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/chemical/ResidueTypeFinder.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/rna/RNA_ResidueLevelTask.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/CustomBaseTypePackerPalette.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 <ObjexxFCL/string.functions.hh>
#include <protocols/rna/denovo/util.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <sstream>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.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 <platform/types.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/Jump.hh>
#include <utility/vector0.hh>
#include <ObjexxFCL/DynamicIndexRange.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <utility/excn/Exceptions.hh>

Namespaces
	ObjexxFCL
	ObjexxFCL::format

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

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

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

void* my_main

(

void *

)

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

Referenced by main().

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

References ObjexxFCL::distance_squared().

Referenced by 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, test.T200_Scoring::ii, pyrosetta.distributed.docs::movers, name, local::nstruct, out::nstruct(), basic::options::option, option, options, erraser_single_res_analysis::outfile, make_symmdef_file_denovo::pos, demo.D010_Pose_structure::pose, basic::options::OptionKeys::packing::resfile, residues_too_distant(), rna_sequence_recovery_metrics(), test.T500_Packing::rotamer_trials, runtime_assert, in::file::s(), basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::suffix, test.G200_Module_Region::task, basic::options::OptionKeys::inout::dbms::user, and value.

Referenced by my_main().

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::ozstream::close(), utility::io::oc::cout, ObjexxFCL::format::F(), ObjexxFCL::format::I(), clean_pdb_keep_ligand::nres, erraser_single_res_analysis::out, demo.D010_Pose_structure::pose, and ObjexxFCL::FArray< typename >::size().

Referenced by rna_design_test(), and ss_ds_ts_assign_test().

void ss_ds_ts_assign_test

(

)

References basic::options::OptionKeys::chemical::chemical, option, options, 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().