evalRepeats.cc File Reference

#include <basic/Tracer.hh>
#include <numeric/conversions.hh>
#include <numeric/trig.functions.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/conformation/Residue.hh>
#include <core/id/NamedAtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/packing/HolesParams.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/types.hh>
#include <core/sequence/ABEGOManager.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <devel/init.hh>
#include <utility/vector1.hh>
#include <protocols/jumping/util.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <basic/database/open.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/holes.OptionKeys.gen.hh>
#include <basic/options/keys/remodel.OptionKeys.gen.hh>
#include <utility/io/ozstream.hh>
#include <iostream>
#include <ObjexxFCL/format.hh>

Functions
void	avg_ca_position (const core::pose::Pose &pose, const protocols::loops::Loop &region, numeric::xyzVector< double > *point)
void	get_helices (core::pose::Pose &pose, protocols::loops::Loops *helices)
Real	get_distance (const core::pose::Pose &pose, const protocols::loops::Loop helix1, const protocols::loops::Loop helix2)
Real	get_distance_midCA (const core::pose::Pose &pose, const protocols::loops::Loop helix1, const protocols::loops::Loop helix2)
Real	get_distance_endpoint (const core::pose::Pose &pose, const protocols::loops::Loop helix1, const protocols::loops::Loop helix2)
Real	get_holes_score (const core::pose::Pose &pose)
void	get_angles (const core::pose::Pose &pose, const protocols::loops::Loop helix1, const protocols::loops::Loop helix2, Real &theta, Real &sigma, Real &phi)
Real	res_type_score (const core::pose::Pose &pose)
Real	ala_ct (const core::pose::Pose &pose)
Real	get_hb_srbb_score (const core::pose::Pose &pose)
Size	get_helixCAInContact (const core::pose::Pose &pose, protocols::loops::Loops helices, Size maxToCheck)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	tr ("evalRepeats")

Function Documentation

ala_ct()

Real ala_ct

(

const core::pose::Pose &

pose

)

References utility::io::oc::cout, create_a3b_hbs::ii, beta_nonlocal::pose, and create_a3b_hbs::score.

Referenced by main().

avg_ca_position()

void avg_ca_position	(	const core::pose::Pose &	pose,
		const protocols::loops::Loop &	region,
		numeric::xyzVector< double > *	point
	)

References create_a3b_hbs::i, beta_nonlocal::pose, test.G102_Functions_General::region, and numeric::xyzVector< T >::zero().

Referenced by get_angles(), get_distance(), and get_distance_endpoint().

get_angles()

void get_angles	(	const core::pose::Pose &	pose,
		const protocols::loops::Loop	helix1,
		const protocols::loops::Loop	helix2,
		Real &	theta,
		Real &	sigma,
		Real &	phi
	)

References numeric::arccos(), avg_ca_position(), numeric::xyzVector< T >::cross_product(), numeric::conversions::degrees(), numeric::xyzVector< T >::dot_product(), oop_conformations::phi, beta_nonlocal::pose, create_a3b_hbs::r, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::sigma, tr, oop_scan::v1, oop_scan::v2, and basic::Tracer::Warning.

get_distance()

Real get_distance	(	const core::pose::Pose &	pose,
		const protocols::loops::Loop	helix1,
		const protocols::loops::Loop	helix2
	)

References a, avg_ca_position(), compute_difference::b, beta_nonlocal::pose, tr, and basic::Tracer::Warning.

Referenced by main().

get_distance_endpoint()

Real get_distance_endpoint	(	const core::pose::Pose &	pose,
		const protocols::loops::Loop	helix1,
		const protocols::loops::Loop	helix2
	)

References a, avg_ca_position(), compute_difference::b, beta_nonlocal::pose, tr, and basic::Tracer::Warning.

get_distance_midCA()

Real get_distance_midCA	(	const core::pose::Pose &	pose,
		const protocols::loops::Loop	helix1,
		const protocols::loops::Loop	helix2
	)

References a, compute_difference::b, beta_nonlocal::pose, tr, and basic::Tracer::Warning.

get_hb_srbb_score()

Real get_hb_srbb_score

(

const core::pose::Pose &

pose

)

References utility::io::oc::cout, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

get_helices()

void get_helices	(	core::pose::Pose &	pose,
		protocols::loops::Loops *	helices
	)

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

Referenced by main().

get_helixCAInContact()

Size get_helixCAInContact	(	const core::pose::Pose &	pose,
		protocols::loops::Loops	helices,
		Size	maxToCheck
	)

References a, aa, compute_difference::b, create_a3b_hbs::ii, kk, beta_nonlocal::pose, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by main().

get_holes_score()

Real get_holes_score

(

const core::pose::Pose &

pose

)

References basic::database::full_name(), and beta_nonlocal::pose.

Referenced by main().

main()

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

References ala_ct(), argv, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, test.T009_Exceptions::e, ObjexxFCL::format::F(), get_distance(), get_helices(), get_helixCAInContact(), get_holes_score(), ObjexxFCL::format::I(), create_a3b_hbs::ii, basic::init(), gaussian-sampling::input, out::file::o(), option, bin_torsions::output, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, basic::options::OptionKeys::remodel::repeat_structure, res_type_score(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, tag, and tag_from_pose().

res_type_score()

Real res_type_score

(

const core::pose::Pose &

pose

)

References utility::io::oc::cout, create_a3b_hbs::ii, beta_nonlocal::pose, and create_a3b_hbs::score.

Referenced by main().

Variable Documentation

tr

basic::Tracer tr("evalRepeats") ( "evalRepeats"  )

static

Referenced by get_angles(), get_distance(), get_distance_endpoint(), and get_distance_midCA().