Module _protocols_dna_

add_constraints_from_file( (Pose)pose) -> None :
    protocols/dna/util.hh:231

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

argrot_dna_dis2( (Pose)pose, (int)presid, (Residue)pres, (Residue)dres, (float)threshold [, (bool)base_only=False]) -> float :
    arginine rotamer sweep at a protein residue to see if it should be considered a (potentially) 'dna-contacting' residue
    ashworth
    

    C++ signature :
        double argrot_dna_dis2(core::pose::Pose,unsigned long,core::conformation::Residue,core::conformation::Residue,double [,bool=False])

    protocols/dna/util.hh:202

    C++ signature :
        void checkpoint_cleanup()

Returns: None :

close_to_dna( (Residue)pres, (Residue)dres, (float)cut2 [, (bool)base_only=False]) -> bool :
    checks c-beta (except glycine) to base atom-atom distances, not including ribose or phosphate backbone.
    ashworth
    

    C++ signature :
        bool close_to_dna(core::conformation::Residue,core::conformation::Residue,double [,bool=False])

contact_distance2( (object)a_begin, (object)a_end, (object)b_begin, (object)b_end [, (float)threshold=0.0]) -> float :
    distance check for contact between two sets of atoms
    ashworth
    

    C++ signature :
        double contact_distance2(__gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >,__gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >,__gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >,__gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > > [,double=0.0])

design_residues_list( (object)design_residues, (Pose)pose, (PackerTask)ptask) -> None :
    protocols/dna/util.hh:141

    C++ signature :
        void design_residues_list(std::list<protocols::dna::PositionType, std::allocator<protocols::dna::PositionType> > {lvalue},core::pose::Pose,core::pack::task::PackerTask)

dna_base_partner( (AA)na) -> AA :
    protocols/dna/util.hh:109

    C++ signature :
        core::chemical::AA dna_base_partner(core::chemical::AA)

dna_comp_name_str( (str)dna) -> str :
    also consider using the dna_base_partner function below
    ashworth
    

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

dna_full_name3( (str)name3) -> str :
    intended to convert any DNA "threeletter code" into the full three-letter code. Note that this does not (necessarily) return the same thing as residue_type::name3 (which returns "  N" format as of Dec 2008)
    

    C++ signature :
        std::string dna_full_name3(std::string)

find_basepairs( (Pose)pose, (DnaChains)dna_chains [, (bool)include_unpaired=True]) -> None :
    DnaChains version, adapted from pbradley's code.  More paranoid geometry checks, in order to allow highly distorted basepairs without making mistakes
    ashworth
    

    C++ signature :
        void find_basepairs(core::pose::Pose,protocols::dna::DnaChains {lvalue} [,bool=True])

load_checkpoint( (Pose)pose, (int)iter) -> None :
    protocols/dna/util.hh:201

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

load_dna_design_defs_from_file( (object)defs, (str)filename, (str)pdb_prefix) -> None :
    protocols/dna/util.hh:220

    C++ signature :
        void load_dna_design_defs_from_file(utility::vector1<boost::shared_ptr<protocols::dna::DnaDesignDef>, std::allocator<boost::shared_ptr<protocols::dna::DnaDesignDef> > > {lvalue},std::string,std::string)

load_dna_design_defs_from_options( (object)defs, (str)pdb_prefix) -> None :
    protocols/dna/util.hh:226

    C++ signature :
        void load_dna_design_defs_from_options(utility::vector1<boost::shared_ptr<protocols::dna::DnaDesignDef>, std::allocator<boost::shared_ptr<protocols::dna::DnaDesignDef> > > {lvalue},std::string)

load_dna_design_defs_from_strings( (object)defs, (vector1_string)str_defs) -> None :
    loads command-line dna design definitions (shorthand alternative to using resfile)
    option value is string vector
      i.e. -dna_defs C.-6 C.-5
      or   -dna_defs C.-6.GUA C.-5.CYT
    ashworth
    

    C++ signature :
        void load_dna_design_defs_from_strings(utility::vector1<boost::shared_ptr<protocols::dna::DnaDesignDef>, std::allocator<boost::shared_ptr<protocols::dna::DnaDesignDef> > > {lvalue},utility::vector1<std::string, std::allocator<std::string> >)

make_base_pair_aware_fold_tree( (Pose)pose) -> FoldTree :
    protocols/dna/util.hh:236

