findNaturallyOccuringAlphaRepeats.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/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 <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 <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)
void	get_sheets (core::pose::Pose &pose, protocols::loops::Loops *sheets)
Real	get_distance (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)
int	main (int argc, char *argv[])

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

Function Documentation

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_distance(), and get_distance_endpoint().

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.

Referenced by main().

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_sheets()

void get_sheets	(	core::pose::Pose &	pose,
		protocols::loops::Loops *	sheets
	)

References create_a3b_hbs::ii, beta_nonlocal::pose, and basic::options::OptionKeys::jumps::sheets.

Referenced by main().

main()

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

References argv, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, ObjexxFCL::distance(), test.T009_Exceptions::e, ObjexxFCL::format::F(), get_distance(), get_distance_endpoint(), get_helices(), get_sheets(), ObjexxFCL::format::I(), basic::init(), gaussian-sampling::input, oop_conformations::length, out::file::o(), option, bin_torsions::output, pyrosetta.distributed.io::pose_from_file(), basic::options::OptionKeys::mp::assembly::poses, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::jumps::sheets, tag, and tag_from_pose().

Variable Documentation

tr

basic::Tracer tr("alphaRepeatIdenfier") ( "alphaRepeatIdenfier"  )

static

Referenced by get_distance(), and get_distance_endpoint().