extractNativeRepeats.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 <numeric/xyzMatrix.hh>
#include <numeric/random/random.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/conformation/Residue.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/SequenceMapping.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/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/types.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <protocols/jumping/util.hh>
#include <protocols/hybridization/TMalign.hh>
#include <protocols/hybridization/util.hh>
#include <devel/init.hh>
#include <utility/vector1.hh>
#include <Eigen/Dense>
#include <basic/database/open.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <utility/io/ozstream.hh>
#include <iostream>
#include <ObjexxFCL/format.hh>

Functions
void	get_change_in_distance (const core::pose::Pose &pose, vector1< Real > &running_average_distance, vector1< Real > &change_in_distance, vector1< Real > &magnitude_of_change)
vector1< Size >	get_inflection_points (vector1< Real > change_in_distance, vector1< Real > change_in_magnitude)
Size	get_nearest_loop_to_helix (core::pose::Pose &pose, Size starting_pt)
vector1< Size >	get_loop_to_helix_points (core::pose::Pose &pose, vector1< Size > inflection_points)
Size	find_next_repeat_inflection_point (const core::pose::Pose &pose, vector1< Size > inflection_points, Size starting_inflection_pt, Size MIN_REPEAT_SIZE)
vector1< Size >	gather_repeat (const core::pose::Pose &pose, vector1< Size > inflection_points, Size max_res_variance, Size starting_inflection_pt, Size numb_repeats)
void	matrix3f_to_xyzMatrix (Eigen::Matrix3f const &Re, numeric::xyzMatrix< core::Real > &R)
void	identity_matrix (numeric::xyzMatrix< core::Real > &R)
void	calculate_helical_parameters (core::pose::Pose const &pose, Size startRep1, Size endRep1, Size startRep2, Size endRep2, std::string &handedness, Real &rise_out, Real &radius_out, Real &omega_out)
Real	tm_superimpose (core::pose::Pose &pose, core::pose::Pose &ref_pose)
void	calculate_helical_parameters_helper (core::pose::Pose const &pose, Size startRep1, Size endRep1, Size startRep2, Size endRep2, std::string &handedness, Real &rise_out, Real &radius_out, Real &omega_out, Real &tm_out)
Real	calculate_sheet_pct (core::pose::Pose &pose, vector1< Size > repeat_positions)
Real	calculate_rmsd_variance (core::pose::Pose &pose, Size start1_res, Size end1_res, Size start2_res, Size end2_res)
Real	calculate_tm_variance (core::pose::Pose &pose, Size start1_res, Size end1_res, Size start2_res, Size end2_res)
Real	calculate_max_rmsd_variance (core::pose::Pose &pose, vector1< Size > repeat_positions)
Real	calculate_min_tm_variance (core::pose::Pose &pose, vector1< Size > repeat_positions)
vector1< vector1< Size > >	gather_repeats (core::pose::Pose &pose, vector1< Size > inflection_points)
void	gather_info_all_repeats (core::pose::Pose &pose, vector1< vector1< Size > > all_repeats, vector1< vector1< Size > > &selected_repeats, vector1< std::string > &handednesses_v, vector1< Real > &radius_v, vector1< Real > &rise_v, vector1< Real > &omega_v, vector1< Real > &rmsd_v, vector1< Real > &tm_v)
void	gather_info_canonical_repeats (core::pose::Pose &pose, vector1< vector1< Size > > all_repeats, vector1< vector1< Size > > &selected_repeats, vector1< std::string > &handednesses_v, vector1< Real > &radius_v, vector1< Real > &rise_v, vector1< Real > &omega_v, vector1< Real > &rmsd_v, vector1< Real > &tm_v)
void	output_all_repeats (vector1< vector1< Size > > all_repeats, std::string id, vector1< std::string > &handedness, vector1< Real > &radii, vector1< Real > &rises, vector1< Real > &omegas, vector1< Real > rmsd, vector1< Real > tm, std::ostream &output)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("extractNativeRepeats")

Function Documentation

calculate_helical_parameters()

void calculate_helical_parameters	(	core::pose::Pose const &	pose,
		Size	startRep1,
		Size	endRep1,
		Size	startRep2,
		Size	endRep2,
		std::string &	handedness,
		Real &	rise_out,
		Real &	radius_out,
		Real &	omega_out
	)

References ObjexxFCL::format::A(), ObjexxFCL::abs(), numeric::statistics::cov(), basic::Tracer::Debug, build_jacobian::direction, hist2d::H, create_a3b_hbs::i, ObjexxFCL::format::I(), ObjexxFCL::format::L(), N, basic::options::OptionKeys::AnchoredDesign::filters::omega, beta_nonlocal::pose, docking::R, basic::options::OptionKeys::cluster::radius, predPRE::t, and TR.

