util.cc File Reference

#include <protocols/dna/util.hh>
#include <protocols/dna/DnaChains.hh>
#include <protocols/dna/DnaDesignDef.hh>
#include <protocols/dna/DNAParameters.hh>
#include <core/conformation/Atom.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/graph/Graph.hh>
#include <basic/options/option.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSets.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/dna/base_geometry.hh>
#include <basic/Tracer.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/vector1.hh>
#include <utility/vector0.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <algorithm>
#include <iostream>
#include <sstream>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/dna.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <core/chemical/VariantType.hh>
#include <core/import_pose/import_pose.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>

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

Typedefs
typedef numeric::xyzVector < core::Real >	xyzVec
typedef utility::vector1 < std::string >	protocols::dna::Strings

Functions
static THREAD_LOCAL basic::Tracer	protocols::dna::TR ("protocols.dna.util", basic::t_info)
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)
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)
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_sequence_combinations (utility::vector1< Size >::const_iterator seqset_iter, utility::vector1< Size > const &seq_indices, task::PackerTaskCOP ptask, ResTypeSequence &sequence, ResTypeSequences &sequences)
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...
void	protocols::dna::design_residues_list (std::list< PositionType > &design_residues, pose::Pose const &pose, task::PackerTask const &ptask)
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 (RotamerSetsCOP rotamer_sets, ResTypeSequence const &seq, utility::vector0< int > &rot_to_pack)
void	protocols::dna::restrict_to_single_sequence (rotamer_set::RotamerSetsCOP rotamer_sets, vector1< 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, 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...
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)

Typedef Documentation

typedef numeric::xyzVector< core::Real > xyzVec