repeat_dock.cc File Reference

#include <basic/Tracer.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/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/SequenceMapping.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.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/kinematics/MoveMap.hh>
#include <core/kinematics/util.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/Minimizer.hh>
#include <core/optimization/CartesianMinimizer.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/motif/motif_hash_stuff.hh>
#include <core/scoring/motif/util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/pose/motif/reference_frames.hh>
#include <numeric/xyzTransform.hh>
#include <core/types.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <protocols/jumping/util.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <devel/init.hh>
#include <utility/string_constants.hh>
#include <utility/vector1.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <utility/io/ozstream.hh>
#include <iostream>
#include <ObjexxFCL/format.hh>
#include <sstream>

Classes
struct	Dock

Functions
void	get_helices (core::pose::Pose &pose, protocols::loops::LoopsOP helicesOP)
Real	calculate_helical_tail_variance (core::pose::Pose pose, core::pose::Pose native_pose, Dock testDock)
core::pose::Pose	minimize_to_close (core::pose::Pose pose)
void	generate_combined_model (core::pose::Pose pose, core::pose::Pose native_pose, Dock &testDock)
vector1< Dock >	get_all_2helix_docks (core::pose::Pose &pose, core::pose::Pose &native_pose)
vector1< Dock >	get_all_1helix_docks (core::pose::Pose &pose, core::pose::Pose &native_pose)
core::Real	compute_motif_score (core::pose::Pose const &pose, Size start_res, Size end_res, core::scoring::motif::MotifHashManager *mman_)
void	get_second_2_helices (Dock &dock, core::pose::Pose pose, Size &start_res, Size &end_res)
core::pose::Pose	superimpose_A_to_all (Dock &dock, core::pose::Pose native_pose)
void	calculate_motif_scores (Dock &dock, core::scoring::motif::MotifHashManager *mman_)
int	main (int argc, char *argv[])

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

Function Documentation

calculate_helical_tail_variance()

Real calculate_helical_tail_variance	(	core::pose::Pose	pose,
		core::pose::Pose	native_pose,
		Dock	testDock
	)

References ObjexxFCL::abs(), Dock::h1_nat_end, Dock::h1_nat_start, Dock::h1_pos_end, Dock::h1_pos_start, Dock::h2_nat_end, Dock::h2_nat_start, Dock::h2_pos_end, Dock::h2_pos_start, create_a3b_hbs::ii, enumerate_junctions::int, docking::native_pose, beta_nonlocal::pose, execute::residues, average_rmsds::rmsd, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

calculate_motif_scores()

void calculate_motif_scores	(	Dock &	dock,
		core::scoring::motif::MotifHashManager *	mman_
	)

References compute_motif_score(), basic::options::OptionKeys::matdes::dock::dock, indel::end_res, get_second_2_helices(), and indel::start_res.

Referenced by main().

compute_motif_score()

core::Real compute_motif_score	(	core::pose::Pose const &	pose,
		Size	start_res,
		Size	end_res,
		core::scoring::motif::MotifHashManager *	mman_
	)

References basic::options::OptionKeys::mh::match::aa1, basic::options::OptionKeys::mh::match::aa2, dist(), basic::options::OptionKeys::in::file::dssp, indel::end_res, numeric::xyzTransform< T >::inverse(), beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::mh::match::ss1, basic::options::OptionKeys::mh::match::ss2, and indel::start_res.

