coiled_coil_search.cc File Reference

#include <core/id/AtomID_Map.hh>
#include <devel/init.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/types.hh>
#include <fstream>
#include <numeric/random/random.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/moves/Mover.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <basic/Tracer.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/string_util.hh>
#include <apps/pilot/will/will_util.hh>

Typedefs
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat
typedef vector1< Size >	Sizes

Functions
void	strip_termini (core::pose::Pose &pose)
Vec	get_helix_axis (core::pose::Pose const &pose, Size start, Size end)
Vec	get_helix_center (core::pose::Pose const &pose, Size start, Size end)
void	make_pdb_atom (numeric::xyzVector< Real > const &coords, std::ostream &out, Size &atom_id)
int	main (int argc, char *argv[])

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

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

Sizes

typedef vector1<Size> Sizes

Vec

typedef numeric::xyzVector<Real> Vec

Function Documentation

get_helix_axis()

Vec get_helix_axis	(	core::pose::Pose const &	pose,
		Size	start,
		Size	end
	)

References end, beta_nonlocal::pose, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by main().

get_helix_center()

Vec get_helix_center	(	core::pose::Pose const &	pose,
		Size	start,
		Size	end
	)

References end, beta_nonlocal::pose, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by apps::pilot::HelixMover::get_helix_centers(), and main().

main()

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

References a, kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, numeric::angle_degrees(), argv, numeric::xyzVector< T >::cross(), basic::options::OptionKeys::in::file::dssp, test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, PREcst::fname, get_helix_axis(), get_helix_center(), create_a3b_hbs::i, basic::init(), subloop_histogram::iterator, create_a3b_hbs::j, make_symmdef_file_denovo::jump_num, numeric::xyzVector< T >::length(), numeric::xyzVector< T >::normalize(), basic::options::OptionKeys::matdes::num_subs_building_block, basic::options::option, option, P, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, create_a3b_hbs::r, rot, in::file::s(), subloop_histogram::size, ObjexxFCL::string_of(), make_symmdef_file_denovo::subunits, basic::options::OptionKeys::symmetry::symmetry, TR, trans, utility_exit_with_message, w, x, numeric::x_rotation_matrix_degrees(), and predPRE::z.

make_pdb_atom()

void make_pdb_atom	(	numeric::xyzVector< Real > const &	coords,
		std::ostream &	out,
		Size &	atom_id
	)

References ObjexxFCL::format::F(), and test.T110_numeric::I.

strip_termini()

void strip_termini

(

core::pose::Pose &

pose

)

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

Variable Documentation

TR

basic::Tracer TR("coiled_coil_search") ( "coiled_coil_search"  )

static

Referenced by main().