#include <basic/options/option.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <utility/io/ozstream.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option_macros.hh>

Functions
void	check_pose_length (core::Size const num_res, core::Size const min_seq_length)

void	check_pose_size (core::Size const num_res_current, core::Size const num_res)

void	check_single_chain (core::pose::PoseOP const &mypose)

void	check_sequence (core::pose::PoseOP const &pose, core::pose::PoseOP const &pose_current)

void	check_number_of_poses (core::Size const n_poses)

void	calculate_average_residue_scores (utility::vector1< core::pose::PoseOP > const &poses, utility::vector1< core::Real > &average_res_scores, std::string &sequence, core::Size const num_res, core::Size const n_poses)

void	calculate_order_scores (utility::vector1< core::Real > &ORDER_RES_Score, utility::vector1< core::Real > const &average_res_scores, core::Size const num_res, core::Size const ORDER)

void	predict_disorder (utility::vector1< std::string > &PREDICTION, utility::vector1< core::Real > const &ORDER_RES_Score, std::string const &sequence, core::Size const num_res, utility::vector1< core::Real > const &cutoffs, bool const terminal)

core::Real	calculate_percent_disorder (utility::vector1< std::string > const &PREDICTION, core::Size const num_res)

void	do_terminal_opt (utility::vector1< core::Real > &cutoffs_new, core::Size const num_res, core::Real const CUTOFF, core::Real const term_cutoff, core::Real const endpoint)

void	output_results (core::Size const num_res, std::string const &sequence, utility::vector1< std::string > const &PREDICTION, utility::vector1< core::Real > const &ORDER_RES_Score, utility::vector1< core::Real > const average_res_scores, core::Size const num_output)

void	calculate_disorder (utility::vector1< core::pose::PoseOP > const &poses, core::Size const num_res, core::Size const n_poses, core::Size const n_output, utility::vector1< core::Real > &vector_percent_disorder, core::Size const ORDER, core::Real const CUTOFF, core::Real const term_cutoff, core::Real const endpoint, core::Real const perc_cut)

void	do_disorder_prediction (utility::vector1< core::Real > &vector_percent_disorder, core::Size const ORDER, core::Real const CUTOFF, core::Real const term_cutoff, core::Real const endpoint, core::Real const perc_cut)

void	measure_disorder (utility::vector1< core::Real > &vector_percent_disorder, core::Size const ORDER, core::Real const CUTOFF, core::Real const term_cutoff, core::Real const endpoint, core::Real const perc_cut)

void	do_event_prediction (utility::vector1< core::Real > const &vector_percent_disorder)

void	define_variables (core::Size &win_size, core::Real &cutoff, core::Real &term_cutoff, core::Real &term_endpoint, core::Real &perc_cut)

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

Variables
static basic::Tracer	TR ("apps.public.analysis.ResidueDisorder")

Function Documentation

◆ calculate_average_residue_scores()

void calculate_average_residue_scores	(	utility::vector1< core::pose::PoseOP > const &	poses,
		utility::vector1< core::Real > &	average_res_scores,
		std::string &	sequence,
		core::Size const	num_res,
		core::Size const	n_poses
	)

References check_sequence(), create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::mp::assembly::poses, basic::options::OptionKeys::relax::sequence, test.T120_core::sfxn, and basic::options::TR.

Referenced by calculate_disorder().

◆ calculate_disorder()

void calculate_disorder	(	utility::vector1< core::pose::PoseOP > const &	poses,
		core::Size const	num_res,
		core::Size const	n_poses,
		core::Size const	n_output,
		utility::vector1< core::Real > &	vector_percent_disorder,
		core::Size const	ORDER,
		core::Real const	CUTOFF,
		core::Real const	term_cutoff,
		core::Real const	endpoint,
		core::Real const	perc_cut
	)

References calculate_average_residue_scores(), calculate_order_scores(), calculate_percent_disorder(), do_terminal_opt(), output_results(), basic::options::OptionKeys::mp::assembly::poses, predict_disorder(), basic::options::OptionKeys::relax::sequence, and basic::options::TR.

Referenced by do_disorder_prediction(), and measure_disorder().

◆ calculate_order_scores()

void calculate_order_scores	(	utility::vector1< core::Real > &	ORDER_RES_Score,
		utility::vector1< core::Real > const &	average_res_scores,
		core::Size const	num_res,
		core::Size const	ORDER
	)

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by calculate_disorder().

◆ calculate_percent_disorder()

core::Real calculate_percent_disorder	(	utility::vector1< std::string > const &	PREDICTION,
		core::Size const	num_res
	)

References count, and basic::options::TR.

Referenced by calculate_disorder().

◆ check_number_of_poses()

void check_number_of_poses ( core::Size const n_poses )

References basic::options::TR, and basic::Tracer::Warning.

Referenced by do_disorder_prediction().

◆ check_pose_length()

void check_pose_length	(	core::Size const	num_res,
		core::Size const	min_seq_length
	)

References numeric::interpolation::to_string(), and utility_exit_with_message.

Referenced by do_disorder_prediction(), and measure_disorder().

