Module _protocols_farna_

assert_phosphate_nomenclature_matches_mini( (Pose)pose) -> None :
    protocols/farna/util.hh:77

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

check_base_pair( (Pose)pose, (object)struct_type) -> None :
    protocols/farna/util.hh:94

    C++ signature :
        void check_base_pair(core::pose::Pose {lvalue},ObjexxFCL::FArray1D<int> {lvalue})

compare_RNA_char( (str)char1, (str)char2) -> bool :
    protocols/farna/util.hh:109

    C++ signature :
        bool compare_RNA_char(char,char)

compare_RNA_secstruct( (str)char1, (str)char2) -> bool :
    protocols/farna/util.hh:112

    C++ signature :
        bool compare_RNA_secstruct(char,char)

convert_based_on_match_type( (str)RNA_string, (int)type) -> str :
    protocols/farna/util.hh:106

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

create_rna_vall_torsions( (Pose)pose, (str)outfile, (vector1_Size)exclude_res_list) -> None :
    protocols/farna/util.hh:68

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

create_rna_vall_torsions( (Pose)pose, (object)torsions_out, (vector1_Size)exclude_res_list) -> None :
    protocols/farna/util.hh:63

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

ensure_phosphate_nomenclature_matches_mini( (Pose)pose) -> None :
    protocols/farna/util.hh:80

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

export_packer_results( (vector1_pair_Real_string)results, (vector1_PoseOP)pose_list, (__CPP_ScoreFunction__)scorefxn, (str)outfile [, (bool)dumo=False]) -> None :
    protocols/farna/util.hh:91

    C++ signature :
        void export_packer_results(utility::vector1<std::pair<double, std::string>, std::allocator<std::pair<double, std::string> > > {lvalue},utility::vector1<boost::shared_ptr<core::pose::Pose>, std::allocator<boost::shared_ptr<core::pose::Pose> > >,boost::shared_ptr<core::scoring::ScoreFunction> {lvalue},std::string [,bool=False])

figure_out_base_pair_partner( (Pose)pose, (map_Size_Size)partner [, (bool)strict=True]) -> None :
    protocols/farna/util.hh:162

    C++ signature :
        void figure_out_base_pair_partner(core::pose::Pose {lvalue},std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > > {lvalue} [,bool=True])

figure_out_secstruct( (Pose)pose) -> None :
    protocols/farna/util.hh:48

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

get_base_pairing_info( (Pose)pose, (int)seqpos, (str)secstruct, (object)edge_is_base_pairing) -> None :
    protocols/farna/util.hh:54

    C++ signature :
        void get_base_pairing_info(core::pose::Pose,unsigned long,char {lvalue},ObjexxFCL::FArray1D<bool> {lvalue})

get_base_pairing_list( (Pose)pose, (vector1_pair_Size_Size)base_pairing_list) -> None :
    protocols/farna/util.hh:58

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

get_op2_op1_sign( (Pose)pose, (int)res_num) -> float :
    protocols/farna/util.hh:74

    C++ signature :
        double get_op2_op1_sign(core::pose::Pose,unsigned long)

get_op2_op1_sign( (Pose)pose) -> float :
    protocols/farna/util.hh:71

    C++ signature :
        double get_op2_op1_sign(core::pose::Pose)

get_rigid_body_jumps( (Pose)pose) -> vector1_Size :
    protocols/farna/util.hh:142

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

get_rna_secstruct( (Pose)pose) -> str :
    protocols/farna/RNA_SecStructInfo.hh:97

    C++ signature :
        std::string get_rna_secstruct(core::pose::Pose {lvalue})

get_sugar_centroid( (Residue)rsd) -> xyzVector_Real :
    protocols/farna/util.hh:115

    C++ signature :
        numeric::xyzVector<double> get_sugar_centroid(core::conformation::Residue)

involved_in_phosphate_torsion( (str)atomname) -> bool :
    protocols/farna/util.hh:154

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

is_num_in_list( (int)i, (vector1_Size)list) -> bool :
    protocols/farna/util.hh:136

    C++ signature :
        bool is_num_in_list(unsigned long,utility::vector1<unsigned long, std::allocator<unsigned long> >)

let_rigid_body_jumps_move( (MoveMap)movemap, (Pose)pose [, (bool)move_first_rigid_body=False]) -> bool :
    protocols/farna/util.hh:147

