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| static basic::Tracer | protocols::dna::TR ("protocols.dna.util", basic::t_info) |
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| bool | protocols::dna::close_to_dna (Residue const &pres, Residue const &dres, Real threshold, bool base_only) |
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| Real | protocols::dna::argrot_dna_dis2 (pose::Pose const &pose, core::Size presid, Residue const &, Residue const &dres, Real threshold, bool base_only) |
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| Real | protocols::dna::contact_distance2 (Atoms::const_iterator a_begin, Atoms::const_iterator a_end, Atoms::const_iterator b_begin, Atoms::const_iterator b_end, Real threshold) |
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| Real | protocols::dna::z_axis_dist (Residue const &pres, Residue const &dres) |
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| std::string | protocols::dna::dna_comp_name_str (std::string const &dna) |
| | also consider using the dna_base_partner function below More...
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| std::string | protocols::dna::dna_full_name3 (std::string const &name3) |
| | 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) More...
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| chemical::AA | protocols::dna::dna_base_partner (chemical::AA const &na) |
| | helper function More...
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| void | protocols::dna::find_basepairs (pose::Pose const &pose, DnaChains &dna_chains, bool include_unpaired) |
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| void | protocols::dna::make_sequence_combinations (utility::vector1< core::Size >::const_iterator seqset_iter, utility::vector1< core::Size > const &seq_indices, task::PackerTaskCOP ptask, ResTypeSequence &sequence, ResTypeSequences &sequences) |
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| void | protocols::dna::make_single_mutants (ResTypeSequence const &sequence, task::PackerTaskCOP ptask, ResTypeSequences &sequences) |
| | make a list of all single mutants from a base sequence More...
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| void | protocols::dna::design_residues_list (std::list< PositionType > &design_residues, pose::Pose const &pose, task::PackerTask const &ptask) |
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| std::ostream & | protocols::dna::operator<< (std::ostream &os, ResTypeSequence const &seq) |
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| std::string | protocols::dna::seq_to_str (ResTypeSequence const &seq) |
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| std::ostream & | protocols::dna::operator<< (std::ostream &os, ResTypeSequences const &seqs) |
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| std::string | protocols::dna::seq_pdb_str (ResTypeSequence const &seq, pose::Pose const &pose) |
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| void | protocols::dna::print_sequence_pdb_nums (ResTypeSequence const &seq, pose::Pose const &pose, std::ostream &os) |
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| void | protocols::dna::print_sequences_pdb_nums (ResTypeSequences const &seqs, pose::Pose const &pose, std::ostream &os) |
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| void | protocols::dna::restrict_dna_rotamers (RotamerSetsCOP rotamer_sets, ResTypeSequence const &seq, utility::vector0< int > &rot_to_pack) |
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| void | protocols::dna::restrict_to_single_sequence (rotamer_set::RotamerSetsCOP rotamer_sets, vector1< ResidueTypeCOP > const &single_sequence, utility::vector0< int > &rot_to_pack) |
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| void | protocols::dna::substitute_residue (pose::Pose &pose, core::Size index, ResidueType const &new_type) |
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| void | protocols::dna::write_checkpoint (pose::Pose &pose, core::Size iter) |
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| void | protocols::dna::load_checkpoint (pose::Pose &pose, core::Size &iter) |
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| void | protocols::dna::checkpoint_cleanup () |
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| void | protocols::dna::load_dna_design_defs_from_strings (DnaDesignDefOPs &defs, Strings const &str_defs) |
| | 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 More...
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| void | protocols::dna::load_dna_design_defs_from_file (DnaDesignDefOPs &defs, std::string const &filename, std::string const &pdb_prefix) |
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| void | protocols::dna::load_dna_design_defs_from_options (DnaDesignDefOPs &defs, std::string const &pdb_prefix) |
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| void | protocols::dna::add_constraints_from_file (pose::Pose &pose) |
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| kinematics::FoldTree | protocols::dna::make_base_pair_aware_fold_tree (pose::Pose const &pose) |
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| bool | protocols::dna::not_already_connected (pose::Pose const &pose, core::Size const num_jumps, char const this_chain, char const other_chain, ObjexxFCL::FArray2D< core::Size > &jump_pairs) |
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| void | protocols::dna::set_base_segment_chainbreak_constraints (pose::Pose &pose, core::Size const start_base, core::Size const end_base) |
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| void | protocols::dna::show_dna_geometry (core::pose::Pose const &pose, std::ostream &out) |
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| void | protocols::dna::show_dna_geometry_extra_details (pose::Pose const &pose, std::string tag, std::ostream &out) |
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