test_CCD_loop_closure.cc File Reference

Integration test application for testing CCD loop closure. More...

#include <devel/init.hh>
#include <core/types.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/pose/Pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/TorsionID.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/loop_closure/ccd/CCDLoopClosureMover.hh>
#include <numeric/random/random.hh>
#include <utility/excn/Exceptions.hh>
#include <iostream>

Functions
PoseOP	get_n_mer_polyalanine (Size n)
PoseOP	get_n_mer_maltose (Size n)
MoveMapOP	get_phi_psi_mm (Size n)
Loop	get_loop_for_n_mer (Size n)
void	randomly_open_pose_loop (Pose &pose, Loop const &loop)
int	main (int argc, char *argv[])

Variables
string const	PATH = "output/"

Detailed Description

Integration test application for testing CCD loop closure.

This application... ...creates polyalanine and polyglucose (maltose) chains of varying lengths, ...randomly opens the chains, and ...uses CCD to close the broken loops.

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

Function Documentation

get_loop_for_n_mer()

Loop get_loop_for_n_mer

(

Size

n

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

Referenced by main().

get_n_mer_maltose()

PoseOP get_n_mer_maltose

(

Size

n

)

References create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, and basic::options::OptionKeys::relax::sequence.

Referenced by main().

get_n_mer_polyalanine()

PoseOP get_n_mer_polyalanine

(

Size

n

)

References create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, and basic::options::OptionKeys::relax::sequence.

Referenced by main().

get_phi_psi_mm()

MoveMapOP get_phi_psi_mm

(

Size

n

)

References create_a3b_hbs::i, beta_nonlocal::mm, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

Referenced by main().

main()

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

References argv, utility::io::oc::cout, test.T009_Exceptions::e, get_loop_for_n_mer(), get_n_mer_maltose(), get_n_mer_polyalanine(), get_phi_psi_mm(), basic::init(), internal_coordinates::loop, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, PATH, beta_nonlocal::pose, randomly_open_pose_loop(), and numeric::interpolation::to_string().

randomly_open_pose_loop()

void randomly_open_pose_loop	(	Pose &	pose,
		Loop const &	loop
	)

References create_a3b_hbs::i, internal_coordinates::loop, beta_nonlocal::pose, numeric::random::rg(), and numeric::random::uniform().

Referenced by main().

Variable Documentation

PATH

string const PATH = "output/"

Referenced by main().