r_frag_quality.cc File Reference

#include <core/conformation/Conformation.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FrameIterator.hh>
#include <core/fragment/FragID_Iterator.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/OrderedFragSet.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/RT.hh>
#include <core/fragment/util.hh>
#include <basic/Tracer.hh>
#include <protocols/jumping/JumpSample.hh>
#include <protocols/jumping/JumpSetup.hh>
#include <core/fragment/SecondaryStructure.hh>
#include <core/scoring/rms_util.hh>
#include <core/pose/Pose.hh>
#include <devel/init.hh>
#include <core/chemical/ChemicalManager.hh>
#include <numeric/angle.functions.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <protocols/toolbox/Cluster.hh>
#include <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/fragment/FragData.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/format.hh>
#include <core/kinematics/AtomTree.hh>
#include <protocols/jumping/PairingLibrary.hh>
#include <core/fragment/Frame.hh>

Classes
class	ThisApplication

Functions
Real	check_jump (pose::Pose const &pose, pose::Pose const &native, JumpSample const &, int downstream_res_nr)
Real	compare_cartesian_rmsd (Pose const &orig_frag, Pose const &pred_frag)
Real	sqr (Real x)
Real	compare_torsion_rmsd (Pose const &orig_frag, Pose const &pred_frag)
Real	compare_frags_pose (Pose const &native, Pose const &test_pose, Frame const &frame, utility::vector1< Size > const &excl)
bool	compute_min_mean_rmsd_frag (FrameList &frames, Pose const &native_pose, Real &min_rmsd, Real &mean_rmsd, Real &max_rmsd)
void	check_quality_of_cluster_frags (Pose const &native_pose, FragSetOP decoy_frags, FragSetOP fill_frags, FragSetOP new_frags)
void	write_cluster_frags (FragSetOP predicted_frags, FragSetOP fill_frags, FragSetOP new_frags)
void	compute_intrinsic_deviation (Pose &test_pose, FragSetOP predicted_frags, Pose const &native_pose)
Real	compare_frags (Pose const &orig_frag, Pose const &pred_frag)
FragSetOP	filter_frags (FragSet const &frags_in, std::string const &filter_file)
int	main (int argc, char **argv)

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

Function Documentation

check_jump()

Real check_jump	(	pose::Pose const &	pose,
		pose::Pose const &	native,
		JumpSample const &	,
		int	downstream_res_nr
	)

References docking::a1, docking::a2, docking::a3, docking::b1, docking::b2, docking::b3, ObjexxFCL::format::F(), create_a3b_hbs::i, basic::Tracer::Info, numeric::xyzVector< T >::length(), surface_app::native, beta_nonlocal::pose, erraser_analysis::res1, erraser_analysis::res2, ObjexxFCL::format::RJ(), loops_kic::rms, and tr.

Referenced by main().

check_quality_of_cluster_frags()

void check_quality_of_cluster_frags	(	Pose const &	native_pose,
		FragSetOP	decoy_frags,
		FragSetOP	fill_frags,
		FragSetOP	new_frags
	)

References compute_min_mean_rmsd_frag(), score_vs_rmsd::frames, BundlePairRmsdCalculator::max_rmsd, docking::native_pose, option, make_symmdef_file_denovo::pos, and ObjexxFCL::format::RJ().

Referenced by main().

compare_cartesian_rmsd()

Real compare_cartesian_rmsd	(	Pose const &	orig_frag,
		Pose const &	pred_frag
	)

References cmp(), basic::Tracer::Debug, create_a3b_hbs::i, create_a3b_hbs::nres, and tr.

Referenced by compare_frags().

compare_frags()

Real compare_frags	(	Pose const &	orig_frag,
		Pose const &	pred_frag
	)

References compare_cartesian_rmsd(), compare_torsion_rmsd(), option, and internal_coordinates::torsion().

compare_frags_pose()

Real compare_frags_pose	(	Pose const &	native,
		Pose const &	test_pose,
		Frame const &	frame,
		utility::vector1< Size > const &	excl
	)

References cmp(), basic::Tracer::Debug, numeric::kinematic_closure::frame(), create_a3b_hbs::i, surface_app::native, option, basic::options::OptionKeys::cutoutdomain::start, create_a3b_hbs::test_pose, tr, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by compute_intrinsic_deviation(), compute_min_mean_rmsd_frag(), and main().

compare_torsion_rmsd()

Real compare_torsion_rmsd	(	Pose const &	orig_frag,
		Pose const &	pred_frag
	)

References numeric::nearest_angle_degrees(), make_symmdef_file_denovo::pos, and sqr().