    C++ signature :
        core::kinematics::FoldTree make_base_pair_aware_fold_tree(core::pose::Pose)

make_sequence_combinations( (object)seqset_iter, (vector1_Size)seq_indices, (PackerTask)ptask, (object)sequence, (object)sequences) -> None :
    protocols/dna/util.hh:150

    C++ signature :
        void make_sequence_combinations(__gnu_cxx::__normal_iterator<unsigned long const*, std::vector<unsigned long, std::allocator<unsigned long> > >,utility::vector1<unsigned long, std::allocator<unsigned long> >,boost::shared_ptr<core::pack::task::PackerTask const>,std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > > {lvalue},utility::vector1<std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > >, std::allocator<std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > > > > {lvalue})

make_single_mutants( (object)sequence, (PackerTask)ptask, (object)sequences) -> None :
    make a list of all single mutants from a base sequence
    ashworth
    

    C++ signature :
        void make_single_mutants(std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > >,boost::shared_ptr<core::pack::task::PackerTask const>,utility::vector1<std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > >, std::allocator<std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > > > > {lvalue})

make_subdirs( (str)) -> None :
    protocols/dna/PDBOutput.hh:98

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

not_already_connected( (Pose)pose, (int)num_jumps, (str)this_chain, (str)other_chain, (object)jump_pairs) -> bool :
    protocols/dna/util.hh:245

    C++ signature :
        bool not_already_connected(core::pose::Pose,unsigned long,char,char,ObjexxFCL::FArray2D<int> {lvalue})

print_sequence_pdb_nums( (object), (Pose), (OStream)) -> None :
    protocols/dna/util.hh:167

    C++ signature :
        void print_sequence_pdb_nums(std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > >,core::pose::Pose,std::ostream {lvalue})

print_sequences_pdb_nums( (object), (Pose), (OStream)) -> None :
    protocols/dna/util.hh:173

    C++ signature :
        void print_sequences_pdb_nums(utility::vector1<std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > >, std::allocator<std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > > > >,core::pose::Pose,std::ostream {lvalue})

restrict_dna_rotamers( (__CPP_RotamerSets__)rotsets, (object)seq, (vector0_T_int_std_allocator_T_int_T__T)rot_to_pack) -> None :
    for packing a single DNA sequence out of a multi-DNA-sequence RotamerSet
    ashworth
    

    C++ signature :
        void restrict_dna_rotamers(boost::shared_ptr<core::pack::rotamer_set::RotamerSets const>,std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > >,utility::vector0<int, std::allocator<int> > {lvalue})

restrict_to_single_sequence( (__CPP_RotamerSets__)rotamer_sets, (object)single_sequence, (vector0_T_int_std_allocator_T_int_T__T)rot_to_pack) -> None :
    for packing a single sequence out of a RotamerSets that (potentially) represents sequence variability
    ashworth
    

    C++ signature :
        void restrict_to_single_sequence(boost::shared_ptr<core::pack::rotamer_set::RotamerSets const>,utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > >,utility::vector0<int, std::allocator<int> > {lvalue})

seq_pdb_str( (object), (Pose)) -> str :
    protocols/dna/util.hh:161

    C++ signature :
        std::string seq_pdb_str(std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > >,core::pose::Pose)

seq_to_str( (object)seq) -> str :
    protocols/dna/util.hh:154

    C++ signature :
        std::string seq_to_str(std::map<unsigned long, boost::shared_ptr<core::chemical::ResidueType const>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, boost::shared_ptr<core::chemical::ResidueType const> > > >)

set_base_segment_chainbreak_constraints( (Pose)pose, (int)this_base, (int)end_base) -> None :
    protocols/dna/util.hh:253

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

substitute_residue( (Pose)pose, (int)index, (ResidueType)new_type) -> None :
    protocols/dna/util.hh:198

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

write_checkpoint( (Pose)pose, (int)iter) -> None :
    protocols/dna/util.hh:200

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

z_axis_dist( (Residue)pres, (Residue)dres) -> float :
    A sanity check for the arginine rotamer screen. Can prevent the design of positions that are best left alone because they are too far away along the helical axis ('laterally').
    ashworth
    

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