HDXEnergy.cc File Reference

Scores Ab Initio Models using HDX-NMR rate Data. More...

#include <devel/init.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Atom.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/prof.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/TwelveANeighborGraph.hh>
#include <core/scoring/ContextGraphTypes.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/chemical/AtomType.hh>
#include <core/scoring/func/FadeFunc.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/sasa/SasaCalc.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/util.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/evaluation.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <utility/string_util.hh>
#include <core/pose/util.hh>
#include <core/scoring/sasa/util.hh>
#include <utility/io/izstream.hh>
#include <utility/file/FileName.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/vector1.hh>
#include <numeric/NumericTraits.hh>
#include <utility/io/ozstream.hh>

Functions
void	register_options ()
void	output_results (std::string const &outf)
core::Real	count_neighbors (std::string neighbor_oxygen, core::pose::Pose pose, core::Size res_count_target, std::string target_atom_vector_start, core::Real const distance_internal, numeric::xyzVector< core::Real > target_vector, core::Size res_count_neighbor)
void	calculate_average_residue_scores (core::pose::Pose pose, utility::vector1< core::Real > &average_res_scores, core::Size num_res)
void	calculate_order_scores (utility::vector1< core::Real > &ORDER_RES_Score, const utility::vector1< core::Real > &average_res_scores, core::Size num_res)
core::Real	order_score_score (utility::vector1< core::Real > &ORDER_RES_Score, core::Size strong_resi, core::Real os_pf, bool cate, bool num)
core::Real	nc_score (core::pose::Pose pose, core::Size nc_res, core::Real nc_pf, bool cate, bool num)
core::Real	rel_sasa_score (core::pose::Pose pose, std::string sapseq, std::map< char, core::Real > left, std::map< char, core::Real > right, utility::vector1< Real > rel_sasa, core::Size sasa_res, core::Real sasa_pf, bool cate, bool num)
core::Real	hb_score (std::string sapseq, std::list< core::Size > strong_residues_cat, std::vector< core::Size > strong_residues_pf, std::vector< core::Real > pf_list, core::pose::Pose pose, std::map< char, core::Real > left, std::map< char, core::Real > right, core::scoring::ScoreFunctionOP scorefunc, bool cate, bool num)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.marzolf-daniel.HDXEnergy")

Detailed Description

Scores Ab Initio Models using HDX-NMR rate Data.

Author

DMarzolf (marzo.nosp@m.lf.4.nosp@m.@osu..nosp@m.edu)

Function Documentation

calculate_average_residue_scores()

void calculate_average_residue_scores	(	core::pose::Pose	pose,
		utility::vector1< core::Real > &	average_res_scores,
		core::Size	num_res
	)

References create_a3b_hbs::j, and beta_nonlocal::pose.

Referenced by main().

calculate_order_scores()

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

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

Referenced by main().

count_neighbors()

core::Real count_neighbors	(	std::string	neighbor_oxygen,
		core::pose::Pose	pose,
		core::Size	res_count_target,
		std::string	target_atom_vector_start,
		core::Real const	distance_internal,
		numeric::xyzVector< core::Real >	target_vector,
		core::Size	res_count_neighbor
	)

References numeric::xyzVector< T >::dot(), and beta_nonlocal::pose.

Referenced by average_degree(), and nc_score().

hb_score()

core::Real hb_score	(	std::string	sapseq,
		std::list< core::Size >	strong_residues_cat,
		std::vector< core::Size >	strong_residues_pf,
		std::vector< core::Real >	pf_list,
		core::pose::Pose	pose,
		std::map< char, core::Real >	left,
		std::map< char, core::Real >	right,
		core::scoring::ScoreFunctionOP	scorefunc,
		bool	cate,
		bool	num
	)

References detail::find(), basic::options::OptionKeys::ufv::left, beta_nonlocal::pose, ObjexxFCL::pow(), and basic::options::OptionKeys::ufv::right.

Referenced by main(), output_single_motif(), and process_for_motifs().

main()

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

References argv, calculate_average_residue_scores(), calculate_order_scores(), CREATE_EXCEPTION, test.T009_Exceptions::e, detail::find(), getline(), hb_score(), basic::options::OptionKeys::in::file::HDX, basic::init(), gaussian-sampling::input, line, nc_score(), NEW_OPT, predPRE::numer, option, order_score_score(), bin_torsions::output, output_results(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, register_options(), rel_sasa_score(), pna::resi, docking::s, basic::options::OptionKeys::AnchoredDesign::filters::sasa, basic::options::OptionKeys::relax::sequence, test.T120_core::sfxn, challenge::ss, and basic::options::OptionKeys::inout::dbms::user.

nc_score()

core::Real nc_score	(	core::pose::Pose	pose,
		core::Size	nc_res,
		core::Real	nc_pf,
		bool	cate,
		bool	num
	)

References count_neighbors(), neighbor_count(), beta_nonlocal::pose, and ObjexxFCL::pow().

Referenced by main().

order_score_score()

core::Real order_score_score	(	utility::vector1< core::Real > &	ORDER_RES_Score,
		core::Size	strong_resi,
		core::Real	os_pf,
		bool	cate,
		bool	num
	)

References ObjexxFCL::pow().

Referenced by main().

output_results()

void output_results

(

std::string const &

outf

)

References job_manager::app, out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

register_options()

void register_options

(

)

References in::file::HDX(), and option.

Referenced by main().

rel_sasa_score()

core::Real rel_sasa_score	(	core::pose::Pose	pose,
		std::string	sapseq,
		std::map< char, core::Real >	left,
		std::map< char, core::Real >	right,
		utility::vector1< Real >	rel_sasa,
		core::Size	sasa_res,
		core::Real	sasa_pf,
		bool	cate,
		bool	num
	)

References basic::options::OptionKeys::ufv::left, beta_nonlocal::pose, ObjexxFCL::pow(), basic::options::OptionKeys::ufv::right, and extract_by_sidechain_sasa_score::sasa_score.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.marzolf-daniel.HDXEnergy") ( "apps.pilot.marzolf-daniel.HDXEnergy"  )

static

Referenced by output_results().