symdock_enum_3_1.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/string_util.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>

Typedefs
typedef xyzVector< core::Real >	Vec
typedef xyzMatrix< core::Real >	Mat
typedef xyzVector< double >	Vecf
typedef xyzMatrix< double >	Matf

Functions
void	trans_pose (Pose &pose, Vec const &trans)
void	rot_pose (Pose &pose, Mat const &rot)
void	rot_pose (Pose &pose, Mat const &rot, Vec const &cen)
void	rot_pose (Pose &pose, Vec const &axis, core::Real const &ang)
void	rot_pose (Pose &pose, Vec const &axis, core::Real const &ang, Vec const &cen)
void	alignaxis (Pose &pose, Vec newaxis, Vec oldaxis, Vec cen=Vec(0, 0, 0))
int	cbcount_vec (vector1< Vecf > &cba, vector1< Vecf > &cbb)
void	set_cb_pairs (vector1< Vecf > &cba, vector1< Vecf > &cbb)
int	pose_cbcount (Pose const &a, Pose const &b)
core::Real	angle_degrees (Vec u, Vec v, Vec w)
double	sicfast (vector1< Vecf > pa, vector1< Vecf > pb, vector1< Vecf > &cba, vector1< Vecf > &cbb, Vecf ori, int &cbcount, bool debug=false)
double	sicfast (Pose const &a, Pose const &b, Vecf ori_in, int &cbcount)
void	run ()
int	main (int argc, char *argv[])

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

Typedef Documentation

Mat

typedef xyzMatrix<core::Real> Mat

Matf

typedef xyzMatrix<double> Matf

Vec

typedef xyzVector<core::Real> Vec

Vecf

typedef xyzVector<double> Vecf

Function Documentation

alignaxis()

void alignaxis	(	Pose &	pose,
		Vec	newaxis,
		Vec	oldaxis,
		Vec	cen = Vec(0,0,0)
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, numeric::xyzVector< T >::cross(), numeric::xyzVector< T >::dot(), numeric::max(), numeric::min(), numeric::xyzVector< T >::normalize(), numeric::xyzVector< T >::normalized(), numeric::constants::d::pi, beta_nonlocal::pose, and rot_pose().

Referenced by TCDock::TCDock().

angle_degrees()

core::Real angle_degrees	(	Vec	u,
		Vec	v,
		Vec	w
	)

References numeric::angle_radians(), numeric::conversions::degrees(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, and w.

Referenced by TCDock::run(), and TCDock::TCDock().

cbcount_vec()

int cbcount_vec	(	vector1< Vecf > &	cba,
		vector1< Vecf > &	cbb
	)

main()

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

References argv, test.T009_Exceptions::e, basic::init(), and run().

pose_cbcount()

int pose_cbcount	(	Pose const &	a,
		Pose const &	b
	)

References a, compute_difference::b, count, create_a3b_hbs::i, and create_a3b_hbs::j.

rot_pose() [1/4]

void rot_pose	(	Pose &	pose,
		Mat const &	rot
	)

References natoms(), beta_nonlocal::pose, and rot.

Referenced by alignaxis(), TCDock::dump_pdb(), TCDock::make_dimer(), TCDock::make_pentamer(), TCDock::make_tetramer(), TCDock::make_trimer(), rot_pose(), run(), and TCDock::TCDock().

rot_pose() [2/4]

void rot_pose	(	Pose &	pose,
		Mat const &	rot,
		Vec const &	cen
	)

References beta_nonlocal::pose, rot, rot_pose(), and trans_pose().

rot_pose() [3/4]

void rot_pose	(	Pose &	pose,
		Vec const &	axis,
		core::Real const &	ang
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, beta_nonlocal::pose, rot_pose(), and numeric::rotation_matrix_degrees().

rot_pose() [4/4]

void rot_pose	(	Pose &	pose,
		Vec const &	axis,
		core::Real const &	ang,
		Vec const &	cen
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, beta_nonlocal::pose, rot_pose(), and numeric::rotation_matrix_degrees().

run()

void run

(

)

References compute_difference::alpha, numeric::angle_degrees(), numeric::angle_radians(), begin, numeric::xyzVector< T >::cross(), numeric::distance_squared(), basic::options::OptionKeys::matdes::dock::dump_pdb, utility::file_basename(), PREcst::fname, loops::gamma, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, ObjexxFCL::lead_zero_string_of(), numeric::max(), numeric::xyzVector< T >::normalized(), basic::options::option, option, adapt_rotamers::ori, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, pna::pnt, pyrosetta.distributed.io::pose_from_file, create_a3b_hbs::r, numeric::conversions::radians(), rot_pose(), numeric::rotation_matrix_degrees(), in::file::s(), set_cb_pairs(), sicfast(), ObjexxFCL::FArray< T >::size(), ObjexxFCL::string_of(), symm, predPRE::t, tan, TR, trans_pose(), utility_exit_with_message, w, x, predPRE::y, and predPRE::z.

Referenced by main().

set_cb_pairs()

void set_cb_pairs	(	vector1< Vecf > &	cba,
		vector1< Vecf > &	cbb
	)

References a, and compute_difference::b.

Referenced by run().

sicfast() [1/2]

double sicfast	(	Pose const &	a,
		Pose const &	b,
		Vecf	ori_in,
		int &	cbcount
	)

References a, compute_difference::b, numeric::cross(), numeric::dot(), create_a3b_hbs::i, numeric::xyzMatrix< Real >::identity(), enumerate_junctions::int, create_a3b_hbs::j, numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, rot, numeric::rotation_matrix(), and sicfast().

sicfast() [2/2]

double sicfast	(	vector1< Vecf >	pa,
		vector1< Vecf >	pb,
		vector1< Vecf > &	cba,
		vector1< Vecf > &	cbb,
		Vecf	ori,
		int &	cbcount,
		bool	debug = false
	)

References BIN, numeric::cross(), basic::options::OptionKeys::msd::debug, numeric::dot(), 3d_histogram::dz, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, numeric::xyzMatrix< Real >::identity(), enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, numeric::max(), numeric::min(), adapt_rotamers::ori, erraser_single_res_analysis::out, rot, numeric::rotation_matrix(), numeric::xyzVector< T >::x(), xmn, xmx, numeric::xyzVector< T >::y(), ymn, ymx, and numeric::xyzVector< T >::z().

Referenced by run(), and sicfast().

trans_pose()

void trans_pose	(	Pose &	pose,
		Vec const &	trans
	)

References natoms(), beta_nonlocal::pose, and trans.

Referenced by TCDock::dump_pdb(), rot_pose(), and run().

Variable Documentation

TR

basic::Tracer TR("symdock_enum") ( "symdock_enum"  )

static

Referenced by run().