Referenced by calculate_helical_parameters_helper().

calculate_helical_parameters_helper()

void calculate_helical_parameters_helper	(	core::pose::Pose const &	pose,
		Size	startRep1,
		Size	endRep1,
		Size	startRep2,
		Size	endRep2,
		std::string &	handedness,
		Real &	rise_out,
		Real &	radius_out,
		Real &	omega_out,
		Real &	tm_out
	)

References calculate_helical_parameters(), create_a3b_hbs::ii, basic::options::OptionKeys::mh::harvest::max_res, numeric::min(), pdbslice(), beta_nonlocal::pose, basic::options::OptionKeys::stepwise::slice_res1, basic::options::OptionKeys::stepwise::slice_res2, and tm_superimpose().

Referenced by gather_info_all_repeats(), and gather_info_canonical_repeats().

calculate_max_rmsd_variance()

Real calculate_max_rmsd_variance	(	core::pose::Pose &	pose,
		vector1< Size >	repeat_positions
	)

References calculate_rmsd_variance(), create_a3b_hbs::ii, and beta_nonlocal::pose.

Referenced by gather_info_all_repeats(), gather_info_canonical_repeats(), and gather_repeats().

calculate_min_tm_variance()

Real calculate_min_tm_variance	(	core::pose::Pose &	pose,
		vector1< Size >	repeat_positions
	)

References calculate_tm_variance(), create_a3b_hbs::ii, and beta_nonlocal::pose.

Referenced by gather_info_canonical_repeats(), and gather_repeats().

calculate_rmsd_variance()

Real calculate_rmsd_variance	(	core::pose::Pose &	pose,
		Size	start1_res,
		Size	end1_res,
		Size	start2_res,
		Size	end2_res
	)

References create_a3b_hbs::ii, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::relax::sequence.

Referenced by calculate_max_rmsd_variance().

calculate_sheet_pct()

Real calculate_sheet_pct	(	core::pose::Pose &	pose,
		vector1< Size >	repeat_positions
	)

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

Referenced by gather_repeats().

calculate_tm_variance()

Real calculate_tm_variance	(	core::pose::Pose &	pose,
		Size	start1_res,
		Size	end1_res,
		Size	start2_res,
		Size	end2_res
	)

References create_a3b_hbs::ii, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, and tm_superimpose().

Referenced by calculate_min_tm_variance().

find_next_repeat_inflection_point()

Size find_next_repeat_inflection_point	(	const core::pose::Pose &	pose,
		vector1< Size >	inflection_points,
		Size	starting_inflection_pt,
		Size	MIN_REPEAT_SIZE
	)

References numeric::xyzVector< T >::distance(), create_a3b_hbs::ii, beta_nonlocal::pose, erraser_analysis::res1, and erraser_analysis::res2.

Referenced by gather_repeat().

gather_info_all_repeats()

void gather_info_all_repeats	(	core::pose::Pose &	pose,
		vector1< vector1< Size > >	all_repeats,
		vector1< vector1< Size > > &	selected_repeats,
		vector1< std::string > &	handednesses_v,
		vector1< Real > &	radius_v,
		vector1< Real > &	rise_v,
		vector1< Real > &	omega_v,
		vector1< Real > &	rmsd_v,
		vector1< Real > &	tm_v
	)

References calculate_helical_parameters_helper(), calculate_max_rmsd_variance(), utility::io::oc::cout, detail::find(), create_a3b_hbs::ii, kk, basic::options::OptionKeys::AnchoredDesign::filters::omega, beta_nonlocal::pose, and basic::options::OptionKeys::cluster::radius.

Referenced by main().

gather_info_canonical_repeats()

void gather_info_canonical_repeats	(	core::pose::Pose &	pose,
		vector1< vector1< Size > >	all_repeats,
		vector1< vector1< Size > > &	selected_repeats,
		vector1< std::string > &	handednesses_v,
		vector1< Real > &	radius_v,
		vector1< Real > &	rise_v,
		vector1< Real > &	omega_v,
		vector1< Real > &	rmsd_v,
		vector1< Real > &	tm_v
	)

References calculate_helical_parameters_helper(), calculate_max_rmsd_variance(), calculate_min_tm_variance(), create_a3b_hbs::ii, kk, basic::options::OptionKeys::AnchoredDesign::filters::omega, beta_nonlocal::pose, and basic::options::OptionKeys::cluster::radius.