Referenced by calculate_motif_scores().

generate_combined_model()

void generate_combined_model	(	core::pose::Pose	pose,
		core::pose::Pose	native_pose,
		Dock &	testDock
	)

References ObjexxFCL::abs(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, Dock::centroid_score, pyrosetta::create_score_function, test.T009_Exceptions::e, Dock::h1_nat_end, Dock::h1_nat_start, Dock::h1_pos_end, Dock::h1_pos_start, Dock::h2_nat_end, Dock::h2_nat_start, Dock::h2_pos_end, Dock::h2_pos_start, create_a3b_hbs::ii, numeric::max(), numeric::min(), Dock::nat_final_natCoords_end, Dock::nat_final_natCoords_start, Dock::nat_final_poseCoords_end, Dock::nat_final_poseCoords_start, docking::native_pose, pdbslice(), beta_nonlocal::pose, Dock::redesign_final_poseCoords_end, Dock::redesign_final_poseCoords_start, Dock::repeat_final_poseCoords_end, Dock::repeat_final_poseCoords_start, create_a3b_hbs::score, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, Dock::single_helix, superimpose_pose(), Dock::unclosed_pose, Dock::unclosed_pose_full, basic::options::OptionKeys::remodel::vdw, and Dock::vdw_score.

Referenced by main().

get_all_1helix_docks()

vector1<Dock> get_all_1helix_docks	(	core::pose::Pose &	pose,
		core::pose::Pose &	native_pose
	)

References get_helices(), create_a3b_hbs::ii, docking::native_pose, beta_nonlocal::pose, range, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by main().

get_all_2helix_docks()

vector1<Dock> get_all_2helix_docks	(	core::pose::Pose &	pose,
		core::pose::Pose &	native_pose
	)

References get_helices(), create_a3b_hbs::ii, kk, docking::native_pose, beta_nonlocal::pose, range, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by main().

get_helices()

void get_helices	(	core::pose::Pose &	pose,
		protocols::loops::LoopsOP	helicesOP
	)

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

Referenced by get_all_1helix_docks(), get_all_2helix_docks(), and get_second_2_helices().

get_second_2_helices()

void get_second_2_helices	(	Dock &	dock,
		core::pose::Pose	pose,
		Size &	start_res,
		Size &	end_res
	)

References basic::options::OptionKeys::matdes::dock::dock, indel::end_res, get_helices(), numeric::max(), numeric::min(), beta_nonlocal::pose, and indel::start_res.

Referenced by calculate_motif_scores().

main()

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

References argv, calculate_helical_tail_variance(), calculate_motif_scores(), Dock::centroid_score, Dock::chainA_motif_score, basic::options::OptionKeys::chemical::chemical, demo.D060_Folding::counter, test.T009_Exceptions::e, Dock::final_pose, generate_combined_model(), get_all_1helix_docks(), get_all_2helix_docks(), create_a3b_hbs::ii, basic::init(), gaussian-sampling::input, Dock::nat_final_poseCoords_end, Dock::nat_final_poseCoords_start, in::file::native(), docking::native_pose, option, Dock::overall_motif_score, make_symmdef_file_denovo::pos, pyrosetta.distributed.io::pose_from_file, Dock::redesign_final_poseCoords_end, Dock::redesign_final_poseCoords_start, Dock::repeat_final_poseCoords_end, Dock::repeat_final_poseCoords_start, average_rmsds::rmsd, basic::options::OptionKeys::stepwise::s2, basic::options::OptionKeys::frags::scoring::scoring, sfd, basic::options::OptionKeys::out::file::silent, Dock::single_helix, challenge::ss, utility::string_split(), superimpose_A_to_all(), tag, tag_from_pose(), and Dock::vdw_score.

minimize_to_close()

core::pose::Pose minimize_to_close

(

core::pose::Pose

pose

)

References utility::io::oc::cout, pyrosetta::create_score_function, beta_nonlocal::mm, basic::options::OptionKeys::optimization::optimization, and beta_nonlocal::pose.

superimpose_A_to_all()

core::pose::Pose superimpose_A_to_all	(	Dock &	dock,
		core::pose::Pose	native_pose
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, pyrosetta::create_score_function, basic::options::OptionKeys::matdes::dock::dock, test.T009_Exceptions::e, create_a3b_hbs::ii, utility::LETTERS(), docking::native_pose, create_a3b_hbs::score, basic::options::OptionKeys::frags::scoring::scoring, and superimpose_pose().

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("repeat_dock") ( "repeat_dock"  )

static