Module _core_pose_rna_

apply_Aform_torsions( (Pose)pose, (int)n) -> None :
    core/pose/rna/util.hh:139

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

apply_ideal_c2endo_sugar_coords( (Pose)pose, (int)i) -> None :
    core/pose/rna/util.hh:105

    C++ signature :
        void apply_ideal_c2endo_sugar_coords(core::pose::Pose {lvalue},unsigned long)

apply_non_main_chain_sugar_coords( (vector1_xyzVector_Real)non_main_chain_sugar_coords, (Pose)pose, (Pose)reference_pose, (int)i) -> None :
    core/pose/rna/util.hh:81

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

apply_pucker( (Pose)pose, (int)i [, (PuckerState)pucker_state=rosetta.core.chemical.rna._core_chemical_rna_.PuckerState.ANY_PUCKER [, (bool)skip_same_state=False [, (bool)idealize_coord=True]]]) -> None :
    core/pose/rna/util.hh:99

    C++ signature :
        void apply_pucker(core::pose::Pose {lvalue},unsigned long [,core::chemical::rna::PuckerState=rosetta.core.chemical.rna._core_chemical_rna_.PuckerState.ANY_PUCKER [,bool=False [,bool=True]]])

apply_virtual_rna_residue_variant_type( (Pose)pose, (int)seq_num, (vector1_Size)working_cutpoint_closed_list [, (bool)apply_check=True]) -> None :
    core/pose/rna/util.hh:128

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

apply_virtual_rna_residue_variant_type( (Pose)pose, (int)seq_num [, (bool)apply_check=True]) -> None :
    core/pose/rna/util.hh:124

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

assign_pucker( (Pose)pose, (int)rsd_id) -> PuckerState :
    core/pose/rna/util.hh:91

    C++ signature :
        core::chemical::rna::PuckerState assign_pucker(core::pose::Pose,unsigned long)

classify_base_pairs( (Pose)pose, (object)base_pair_list, (vector1_bool)is_bulged) -> None :
    core/pose/rna/RNA_BasePairClassifier.hh:35

    C++ signature :
        void classify_base_pairs(core::pose::Pose,utility::vector1<core::pose::rna::BasePair, std::allocator<core::pose::rna::BasePair> > {lvalue},utility::vector1<bool, std::allocator<bool> > {lvalue})

correctly_position_cutpoint_phosphate_torsions( (Pose)current_pose, (int)five_prime_chainbreak) -> None :
    core/pose/rna/util.hh:108

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

figure_out_reasonable_rna_fold_tree( (Pose)pose) -> None :
    core/pose/rna/util.hh:36

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

fix_sugar_coords( (vector1_string)atoms_for_which_we_need_new_dofs, (vector1_xyzVector_Real)non_main_chain_sugar_coords, (Pose)pose, (Pose)reference_pose, (int)i) -> None :
    core/pose/rna/util.hh:68

    C++ signature :
        void fix_sugar_coords(utility::vector1<std::string, std::allocator<std::string> >,utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > >,core::pose::Pose {lvalue},core::pose::Pose,unsigned long)

fix_sugar_coords_WORKS_BUT_SLOW( (vector1_string)atoms_for_which_we_need_new_dofs, (object)which_dofs, (vector1_xyzVector_Real)non_main_chain_sugar_coords, (Pose)pose, (int)i) -> None :
    core/pose/rna/util.hh:53

    C++ signature :
        void fix_sugar_coords_WORKS_BUT_SLOW(utility::vector1<std::string, std::allocator<std::string> >,utility::vector1<utility::vector1<core::id::DOF_Type, std::allocator<core::id::DOF_Type> >, std::allocator<utility::vector1<core::id::DOF_Type, std::allocator<core::id::DOF_Type> > > >,utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > >,core::pose::Pose {lvalue},unsigned long)

get_number_base_stacks( (Pose)pose_input) -> int :
    core/pose/rna/RNA_BasePairClassifier.hh:40

    C++ signature :
        unsigned long get_number_base_stacks(core::pose::Pose)

get_residue_base_state( (Pose)pose, (int)seq_num) -> ChiState :
    core/pose/rna/util.hh:142

    C++ signature :
        core::chemical::rna::ChiState get_residue_base_state(core::pose::Pose,unsigned long)

get_residue_pucker_state( (Pose)pose, (int)seq_num) -> PuckerState :
    core/pose/rna/util.hh:145

    C++ signature :
        core::chemical::rna::PuckerState get_residue_pucker_state(core::pose::Pose,unsigned long)

has_virtual_rna_residue_variant_type( (Pose)pose, (int)seq_num) -> bool :
    core/pose/rna/util.hh:136

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

initialize_atoms_for_which_we_need_new_dofs( (vector1_string)atoms_for_which_we_need_new_dofs, (Pose)pose, (int)i) -> None :
    core/pose/rna/util.hh:74

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

is_cutpoint_closed_atom( (Residue)rsd, (AtomID)id) -> bool :
    core/pose/rna/util.hh:112

    C++ signature :
        bool is_cutpoint_closed_atom(core::conformation::Residue,core::id::AtomID)

is_cutpoint_closed_torsion( (Pose)pose, (TorsionID)torsion_id) -> bool :
    core/pose/rna/util.hh:110

    C++ signature :
        bool is_cutpoint_closed_torsion(core::pose::Pose,core::id::TorsionID)

is_cutpoint_open( (Pose)pose, (int)i) -> bool :
    core/pose/rna/util.hh:42

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

is_rna_chainbreak( (Pose)pose, (int)i) -> bool :
    core/pose/rna/util.hh:45

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

is_torsion_valid( (Pose)pose, (TorsionID)torsion_id [, (bool)verbose=False [, (bool)skip_chainbreak_torsions=False]]) -> bool :
    core/pose/rna/util.hh:119

    C++ signature :
        bool is_torsion_valid(core::pose::Pose,core::id::TorsionID [,bool=False [,bool=False]])

mutate_position( (Pose)pose, (int)i, (str)new_seq) -> bool :
    core/pose/rna/util.hh:33

    C++ signature :
        bool mutate_position(core::pose::Pose {lvalue},unsigned long,char)

output_boolean( (str)tag, (bool)boolean) -> None :
    core/pose/rna/util.hh:114

    C++ signature :
        void output_boolean(std::string,bool)

prepare_scratch_residue( (Residue)scratch_rsd, (Residue)start_rsd, (vector1_xyzVector_Real)non_main_chain_sugar_coords, (Pose)pose) -> None :
    core/pose/rna/util.hh:60

    C++ signature :
        void prepare_scratch_residue(boost::shared_ptr<core::conformation::Residue> {lvalue},core::conformation::Residue,utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > >,core::pose::Pose)

print_torsion_info( (Pose)pose, (TorsionID)torsion_id) -> None :
    core/pose/rna/util.hh:116

    C++ signature :
        void print_torsion_info(core::pose::Pose,core::id::TorsionID)

remove_virtual_rna_residue_variant_type( (Pose)pose, (int)seq_num) -> None :
    core/pose/rna/util.hh:132

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

virtualize_5prime_phosphates( (Pose)pose) -> None :
    core/pose/rna/util.hh:39

    C++ signature :
        void virtualize_5prime_phosphates(core::pose::Pose {lvalue})