Referenced by main().

gather_repeat()

vector1<Size> gather_repeat	(	const core::pose::Pose &	pose,
		vector1< Size >	inflection_points,
		Size	max_res_variance,
		Size	starting_inflection_pt,
		Size	numb_repeats
	)

References find_next_repeat_inflection_point(), create_a3b_hbs::ii, and beta_nonlocal::pose.

Referenced by gather_repeats().

gather_repeats()

vector1<vector1 <Size> > gather_repeats	(	core::pose::Pose &	pose,
		vector1< Size >	inflection_points
	)

References calculate_max_rmsd_variance(), calculate_min_tm_variance(), calculate_sheet_pct(), utility::io::oc::cout, gather_repeat(), and beta_nonlocal::pose.

Referenced by main().

get_change_in_distance()

void get_change_in_distance	(	const core::pose::Pose &	pose,
		vector1< Real > &	running_average_distance,
		vector1< Real > &	change_in_distance,
		vector1< Real > &	magnitude_of_change
	)

References ObjexxFCL::abs(), center_of_mass(), numeric::xyzVector< T >::distance(), create_a3b_hbs::ii, enumerate_junctions::int, beta_nonlocal::jj, beta_nonlocal::pose, numeric::random::random_range(), numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Referenced by main().

get_inflection_points()

vector1<Size> get_inflection_points	(	vector1< Real >	change_in_distance,
		vector1< Real >	change_in_magnitude
	)

References ObjexxFCL::abs(), create_a3b_hbs::ii, enumerate_junctions::int, kk, erraser_analysis::res1, and erraser_analysis::res2.

Referenced by main().

get_loop_to_helix_points()

vector1<Size> get_loop_to_helix_points	(	core::pose::Pose &	pose,
		vector1< Size >	inflection_points
	)

References detail::find(), get_nearest_loop_to_helix(), create_a3b_hbs::ii, and beta_nonlocal::pose.

Referenced by main().

get_nearest_loop_to_helix()

Size get_nearest_loop_to_helix	(	core::pose::Pose &	pose,
		Size	starting_pt
	)

References create_a3b_hbs::ii, enumerate_junctions::int, numeric::max(), and beta_nonlocal::pose.

Referenced by get_loop_to_helix_points().

identity_matrix()

void identity_matrix

(

numeric::xyzMatrix< core::Real > &

R

)

References docking::R.

main()

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

References argv, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, test.T009_Exceptions::e, gather_info_all_repeats(), gather_info_canonical_repeats(), gather_repeats(), get_change_in_distance(), get_inflection_points(), get_loop_to_helix_points(), create_a3b_hbs::ii, basic::init(), gaussian-sampling::input, basic::options::OptionKeys::AnchoredDesign::filters::omega, output_all_repeats(), pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::cluster::radius, average_rmsds::rmsd, basic::options::OptionKeys::frags::scoring::scoring, tag, and tag_from_pose().

matrix3f_to_xyzMatrix()

void matrix3f_to_xyzMatrix	(	Eigen::Matrix3f const &	Re,
		numeric::xyzMatrix< core::Real > &	R
	)

References docking::R.

output_all_repeats()

void output_all_repeats	(	vector1< vector1< Size > >	all_repeats,
		std::string	id,
		vector1< std::string > &	handedness,
		vector1< Real > &	radii,
		vector1< Real > &	rises,
		vector1< Real > &	omegas,
		vector1< Real >	rmsd,
		vector1< Real >	tm,
		std::ostream &	output
	)

References create_a3b_hbs::ii, kk, bin_torsions::output, and average_rmsds::rmsd.

Referenced by main().

tm_superimpose()

Real tm_superimpose	(	core::pose::Pose &	pose,
		core::pose::Pose &	ref_pose
	)

References beta_nonlocal::pose.

Referenced by calculate_helical_parameters_helper(), and calculate_tm_variance().

Variable Documentation

TR

basic::Tracer TR("extractNativeRepeats") ( "extractNativeRepeats"  )

static

Referenced by calculate_helical_parameters().