Referenced by compare_frags().

compute_intrinsic_deviation()

void compute_intrinsic_deviation	(	Pose &	test_pose,
		FragSetOP	predicted_frags,
		Pose const &	native_pose
	)

References basic::options::OptionKeys::cluster::cluster, compare_frags_pose(), utility::io::oc::cout, dist(), ObjexxFCL::format::F(), detail::find(), numeric::kinematic_closure::frame(), getline(), utility::io::izstream::good(), utility::io::ozstream::good(), create_a3b_hbs::i, basic::options::OptionKeys::in::in, basic::Tracer::Info, create_a3b_hbs::j, line, min(), basic::options::OptionKeys::docking::ligand::min_rms, docking::native_pose, utility::io::izstream::open(), utility::io::ozstream::open(), option, erraser_single_res_analysis::out, oop_conformations::phi, make_symmdef_file_denovo::pos, test.T008_Serialization::pose2, oop_conformations::psi, cluster::radius(), range, ObjexxFCL::format::RJ(), loops_kic::rms, runtime_assert, str(), create_a3b_hbs::test_pose, internal_coordinates::torsion(), tr, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

compute_min_mean_rmsd_frag()

bool compute_min_mean_rmsd_frag	(	FrameList &	frames,
		Pose const &	native_pose,
		Real &	min_rmsd,
		Real &	mean_rmsd,
		Real &	max_rmsd
	)

References compare_frags_pose(), score_vs_rmsd::frames, BundlePairRmsdCalculator::max_rmsd, docking::native_pose, option, create_a3b_hbs::r, and create_a3b_hbs::test_pose.

Referenced by check_quality_of_cluster_frags().

filter_frags()

FragSetOP filter_frags	(	FragSet const &	frags_in,
		std::string const &	filter_file
	)

References basic::Tracer::Error, filter, score_vs_rmsd::frames, getline(), basic::Tracer::Info, line, make_symmdef_file_denovo::pos, subloop_histogram::size, tr, and utility_exit_with_message.

Referenced by main().

main()

int main	(	int	argc,
		char **	argv
	)

References argv, check_jump(), check_quality_of_cluster_frags(), compare_frags_pose(), compute_intrinsic_deviation(), utility::io::oc::cout, test.T009_Exceptions::e, end, create_a3b_hbs::f, ObjexxFCL::format::F(), evaluate_beta_mutants::file, filter, filter_frags(), basic::options::OptionKeys::in::file::fold_tree, numeric::kinematic_closure::frame(), create_a3b_hbs::i, basic::Tracer::Info, basic::init(), docking::jumps, ObjexxFCL::len(), beta_nonlocal::mm, in::file::native(), surface_app::native, utility::io::ozstream::open(), basic::options::option, option, erraser_single_res_analysis::out, kic_runner::pdb, erraser_single_res_analysis::pdb_id, make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::cluster::radius, ThisApplication::register_options(), ObjexxFCL::format::RJ(), in::file::s(), subloop_histogram::size, create_a3b_hbs::test_pose, internal_coordinates::torsion(), internal_coordinates::torsions, tr, basic::options::OptionKeys::inout::dbms::user, detail::write(), and write_cluster_frags().

sqr()

Real sqr ( Real  x )

inline

References x.

Referenced by compare_torsion_rmsd().

write_cluster_frags()

void write_cluster_frags	(	FragSetOP	predicted_frags,
		FragSetOP	fill_frags,
		FragSetOP	new_frags
	)

References basic::options::OptionKeys::cluster::cluster, count, PREcst::fit(), for(), numeric::kinematic_closure::frame(), getline(), utility::io::izstream::good(), create_a3b_hbs::i, basic::options::OptionKeys::in::in, basic::Tracer::Info, oop_conformations::length, line, max(), beta_nonlocal::mm, N, lactamize::nr, utility::io::izstream::open(), option, make_symmdef_file_denovo::pos, beta_nonlocal::pose, ObjexxFCL::format::RJ(), runtime_assert, str(), sum(), tr, basic::Tracer::Trace, utility_exit_with_message, basic::Tracer::TracerProxy::visible(), and basic::Tracer::Warning.

Referenced by main().

Variable Documentation

tr

basic::Tracer tr("main") ( "main"  )

static

Referenced by check_jump(), compare_cartesian_rmsd(), compare_frags_pose(), compute_intrinsic_deviation(), filter_frags(), main(), and write_cluster_frags().