Module _protocols_motifs_

add_motif_bb_constraints( (__CPP_ConstraintSet__)cst_set, (Pose)pose, (int)this_pos, (Residue)inv_rotamer) -> None :
    protocols/motifs/motif_utils.hh:95

    C++ signature :
        void add_motif_bb_constraints(boost::shared_ptr<core::scoring::constraints::ConstraintSet>,core::pose::Pose {lvalue},unsigned long,core::conformation::Residue)

add_motif_sc_constraints( (__CPP_ConstraintSet__)cst_set, (Pose)pose, (int)this_pos, (Residue)inv_rotamer, (__CPP_Motif__)this_motif, (bool)is_it_forward) -> None :
    protocols/motifs/motif_utils.hh:104

    C++ signature :
        void add_motif_sc_constraints(boost::shared_ptr<core::scoring::constraints::ConstraintSet>,core::pose::Pose {lvalue},unsigned long,core::conformation::Residue,boost::shared_ptr<protocols::motifs::Motif const>,bool)

atom_specific_rms( (Residue)rsd1, (Residue)rsd2, (vector1_Size)atoms) -> float :
    protocols/motifs/motif_utils.hh:242

    C++ signature :
        double atom_specific_rms(core::conformation::Residue,core::conformation::Residue,utility::vector1<unsigned long, std::allocator<unsigned long> >)

atom_specific_rms( (Residue)rsd1, (Residue)rsd2, (vector1_string)atoms) -> float :
    protocols/motifs/motif_utils.hh:235

    C++ signature :
        double atom_specific_rms(core::conformation::Residue,core::conformation::Residue,utility::vector1<std::string, std::allocator<std::string> >)

backbone_stub_match( (Residue)r1, (Residue)r2) -> float :
    protocols/motifs/motif_utils.hh:87

    C++ signature :
        double backbone_stub_match(core::conformation::Residue,core::conformation::Residue)

bools_from_sizes( (int)nres, (vector1_Size)v) -> vector1_bool :
    protocols/motifs/motif_utils.hh:220

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

bpdefs2map( (Pose)pose, (object)targets) -> object :
    protocols/motifs/motif_utils.hh:176

    C++ signature :
        std::map<unsigned long, std::set<std::string, std::less<std::string>, std::allocator<std::string> >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, std::set<std::string, std::less<std::string>, std::allocator<std::string> > > > > bpdefs2map(core::pose::Pose,utility::vector1<boost::shared_ptr<protocols::dna::DnaDesignDef>, std::allocator<boost::shared_ptr<protocols::dna::DnaDesignDef> > >)

build_rotamers_lite( (Pose)pose, (int)rotamer_build_position, (vector1_bool)aa_info, (int)ex_ [, (bool)bump_check=True]) -> RotamerSet :
    protocols/motifs/motif_utils.hh:251

    C++ signature :
        boost::shared_ptr<core::pack::rotamer_set::RotamerSet> build_rotamers_lite(core::pose::Pose {lvalue},unsigned long,utility::vector1<bool, std::allocator<bool> >,unsigned long [,bool=True])

defs2allowedtypes( (Pose)pose, (object)targeted_dna) -> object :
    protocols/motifs/motif_utils.hh:164

    C++ signature :
        utility::vector1<std::pair<unsigned long, utility::vector1<std::string, std::allocator<std::string> > >, std::allocator<std::pair<unsigned long, utility::vector1<std::string, std::allocator<std::string> > > > > defs2allowedtypes(core::pose::Pose,utility::vector1<boost::shared_ptr<protocols::dna::DnaDesignDef>, std::allocator<boost::shared_ptr<protocols::dna::DnaDesignDef> > >)

defs2map( (Pose)pose, (object)targets) -> object :
    protocols/motifs/motif_utils.hh:170

    C++ signature :
        std::map<unsigned long, std::set<std::string, std::less<std::string>, std::allocator<std::string> >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, std::set<std::string, std::less<std::string>, std::allocator<std::string> > > > > defs2map(core::pose::Pose,utility::vector1<boost::shared_ptr<protocols::dna::DnaDesignDef>, std::allocator<boost::shared_ptr<protocols::dna::DnaDesignDef> > >)

defs2vector( (Pose)pose, (object)targeted_dna) -> vector1_Size :
    protocols/motifs/motif_utils.hh:158

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > defs2vector(core::pose::Pose,utility::vector1<boost::shared_ptr<protocols::dna::DnaDesignDef>, std::allocator<boost::shared_ptr<protocols::dna::DnaDesignDef> > >)

    protocols/motifs/motif_utils.hh:123

    C++ signature :
        protocols::motifs::MotifLibrary get_LigandMotifLibrary_user()

Returns: MotifLibrary :

    protocols/motifs/motif_utils.hh:120

    C++ signature :
        protocols::motifs::MotifLibrary get_MotifLibrary_user()

Returns: MotifLibrary :

get_filenames( (object)listnames) -> object :
    protocols/motifs/motif_utils.hh:209

    C++ signature :
        utility::vector1<utility::file::FileName, std::allocator<utility::file::FileName> > get_filenames(utility::vector1<utility::file::FileName, std::allocator<utility::file::FileName> >)

    protocols/motifs/motif_utils.hh:189

    C++ signature :
        utility::vector1<boost::shared_ptr<protocols::dna::DnaDesignDef>, std::allocator<boost::shared_ptr<protocols::dna::DnaDesignDef> > > get_motif_build_position_defs_user()

