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util.hh File Reference
#include <protocols/dna/DnaChains.fwd.hh>
#include <protocols/dna/typedefs.hh>
#include <protocols/dna/DnaDesignDef.fwd.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Atom.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pack/rotamer_set/RotamerSets.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/vector0.fwd.hh>
#include <utility/vector1.hh>
#include <list>
#include <iosfwd>

Classes

class  protocols::dna::PositionType
 basic struct for remembering position/type information before/during/after design More...
 

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::dna
 

Constant Groups

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::dna
 

Typedefs

typedef utility::vector1
< PositionType > 
protocols::dna::PositionTypes
 

Functions

bool protocols::dna::close_to_dna (Residue const &pres, Residue const &dres, Real threshold, bool base_only)
 
Real protocols::dna::argrot_dna_dis2 (pose::Pose const &pose, Size presid, Residue const &pres, Residue const &dres, Real threshold, bool base_only)
 
core::Real protocols::dna::contact_distance2 (core::conformation::Atoms::const_iterator a_begin, core::conformation::Atoms::const_iterator a_end, core::conformation::Atoms::const_iterator b_begin, core::conformation::Atoms::const_iterator b_end, core::Real threshold=0.0)
 
Real protocols::dna::z_axis_dist (Residue const &pres, Residue const &dres)
 
std::string protocols::dna::dna_comp_name_str (std::string const &dna)
 also consider using the dna_base_partner function below More...
 
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...
 
chemical::AA protocols::dna::dna_base_partner (chemical::AA const &na)
 helper function More...
 
void protocols::dna::find_basepairs (pose::Pose const &pose, DnaChains &dna_chains, bool include_unpaired)
 
void protocols::dna::make_single_mutants (ResTypeSequence const &sequence, core::pack::task::PackerTaskCOP ptask, ResTypeSequences &sequences)
 
void protocols::dna::design_residues_list (std::list< PositionType > &design_residues, core::pose::Pose const &pose, core::pack::task::PackerTask const &ptask)
 
void protocols::dna::make_sequence_combinations (utility::vector1< core::Size >::const_iterator seqset_iter, utility::vector1< core::Size > const &seq_indices, core::pack::task::PackerTaskCOP ptask, ResTypeSequence &sequence, ResTypeSequences &sequences)
 
std::ostream & protocols::dna::operator<< (std::ostream &os, ResTypeSequence const &seq)
 
std::string protocols::dna::seq_to_str (ResTypeSequence const &seq)
 
std::ostream & protocols::dna::operator<< (std::ostream &os, ResTypeSequences const &seqs)
 
std::string protocols::dna::seq_pdb_str (ResTypeSequence const &seq, pose::Pose const &pose)
 
void protocols::dna::print_sequence_pdb_nums (ResTypeSequence const &seq, pose::Pose const &pose, std::ostream &os)
 
void protocols::dna::print_sequences_pdb_nums (ResTypeSequences const &seqs, pose::Pose const &pose, std::ostream &os)
 
void protocols::dna::restrict_dna_rotamers (core::pack::rotamer_set::RotamerSetsCOP rotsets, ResTypeSequence const &seq, utility::vector0< int > &rot_to_pack)
 
void protocols::dna::restrict_to_single_sequence (core::pack::rotamer_set::RotamerSetsCOP rotamer_sets, utility::vector1< core::chemical::ResidueTypeCOP > const &single_sequence, utility::vector0< int > &rot_to_pack)
 
void protocols::dna::substitute_residue (pose::Pose &pose, Size index, ResidueType const &new_type)
 
void protocols::dna::write_checkpoint (pose::Pose &pose, Size iter)
 
void protocols::dna::load_checkpoint (pose::Pose &pose, Size &iter)
 
void protocols::dna::checkpoint_cleanup ()
 
void protocols::dna::load_dna_design_defs_from_strings (DnaDesignDefOPs &defs, utility::vector1< std::string > const &str_defs)
 
void protocols::dna::load_dna_design_defs_from_file (DnaDesignDefOPs &defs, std::string const &filename, std::string const &pdb_prefix)
 
void protocols::dna::load_dna_design_defs_from_options (DnaDesignDefOPs &defs, std::string pdb_prefix)
 
void protocols::dna::add_constraints_from_file (pose::Pose &pose)
 
kinematics::FoldTree protocols::dna::make_base_pair_aware_fold_tree (pose::Pose const &pose)
 
bool protocols::dna::not_already_connected (pose::Pose const &pose, Size const num_jumps, char const this_chain, char const other_chain, ObjexxFCL::FArray2D_int &jump_pairs)
 
void protocols::dna::set_base_segment_chainbreak_constraints (pose::Pose &pose, core::Size const start_base, core::Size const end_base)