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 <core/pack/task/ResfileReader.hh>
#include <utility/vector1.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 <cmath>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/ddg.OptionKeys.gen.hh>
#include <core/chemical/ResidueType.hh>
#include <core/pack/task/ResidueLevelTask.hh>

Typedefs
using	ddGs = std::vector< Real >

Functions
std::ostream &	writeYamlValue (std::ostream &S, std::string const &name, core::Real value)
std::ostream &	writeYamlValue (std::ostream &S, std::string const &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[])

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

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

ddGs

using ddGs = std::vector<Real>

Function Documentation

average()

Real average

(

utility::vector1< Real > &

scores_to_average

)

References create_a3b_hbs::i, and sum().

Referenced by RDCToolMover::apply(), calculate_percent_hydrophobic_stats(), RDCToolMover::dump_averages(), ChallengeMover::extract_chunks_from_alignment_counts(), ChallengeMover::extract_ss_chunks_from_alignment_counts(), main(), register_options(), and run().

average_score_components()

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

References create_a3b_hbs::i, create_a3b_hbs::j, ObjexxFCL::FArray2D< T >::l1(), ObjexxFCL::FArray2D< T >::l2(), ObjexxFCL::FArray2D< T >::u1(), and ObjexxFCL::FArray2D< T >::u2().

Referenced by main().

correlation()

void correlation

(

std::string

ddg_out

)

References correlation_coefficient(), utility::io::oc::cout, basic::Tracer::Error, getline(), res, TR, writeYamlValue(), and orn_macrocycle::wt.

Referenced by main().

correlation_coefficient()

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

References utility::options::OptionKeys::options::exit, create_a3b_hbs::i, TR, x, xx, test.T110_numeric::xy, predPRE::y, and yy.

Referenced by correlation().

main()

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

References job_manager::app, argv, average(), average_score_components(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, correlation(), utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::ddg::debug_output, basic::options::OptionKeys::ddg::dump_pdbs, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, utility::exit(), ObjexxFCL::format::F(), lactamize::filename, header(), create_a3b_hbs::i, basic::options::OptionKeys::in::in, basic::init(), autocorrelation::iterations, create_a3b_hbs::j, create_a3b_hbs::k, line, demo.D090_Ala_scan::mutant_aa, local::num_iterations, basic::options::OptionKeys::out::file::o, option, erraser_single_res_analysis::out, basic::options::OptionKeys::lh::fragpdb::out_path, output_pdb(), parse_resfile(), out::path::pdb(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, enumerate_junctions::q, create_a3b_hbs::r, predPRE::resnum, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), store_energies(), sum(), vancomycin::task, and basic::options::OptionKeys::ddg::weight_file.

store_energies()

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

References ObjexxFCL::FArray2D< T >::dimension(), create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and docking::s.

Referenced by main(), and run().

sum()

Real sum

(

ddGs &

scores_to_sum

)

References create_a3b_hbs::i.

Referenced by pyrosetta.bindings.energies::active_total_energies(), average(), bin_torsions::bin_histograms(), helpers::cache_array(), calc_sdev(), calculate_percent_hydrophobic_stats(), check_intensities(), compare_times::compare_times(), Kernel::dot(), autocorrelation::find_autocorrelation(), get_area_tot(), util::get_surrounding_res(), demo.D060_Folding::guess_disulfides(), Kernel::k_function(), main(), average_rmsds::mean(), build_jacobian::normalize(), nosuper_CA_rmsd(), ObjexxFCL::FArray2< T >::operator*=(), detail::uint128_wrapper::operator+=(), bin_torsions::plot_score_function(), job_manager.JobWindow::refresh(), region_rmsd_structures_aligned(), pyrosetta.bindings.energies::residue_onebody_energies_array(), ObjexxFCL::FArray2< T >::right_multiply_by_transpose(), abbinding::rmsd_frmk_chothia_num_ab(), demo.D090_Ala_scan::scanning_analysis(), evaluate_beta_mutants::score_ensemble(), Solver::Solve(), solve_nu_svr(), detail::bigint::square(), statistics(), svm_predict_values(), pyrosetta.tests.distributed.test_viewer.TestViewer::test_viewer_with_poses(), and write_cluster_frags().

writeYamlValue() [1/2]

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

References pyrosetta.distributed.cluster.converters::S, and value.

writeYamlValue() [2/2]

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

References pyrosetta.distributed.cluster.converters::S, and value.

Referenced by correlation().

Variable Documentation

TR

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

static

Referenced by correlation(), and correlation_coefficient().