ddg_benchmark.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <devel/init.hh>
#include <core/import_pose/import_pose.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <core/pack/task/ResfileReader.hh>
#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <string>
#include <sstream>
#include <cmath>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/ddg.OptionKeys.gen.hh>
#include <core/chemical/ResidueType.hh>
#include <utility/vector0.hh>

Typedefs
typedef std::vector< Real >	ddGs

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.pilot.yiliu.ddg")
std::ostream &	writeYamlValue (std::ostream &S, std::string name, core::Real value)
std::ostream &	writeYamlValue (std::ostream &S, std::string name, bool value)
Real	sum (ddGs &scores_to_sum)
Real	average (utility::vector1< Real > &scores_to_average)
Size	store_energies (ObjexxFCL::FArray2D< Real > &two_d_e_arrays, scoring::ScoreFunction &s, pose::Pose &p, Size next_index, Size size_to_expect)
Size	average_score_components (ObjexxFCL::FArray2D< Real > &scores_to_average, utility::vector1< Real > &averaged_scores)
Real	correlation_coefficient (utility::vector1< Real > sim, utility::vector1< Real > exp)
void	correlation (std::string ddg_out)
int	main (int argc, char *argv[])

Detailed Description

Author

Liz Kellogg ekell.nosp@m.ogg@.nosp@m.u.was.nosp@m.hing.nosp@m.ton.e.nosp@m.du

Typedef Documentation

typedef std::vector<Real> ddGs

Function Documentation

Real average

(

utility::vector1< Real > &

scores_to_average

)

References sum().

Referenced by main().

Size average_score_components	(	ObjexxFCL::FArray2D< Real > &	scores_to_average,
		utility::vector1< Real > &	averaged_scores
	)

References basic::options::OptionKeys::frags::j, ObjexxFCL::FArray2D< typename >::l1(), ObjexxFCL::FArray2D< typename >::l2(), ObjexxFCL::FArray2D< typename >::u1(), and ObjexxFCL::FArray2D< typename >::u2().

Referenced by main().

void correlation

(

std::string

ddg_out

)

References correlation_coefficient(), utility::io::oc::cout, basic::options::OptionKeys::ddg::ddg, basic::Tracer::Error, ObjexxFCL::getline(), app.delta_score_per_mutation::res, fmt::sprintf(), TR(), writeYamlValue(), and revert_app::wt.

Referenced by main().

Real correlation_coefficient	(	utility::vector1< Real >	sim,
		utility::vector1< Real >	exp
	)

References utility::options::OptionKeys::options::exit, TR(), x(), and y().

Referenced by correlation().

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

References average(), average_score_components(), begin, correlation(), utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::ddg::debug_output, basic::options::OptionKeys::ddg::dump_pdbs, utility::options::OptionKeys::options::exit, utility::exit(), ObjexxFCL::format::F(), test.G202_Module_PythonPDB::filename, basic::options::OptionKeys::in::in, devel::init(), basic::options::OptionKeys::ddg::iterations, basic::options::OptionKeys::frags::j, line, utility::excn::EXCN_Base::msg(), demo.D090_Ala_scan::mutant_aa, basic::options::OptionKeys::casp::num_iterations, basic::options::OptionKeys::out::file::o, option, options, basic::options::OptionKeys::canonical_sampling::out::out, basic::options::OptionKeys::lh::fragpdb::out_path, basic::options::OptionKeys::loops::output_pdb, out::path::pdb(), app.surface_docking.surface_docking::pose, clean_pdb_keep_ligand::resnum, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), store_energies(), sum(), app.delta_score_per_mutation::task, and basic::options::OptionKeys::ddg::weight_file.

Size store_energies	(	ObjexxFCL::FArray2D< Real > &	two_d_e_arrays,
		scoring::ScoreFunction &	s,
		pose::Pose &	p,
		Size	next_index,
		Size	size_to_expect
	)

References begin, ObjexxFCL::FArray2D< typename >::dimension(), basic::options::OptionKeys::cutoutdomain::end, basic::options::OptionKeys::frags::j, and basic::options::OptionKeys::in::file::s.

Referenced by main().

Real sum

(

ddGs &

scores_to_sum

)

Referenced by average(), BuildBindings::BuildRosettaOnWindows(), toolbox.cleaning::cleanCRYS(), pyrosetta.toolbox.cleaning::cleanCRYS(), toolbox::cleanCRYS(), pyrosetta.toolbox::cleanCRYS(), compare_times::compare_times(), Kernel::dot(), ObjexxFCL::dot(), ObjexxFCL::dot_product(), demo.D060_Folding::guess_disulfides(), Kernel::k_function(), pyrosetta.toolbox.structural_alignment::kabsch_alignment(), toolbox.structural_alignment::kabsch_alignment(), main(), ObjexxFCL::FArray2< T >::operator*=(), ObjexxFCL::FArray2< T >::right_multiply_by_transpose(), demo.D090_Ala_scan::scanning_analysis(), Solver::Solve(), solve_nu_svr(), statistics(), and svm_predict_values().

static THREAD_LOCAL basic::Tracer TR ( "apps.pilot.yiliu.ddg"  )

static

Referenced by correlation(), and correlation_coefficient().

std::ostream& writeYamlValue	(	std::ostream &	S,
		std::string	name,
		core::Real	value
	)

Referenced by correlation().

std::ostream& writeYamlValue	(	std::ostream &	S,
		std::string	name,
		bool	value
	)