ResidueDisorder.cc File Reference

#include <basic/options/option.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <utility/io/izstream.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.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 <core/scoring/ScoreType.hh>
#include <utility/io/ozstream.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>

Functions
void	check_pose_size (core::Size num_res_current, core::Size num_res)
void	check_single_chain (const core::pose::PoseOP &mypose)
void	check_sequence (const core::pose::PoseOP &pose, const core::pose::PoseOP &pose_current)
void	check_number_of_poses (core::Size n_poses)
void	check_score_function (core::scoring::ScoreFunctionOP sfxn)
void	read_in_pdbs (utility::vector1< core::pose::PoseOP > &poses, core::Size &n_poses, core::Size &num_res)
void	calculate_average_residue_scores (const utility::vector1< core::pose::PoseOP > &poses, utility::vector1< core::Real > &average_res_scores, std::string &sequence, core::Size num_res, core::Size n_poses)
void	caculate_order_scores (utility::vector1< core::Real > &ORDER_RES_Score, const utility::vector1< core::Real > &average_res_scores, core::Size num_res)
void	predict_disorder (utility::vector1< std::string > &PREDICTION, const utility::vector1< core::Real > &ORDER_RES_Score, const std::string &sequence, core::Size num_res, const utility::vector1< core::Real > &cutoffs, bool terminal)
core::Real	calculate_percent_disorder (const utility::vector1< std::string > &PREDICTION, core::Size num_res)
void	do_terminal_opt (utility::vector1< core::Real > &cutoffs_new, core::Size num_res)
void	output_results (core::Size num_res, const std::string &sequence, const utility::vector1< std::string > &PREDICTION, const utility::vector1< core::Real > &ORDER_RES_Score, utility::vector1< core::Real > average_res_scores)
int	main (int argc, char *argv[])

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

Function Documentation

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

References test.T150_PyMOL_Integration::i, and basic::options::OptionKeys::frags::j.

Referenced by main().

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

References check_score_function(), check_sequence(), test.T150_PyMOL_Integration::i, basic::options::OptionKeys::frags::j, erraser_single_res_analysis::score, test.T120_core::sfxn, and TR.

Referenced by main().

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

References clean_pdb_keep_ligand::count, and TR.

Referenced by main().

void check_number_of_poses

(

core::Size

n_poses

)

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

Referenced by read_in_pdbs().

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

References utility_exit_with_message.

Referenced by read_in_pdbs().

void check_score_function

(

core::scoring::ScoreFunctionOP

sfxn

)

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

Referenced by calculate_average_residue_scores().

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

References utility_exit_with_message.

Referenced by calculate_average_residue_scores().

void check_single_chain

(

const core::pose::PoseOP &

mypose

)

References utility_exit_with_message.

Referenced by read_in_pdbs().

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

References test.T150_PyMOL_Integration::i.

Referenced by main().

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

References caculate_order_scores(), calculate_average_residue_scores(), calculate_percent_disorder(), utility::excn::Exception::display(), do_terminal_opt(), test.T009_Exceptions::e, devel::init(), options, output_results(), basic::options::OptionKeys::mp::assembly::poses, predict_disorder(), read_in_pdbs(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, and basic::options::TR.

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

References utility::io::ozstream::close(), test.T150_PyMOL_Integration::i, basic::options::OptionKeys::out::file::o, basic::options::option, options, erraser_single_res_analysis::out, erraser_single_res_analysis::outfile, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

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

References test.T150_PyMOL_Integration::i, and TR.

Referenced by main().

void read_in_pdbs	(	utility::vector1< core::pose::PoseOP > &	poses,
		core::Size &	n_poses,
		core::Size &	num_res
	)

References check_number_of_poses(), check_pose_size(), and check_single_chain().

Referenced by main().

Variable Documentation

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

static

Referenced by calculate_average_residue_scores(), calculate_percent_disorder(), check_number_of_poses(), check_score_function(), and predict_disorder().