◆ check_pose_size()

void check_pose_size	(	core::Size const	num_res_current,
		core::Size const	num_res
	)

References utility_exit_with_message.

Referenced by do_disorder_prediction(), and measure_disorder().

◆ check_sequence()

void check_sequence	(	core::pose::PoseOP const &	pose,
		core::pose::PoseOP const &	pose_current
	)

References beta_nonlocal::pose, and utility_exit_with_message.

Referenced by calculate_average_residue_scores().

◆ check_single_chain()

void check_single_chain ( core::pose::PoseOP const & mypose )

References num_chains(), and utility_exit_with_message.

Referenced by do_disorder_prediction(), and measure_disorder().

◆ define_variables()

void define_variables	(	core::Size &	win_size,
		core::Real &	cutoff,
		core::Real &	term_cutoff,
		core::Real &	term_endpoint,
		core::Real &	perc_cut
	)

References extract_by_sidechain_sasa_score::cutoff, basic::options::option, basic::options::OptionKeys::corrections::restore_talaris_behavior, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

◆ do_disorder_prediction()

void do_disorder_prediction	(	utility::vector1< core::Real > &	vector_percent_disorder,
		core::Size const	ORDER,
		core::Real const	CUTOFF,
		core::Real const	term_cutoff,
		core::Real const	endpoint,
		core::Real const	perc_cut
	)

References calculate_disorder(), check_number_of_poses(), check_pose_length(), check_pose_size(), check_single_chain(), gaussian-sampling::input, and basic::options::OptionKeys::mp::assembly::poses.

Referenced by main().

◆ do_event_prediction()

void do_event_prediction ( utility::vector1< core::Real > const & vector_percent_disorder )

References ObjexxFCL::abs(), utility::io::ozstream::clear(), utility::io::ozstream::close(), count, extract_by_sidechain_sasa_score::cutoff, detail::find(), create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::out::file::o, basic::options::option, erraser_single_res_analysis::out, lactamize::outfile, ObjexxFCL::right_string_of(), subloop_histogram::size, erraser_analysis::temp, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

◆ do_terminal_opt()

void do_terminal_opt	(	utility::vector1< core::Real > &	cutoffs_new,
		core::Size const	num_res,
		core::Real const	CUTOFF,
		core::Real const	term_cutoff,
		core::Real const	endpoint
	)

References create_a3b_hbs::i.

Referenced by calculate_disorder().

◆ main()

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

References argv, extract_by_sidechain_sasa_score::cutoff, define_variables(), do_disorder_prediction(), do_event_prediction(), test.T009_Exceptions::e, basic::init(), measure_disorder(), NEW_OPT, basic::options::option, basic::options::OptionKeys::corrections::restore_talaris_behavior, basic::options::OptionKeys::frags::scoring::scoring, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::Tracer::Warning.

◆ measure_disorder()

void measure_disorder	(	utility::vector1< core::Real > &	vector_percent_disorder,
		core::Size const	ORDER,
		core::Real const	CUTOFF,
		core::Real const	term_cutoff,
		core::Real const	endpoint,
		core::Real const	perc_cut
	)

References calculate_disorder(), check_pose_length(), check_pose_size(), check_single_chain(), count, and gaussian-sampling::input.

Referenced by main().

◆ output_results()

void output_results	(	core::Size const	num_res,
		std::string const &	sequence,
		utility::vector1< std::string > const &	PREDICTION,
		utility::vector1< core::Real > const &	ORDER_RES_Score,
		utility::vector1< core::Real > const	average_res_scores,
		core::Size const	num_output
	)

References utility::io::ozstream::clear(), utility::io::ozstream::close(), create_a3b_hbs::i, basic::options::OptionKeys::out::file::o, basic::options::option, erraser_single_res_analysis::out, lactamize::outfile, basic::options::OptionKeys::out::prefix, ObjexxFCL::right_string_of(), basic::options::OptionKeys::relax::sequence, and basic::options::OptionKeys::inout::dbms::user.

Referenced by calculate_disorder().

◆ predict_disorder()

void predict_disorder	(	utility::vector1< std::string > &	PREDICTION,
		utility::vector1< core::Real > const &	ORDER_RES_Score,
		std::string const &	sequence,
		core::Size const	num_res,
		utility::vector1< core::Real > const &	cutoffs,
		bool const	terminal
	)

References create_a3b_hbs::i, basic::options::OptionKeys::relax::sequence, and basic::options::TR.

Referenced by calculate_disorder().

Variable Documentation

◆ TR

basic::Tracer TR("apps.public.analysis.ResidueDisorder") ( "apps.public.analysis.ResidueDisorder" )

static

Functions

Variables

Function Documentation

◆ calculate_average_residue_scores()

◆ calculate_disorder()

◆ calculate_order_scores()

◆ calculate_percent_disorder()

◆ check_number_of_poses()

◆ check_pose_length()

◆ check_pose_size()

◆ check_sequence()

◆ check_single_chain()

◆ define_variables()

◆ do_disorder_prediction()

◆ do_event_prediction()

◆ do_terminal_opt()

◆ main()

◆ measure_disorder()

◆ output_results()

◆ predict_disorder()

Variable Documentation

◆ TR