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/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 <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 <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/farna/util.hh>
#include <fstream>
#include <iostream>
#include <string>
#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 <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)
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, basic::init(), utility::excn::EXCN_Base::msg(), my_main(), NEW_OPT, and options.

void* my_main

(

void *

)

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

Referenced by main().

void rna_design_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::magnesium::montecarlo::dump, basic::options::OptionKeys::matdes::dock::dump_pdb, pyrosetta::get_score_function, test.T200_Scoring::ii, local::nstruct, out::nstruct(), basic::options::option, option, options, clean_pdb_keep_ligand::outfile, make_symmdef_file_denovo::pos, app.surface_docking.surface_docking::pose, basic::options::OptionKeys::packing::resfile, rna_sequence_recovery_metrics(), in::file::s(), PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, app.delta_score_per_mutation::task, and basic::options::OptionKeys::inout::dbms::user.

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, basic::options::OptionKeys::canonical_sampling::out::out, app.surface_docking.surface_docking::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, rna_sequence_recovery_metrics(), in::file::s(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().