Returns: object :

get_motif_build_positions_user( (Pose)pose) -> vector1_Size :
    protocols/motifs/motif_utils.hh:186

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

get_target_position_map_make_dna_mutations( (Pose)pose) -> object :
    protocols/motifs/motif_utils.hh:141

    C++ signature :
        std::map<unsigned long, std::set<std::string, std::less<std::string>, std::allocator<std::string> >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, std::set<std::string, std::less<std::string>, std::allocator<std::string> > > > > get_target_position_map_make_dna_mutations(core::pose::Pose {lvalue})

get_target_positions_make_dna_mutations( (Pose)pose) -> vector1_Size :
    protocols/motifs/motif_utils.hh:136

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

    protocols/motifs/motif_utils.hh:126

    C++ signature :
        utility::vector1<boost::shared_ptr<core::conformation::Residue>, std::allocator<boost::shared_ptr<core::conformation::Residue> > > get_targetconformers_user()

Returns: object :

load_build_position_data( (BuildPosition)bp, (str)filename, (Pose)pose, (int)ligand_marker) -> None :
    protocols/motifs/motif_utils.hh:204

    C++ signature :
        void load_build_position_data(protocols::motifs::BuildPosition {lvalue},std::string,core::pose::Pose {lvalue},unsigned long)

load_build_position_data( (BuildPosition)bp, (str)filename, (Pose)pose) -> None :
    protocols/motifs/motif_utils.hh:196

    C++ signature :
        void load_build_position_data(protocols::motifs::BuildPosition {lvalue},std::string,core::pose::Pose {lvalue})

make_base_pair_mutation( (Pose)pose, (int)seqpos, (AA)na) -> None :
    protocols/motifs/motif_utils.hh:228

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

make_dna_mutations( (Pose)pose, (object)targeted_dna) -> None :
    protocols/motifs/motif_utils.hh:152

    C++ signature :
        void make_dna_mutations(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<protocols::dna::DnaDesignDef>, std::allocator<boost::shared_ptr<protocols::dna::DnaDesignDef> > >)

make_dna_mutations( (Pose)pose) -> None :
    protocols/motifs/motif_utils.hh:146

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

mutate_loops_for_search( (Pose)pose, (Loops)flex_regions) -> None :
    protocols/motifs/motif_utils.hh:110

    C++ signature :
        void mutate_loops_for_search(core::pose::Pose {lvalue},protocols::loops::Loops {lvalue})

mutate_position_vector_for_search( (Pose)pose, (vector1_Size)trim_positions) -> None :
    protocols/motifs/motif_utils.hh:116

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

name3_from_oneletter( (str)oneletter) -> str :
    protocols/motifs/motif_utils.hh:181

    C++ signature :
        std::string name3_from_oneletter(std::string)

parallel_base_test( (Residue)pose_dna, (Residue)motif_dna) -> float :
    protocols/motifs/motif_utils.hh:80

    C++ signature :
        double parallel_base_test(core::conformation::Residue,core::conformation::Residue)

setup_conformer_map( (object)conformerOPs) -> object :
    protocols/motifs/motif_utils.hh:131

    C++ signature :
        std::map<std::string, utility::vector1<boost::shared_ptr<core::conformation::Residue>, std::allocator<boost::shared_ptr<core::conformation::Residue> > >, std::less<std::string>, std::allocator<std::pair<std::string const, utility::vector1<boost::shared_ptr<core::conformation::Residue>, std::allocator<boost::shared_ptr<core::conformation::Residue> > > > > > setup_conformer_map(utility::vector1<boost::shared_ptr<core::conformation::Residue>, std::allocator<boost::shared_ptr<core::conformation::Residue> > >)

single_ligand_motif_from_stream( (std_istream)motif_info) -> SingleMotif :
    protocols/motifs/motif_utils.hh:72

    C++ signature :
        boost::shared_ptr<protocols::motifs::SingleMotif> single_ligand_motif_from_stream(std::istream {lvalue})

single_motif_from_filename( (FileName)motif_filename) -> SingleMotif :
    protocols/motifs/motif_utils.hh:56

    C++ signature :
        boost::shared_ptr<protocols::motifs::SingleMotif> single_motif_from_filename(utility::file::FileName)

single_motif_from_stream( (std_istream)motif_info) -> SingleMotif :
    protocols/motifs/motif_utils.hh:67

    C++ signature :
        boost::shared_ptr<protocols::motifs::SingleMotif> single_motif_from_stream(std::istream {lvalue})

single_motif_from_stream( (object)motif_info) -> SingleMotif :
    protocols/motifs/motif_utils.hh:62

    C++ signature :
        boost::shared_ptr<protocols::motifs::SingleMotif> single_motif_from_stream(utility::io::izstream {lvalue})

single_residue_from_stream( (object)residueinfo) -> Residue :
    protocols/motifs/motif_utils.hh:214

    C++ signature :
        boost::shared_ptr<core::conformation::Residue> single_residue_from_stream(utility::io::izstream {lvalue})