SID_rescore.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 <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.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 <core/pose/metrics/PoseMetricCalculatorBase.fwd.hh>
#include <protocols/pose_metric_calculators/SaltBridgeCalculator.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <protocols/analysis/InterfaceAnalyzerMover.hh>
#include <protocols/relax/FastRelax.fwd.hh>
#include <protocols/relax/FastRelax.hh>
#include <core/scoring/rms_util.hh>

Functions
void	read_in_pdbs (utility::vector1< core::pose::PoseOP > &poses, core::Size &num_chains)
void	calc_RF (const utility::vector1< core::pose::PoseOP > &pose_by_chain, core::Real &RF)
void	predict_AE (const core::pose::PoseOP &pose, core::Real &AE_pred, const std::string &interface, const core::Real &HSA_weight, const core::Real &NR_weight, const core::Real &RF_weight, const core::Real &RF, const core::Real &n_ints)
void	calc_SID_score (core::Real &SID_score, const core::Real &AE_pred, const core::Real &AE_exp)
void	output_results (const utility::vector1< core::Real > &AE_preds, const utility::vector1< core::Real > &SID_scores, const utility::vector1< core::Real > &Rosetta_scores, const utility::vector1< core::Real > &Rosetta_SID_scores, const utility::vector1< core::Real > &rmsds)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.jtseffer.SID_rescore")
basic::options::StringOptionKey const	interface ("interface")
basic::options::RealOptionKey const	AE ("AE")
basic::options::RealOptionKey const	n_ints ("n_ints")
basic::options::BooleanOptionKey const	skip_relax ("skip_relax")

Function Documentation

calc_RF()

void calc_RF	(	const utility::vector1< core::pose::PoseOP > &	pose_by_chain,
		core::Real &	RF
	)

References create_a3b_hbs::i, create_a3b_hbs::j, num_chains(), and beta_nonlocal::pose.

Referenced by main().

calc_SID_score()

void calc_SID_score	(	core::Real &	SID_score,
		const core::Real &	AE_pred,
		const core::Real &	AE_exp
	)

References ObjexxFCL::abs(), compute_difference::b, erraser_analysis::diff, and ObjexxFCL::pow().

Referenced by main().

main()

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

References utility::options::OptionCollection::add(), AE, argv, calc_RF(), calc_SID_score(), pyrosetta.io::create_score_function, utility::options::ScalarOption_T_< K, T >::def(), test.T009_Exceptions::e, create_a3b_hbs::i, basic::init(), interface, basic::options::OptionKeys::intf::intf, n_ints, surface_app::native, basic::options::OptionKeys::in::file::native, num_chains(), basic::options::option, output_results(), pyrosetta.distributed.io::pose_from_file(), basic::options::OptionKeys::mp::assembly::poses, predict_AE(), read_in_pdbs(), average_rmsds::rmsd, legacy_score_vs_rmsd::rmsds, basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, skip_relax, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and value.

output_results()

void output_results	(	const utility::vector1< core::Real > &	AE_preds,
		const utility::vector1< core::Real > &	SID_scores,
		const utility::vector1< core::Real > &	Rosetta_scores,
		const utility::vector1< core::Real > &	Rosetta_SID_scores,
		const utility::vector1< core::Real > &	rmsds
	)

References create_a3b_hbs::i, basic::options::OptionKeys::out::file::o, basic::options::option, erraser_single_res_analysis::out, lactamize::outfile, legacy_score_vs_rmsd::rmsds, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

predict_AE()

void predict_AE	(	const core::pose::PoseOP &	pose,
		core::Real &	AE_pred,
		const std::string &	interface,
		const core::Real &	HSA_weight,
		const core::Real &	NR_weight,
		const core::Real &	RF_weight,
		const core::Real &	RF,
		const core::Real &	n_ints
	)

References pyrosetta.io::create_score_function, pyrosetta.distributed.io::get_score_function(), interface, n_ints, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::abinitio::relax, test.T120_core::sfxn, skip_relax, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

read_in_pdbs()

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

References gaussian-sampling::input, num_chains(), basic::options::OptionKeys::mp::assembly::poses, and basic::options::TR.

Referenced by main().

Variable Documentation

AE

basic::options::RealOptionKey const AE("AE")

(

"AE"

)

Referenced by main().

interface

basic::options::StringOptionKey const interface("interface")

(

"interface"

)

Referenced by main(), and predict_AE().

n_ints

basic::options::RealOptionKey const n_ints("n_ints")

(

"n_ints"

)

Referenced by main(), and predict_AE().

skip_relax

basic::options::BooleanOptionKey const skip_relax("skip_relax")

(

"skip_relax"

)

Referenced by helix_from_sequence(), main(), predict_AE(), and skipping_relax().

TR

basic::Tracer TR("apps.pilot.jtseffer.SID_rescore") ( "apps.pilot.jtseffer.SID_rescore"  )

static