#include <core/scoring/rms_util.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/RNA_SilentStruct.hh>
#include <core/io/pose_stream/SilentFilePoseInputStream.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/options/option.hh>
#include <core/options/after_opts.hh>
#include <core/options/util.hh>
#include <core/options/option_macros.hh>
#include <protocols/idealize/idealize.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/rna/denovo/setup/RNA_DeNovoPoseInitializer.fwd.hh>
#include <protocols/rna/denovo/setup/RNA_DeNovoPoseInitializer.hh>
#include <protocols/rna/denovo/libraries/RNA_ChunkLibrary.hh>
#include <protocols/rna/denovo/libraries/RNA_ChunkLibrary.fwd.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/rna/movers/RNA_HelixAssembler.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/util/basic.hh>
#include <core/io/database/open.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/exit.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/scoring/Energies.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <core/util/Tracer.hh>
#include <core/options/keys/out.OptionKeys.gen.hh>
#include <core/options/keys/score.OptionKeys.gen.hh>
#include <core/options/keys/in.OptionKeys.gen.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
void	rna_assemble_test ()

std::string	get_tag (utility::vector1< Size > const &chunk_numbers)

void	score_and_minimize (pose::Pose &pose, pose::Pose const &native_pose, std::string const &tag, std::string const &silent_file, protocols::rna::denovo::RNA_ChunkLibrary const &)

void	insert_chunk (pose::Pose &pose, protocols::rna::denovo::RNA_ChunkLibrary const &rna_chunk_library, Size const chunk_set_index, utility::vector1< Size > const &chunk_numbers_in, std::string const &silent_file, pose::Pose const &native_pose)

void	rna_assemble_all_combinations_test ()

void	rna_build_helix_test_OLD ()

void	rna_build_helix_test_precompute ()

void *	my_main (void *)

int	main (int argc, char *argv[])

Typedef Documentation

◆ Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

◆ get_tag()

std::string get_tag ( utility::vector1< Size > const & chunk_numbers )

References create_a3b_hbs::i, ObjexxFCL::string_of(), and tag.

Referenced by insert_chunk().

◆ insert_chunk()

void insert_chunk	(	pose::Pose &	pose,
		protocols::rna::denovo::RNA_ChunkLibrary const &	rna_chunk_library,
		Size const	chunk_set_index,
		utility::vector1< Size > const &	chunk_numbers_in,
		std::string const &	silent_file,
		pose::Pose const &	native_pose
	)

References get_tag(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::native_pose, option, beta_nonlocal::pose, score_and_minimize(), and tag.

Referenced by rna_assemble_all_combinations_test().

◆ main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, build_helix_test(), basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, test.T009_Exceptions::e, basic::init(), basic::options::OptionKeys::dna::design::minimize, my_main(), NEW_OPT, basic::options::OptionKeys::flexPepDocking::params_file, beta_sc_scan::seq, and viewer_main().

◆ my_main()

void* my_main ( void * )

References build_helix_test(), utility::options::OptionKeys::options::exit, option, rna_assemble_all_combinations_test(), rna_assemble_test(), rna_build_helix_test_OLD(), and rna_build_helix_test_precompute().

Referenced by main().

◆ rna_assemble_all_combinations_test()

void rna_assemble_all_combinations_test ( )

Referenced by my_main().

◆ rna_assemble_test()

void rna_assemble_test ( )

◆ rna_build_helix_test_OLD()

void rna_build_helix_test_OLD ( )

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::rna::denovo::denovo, in::file::fasta(), ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, local::nstruct, out::nstruct(), option, basic::options::OptionKeys::ddg::output_silent, beta_nonlocal::pose, docking::s, basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, basic::options::OptionKeys::in::file::silent, out::file::silent(), tag, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.