    C++ signature :
        bool let_rigid_body_jumps_move(core::kinematics::MoveMap {lvalue},core::pose::Pose [,bool=False])

make_coarse_pose( (Pose)pose, (Pose)coarse_pose) -> None :
    protocols/farna/util.hh:121

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

make_extended_coarse_pose( (Pose)coarse_pose, (str)full_sequence) -> None :
    protocols/farna/util.hh:118

    C++ signature :
        void make_extended_coarse_pose(core::pose::Pose {lvalue},std::string)

make_phosphate_nomenclature_matches_mini( (Pose)pose) -> None :
    protocols/farna/util.hh:83

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

moveable_jump( (int)jump_pos1, (int)jump_pos2, (AllowInsert)allow_insert) -> bool :
    protocols/farna/util.hh:181

    C++ signature :
        bool moveable_jump(unsigned long,unsigned long,protocols::toolbox::AllowInsert)

moveable_jump( (AtomID)jump_atom_id1, (AtomID)jump_atom_id2, (AllowInsert)allow_insert) -> bool :
    protocols/farna/util.hh:176

    C++ signature :
        bool moveable_jump(core::id::AtomID,core::id::AtomID,protocols::toolbox::AllowInsert)

possible_root( (FoldTree)f, (int)n) -> bool :
    protocols/farna/util.hh:133

    C++ signature :
        bool possible_root(core::kinematics::FoldTree,unsigned long)

print_hbonds( (Pose)pose) -> None :
    protocols/farna/util.hh:171

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

print_internal_coords( (Pose)pose) -> None :
    protocols/farna/util.hh:124

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

process_input_file( (str)silent_file, (vector1_PoseOP)pose_list [, (bool)is_pdb=False [, (bool)coarse_rna=False]]) -> None :
    protocols/farna/util.hh:168

    C++ signature :
        void process_input_file(std::string,utility::vector1<boost::shared_ptr<core::pose::Pose>, std::allocator<boost::shared_ptr<core::pose::Pose> > > {lvalue} [,bool=False [,bool=False]])

remove_cutpoint_closed( (Pose)pose, (int)i) -> None :
    protocols/farna/util.hh:127

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

remove_cutpoints_closed( (Pose)pose) -> None :
    protocols/farna/util.hh:130

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

set_output_res_num( (Pose)extended_pose, (vector1_Size)output_res_num) -> None :
    protocols/farna/util.hh:158

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

set_rna_secstruct( (Pose)pose, (str)rna_secstruct_string) -> None :
    protocols/farna/RNA_SecStructInfo.hh:100

    C++ signature :
        void set_rna_secstruct(core::pose::Pose {lvalue},std::string)

setup_base_pair_constraints( (Pose)pose, (vector1_pair_Size_Size)pairings [, (float)suppress_factor=1.0]) -> None :
    protocols/farna/util.hh:100

    C++ signature :
        void setup_base_pair_constraints(core::pose::Pose {lvalue},utility::vector1<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > [,double=1.0])

setup_coarse_chainbreak_constraints( (Pose)pose, (int)n) -> None :
    protocols/farna/util.hh:103

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

translate_virtual_anchor_to_first_rigid_body( (Pose)pose) -> None :
    protocols/farna/util.hh:150

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

virtualize_bulges( (Pose)input_pose, (vector1_Size)in_allow_bulge_res_list, (__CPP_ScoreFunction__)scorefxn, (str)tag, (bool)allow_pre_virtualize, (bool)allow_consecutive_bulges, (bool)verbose) -> int :
    protocols/farna/util.hh:190

    C++ signature :
        unsigned long virtualize_bulges(core::pose::Pose {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> >,boost::shared_ptr<core::scoring::ScoreFunction const>,std::string,bool,bool,bool)

MATCH_ALL

Value:

rosetta.protocols.farna._protocols_farna_._RNA_MatchType_.MATCH_ALL

MATCH_EXACT

Value:

rosetta.protocols.farna._protocols_farna_._RNA_MatchType_.MATCH_EXACT

MATCH_YR

Value:

rosetta.protocols.farna._protocols_farna_._RNA_MatchType_.MATCH_YR