unsigned long,core::id::AtomID_Map<core::id::AtomID> {lvalue} [,bool=True])

setup_suite_atom_id_map( (Residue)rsd_1, (Residue)rsd_2, (int)res_num_1, (int)res_num_2, (AtomID_Map_T_core_id_AtomID_T)atom_ID_map [, (bool)base_only=True]) -> None :
    protocols/stepwise/modeler/rna/util.hh:76

    C++ signature :
        void setup_suite_atom_id_map(core::conformation::Residue,core::conformation::Residue,unsigned long,unsigned long,core::id::AtomID_Map<core::id::AtomID> {lvalue} [,bool=True])

setup_suite_atom_id_map( (Residue)rsd_1, (Residue)rsd_2, (AtomID_Map_T_core_id_AtomID_T)atom_ID_map [, (bool)base_only=True]) -> None :
    protocols/stepwise/modeler/rna/util.hh:66

    C++ signature :
        void setup_suite_atom_id_map(core::conformation::Residue,core::conformation::Residue,core::id::AtomID_Map<core::id::AtomID> {lvalue} [,bool=True])

show_scorefxn_weight_lines( (__CPP_ScoreFunction__)scorefxn, (str)title) -> None :
    protocols/stepwise/modeler/rna/util.hh:269

    C++ signature :
        void show_scorefxn_weight_lines(boost::shared_ptr<core::scoring::ScoreFunction>,std::string)

sort_copy_dofs( (object)copy_dofs) -> None :
    protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh:84

    C++ signature :
        void sort_copy_dofs(utility::vector1<protocols::stepwise::modeler::rna::Residue_info, std::allocator<protocols::stepwise::modeler::rna::Residue_info> > {lvalue})

sort_seq_num_list( (vector1_Size)seq_num_list) -> None :
    protocols/stepwise/modeler/rna/util.hh:140

    C++ signature :
        void sort_seq_num_list(utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue})

string_to_int( (str)input_string) -> int :
    protocols/stepwise/modeler/rna/util.hh:129

    C++ signature :
        unsigned long string_to_int(std::string)

string_to_real( (str)input_string) -> float :
    protocols/stepwise/modeler/rna/util.hh:132

    C++ signature :
        double string_to_real(std::string)

suite_rmsd( (Pose)pose1, (Pose)pose2, (int)seq_num, (bool)prepend_res [, (bool)ignore_virtual_atom=False]) -> float :
    protocols/stepwise/modeler/rna/util.hh:163

    C++ signature :
        double suite_rmsd(core::pose::Pose,core::pose::Pose,unsigned long,bool [,bool=False])

suite_square_deviation( (Pose)pose1, (Pose)pose2, (bool)prepend_res, (int)moving_res_1, (int)moving_res_2, (int)atom_count, (float)sum_sd, (bool)verbose, (bool)ignore_virtual_atom) -> None :
    protocols/stepwise/modeler/rna/util.hh:196

    C++ signature :
        void suite_square_deviation(core::pose::Pose,core::pose::Pose,bool,unsigned long,unsigned long,unsigned long {lvalue},double {lvalue},bool,bool)

tokenize( (str)str, (str)delimiters) -> vector1_string :
    protocols/stepwise/modeler/rna/util.hh:135

    C++ signature :
        utility::vector1<std::string, std::allocator<std::string> > tokenize(std::string,std::string)

virtualize_free_rna_moieties( (Pose)pose) -> None :
    protocols/stepwise/modeler/rna/util.hh:315

    C++ signature :
        void virtualize_free_rna_moieties(core::pose::Pose {lvalue})