rna_design.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/palette/PackerPalette.fwd.hh>
#include <core/pack/palette/PackerPaletteFactory.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/init/init.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <core/pose/toolbox/AtomLevelDomainMap.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.hh>
#include <core/import_pose/options/RNA_MinimizerOptions.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <ObjexxFCL/format.hh>
#include <protocols/rna/denovo/util.hh>
#include <iostream>
#include <string>
#include <sstream>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <utility/excn/Exceptions.hh>
#include <core/pack/task/ResidueLevelTask.hh>

Functions
void	rna_sequence_recovery_metrics (pose::Pose const &reference_pose, utility::vector1< pose::PoseOP > const &pose_list, std::string const &sequence_recovery_file)
bool	residues_too_distant (conformation::Residue const &r1, conformation::Residue const &r2, Real const dist)
void	rna_design_test ()
void	ss_ds_ts_assign_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Function Documentation

main()

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

References argv, utility::io::oc::cout, basic::options::OptionKeys::magnesium::montecarlo::dump, test.T009_Exceptions::e, a3b_hbs_creator::final_minimize, basic::options::OptionKeys::full_model::global_seq_file, basic::init(), my_main(), NEW_OPT, option, test.T500_Packing::rotamer_trials, and viewer_main().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, option, rna_design_test(), and ss_ds_ts_assign_test().

Referenced by main().

residues_too_distant()

bool residues_too_distant	(	conformation::Residue const &	r1,
		conformation::Residue const &	r2,
		Real const	dist
	)

References dist(), basic::options::OptionKeys::motifs::r1, and basic::options::OptionKeys::motifs::r2.

Referenced by rna_design_test().

rna_design_test()

void rna_design_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::magnesium::montecarlo::dump, basic::options::OptionKeys::matdes::dock::dump_pdb, a3b_hbs_creator::final_minimize, create_a3b_hbs::ii, pyrosetta.distributed.docs::movers, local::nstruct, out::nstruct(), basic::options::option, option, options, lactamize::outfile, parse_resfile(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, basic::options::OptionKeys::packing::resfile, residues_too_distant(), rna_sequence_recovery_metrics(), test.T500_Packing::rotamer_trials, runtime_assert, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::suffix, vancomycin::task, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

rna_sequence_recovery_metrics()

void rna_sequence_recovery_metrics	(	pose::Pose const &	reference_pose,
		utility::vector1< pose::PoseOP > const &	pose_list,
		std::string const &	sequence_recovery_file
	)

References utility::io::oc::cout, ObjexxFCL::format::F(), create_a3b_hbs::i, ObjexxFCL::format::I(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_sc_scan::name3, create_a3b_hbs::nres, erraser_single_res_analysis::out, beta_nonlocal::pose, test.Workshop8test::reference_pose, and residue.

Referenced by rna_design_test(), and ss_ds_ts_assign_test().

ss_ds_ts_assign_test()

void ss_ds_ts_assign_test

(

)

References basic::options::OptionKeys::chemical::chemical, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, make_symmdef_file_denovo::pos, pyrosetta.distributed.io::pose_from_file, rna_sequence_recovery_metrics(), in::file::s(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().