FunGroupTK.cc File Reference

#include <basic/options/keys/in.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/ResidueFactory.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Stub.hh>
#include <utility/graph/Graph.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <numeric/random/random.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/scoring/ImplicitFastClashCheck.hh>
#include <sstream>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <platform/types.hh>
#include <core/pose/init_id_map.hh>
#include <protocols/moves/MoverStatistics.hh>
#include <apps/pilot/will/will_util.ihh>
#include <algorithm>
#include <cassert>
#include <cmath>
#include <complex>
#include <cstddef>
#include <cstdio>
#include <cstdlib>
#include <execinfo.h>
#include <iomanip>
#include <iosfwd>
#include <iostream>
#include <istream>
#include <limits>
#include <list>
#include <map>
#include <ostream>
#include <set>
#include <string>
#include <utility>
#include <vector>

Classes
struct	KRSQuery
class	FunGroupTK
class	BruteFunGroupTK
class	KinFunGroupTK

Macros
#define	CYS_CB_HG_DIS   2.911171
#define	CYS_SG_CB_H   0.7494478
#define	CYS_HG_SG_PRJLEN   2.088496
#define	CYS_1oSIN_CB_SG_HG   1.09875
#define	CYS_HG_SG_X_DROP   0.0998
#define	CYS_CB_SG_BLEN   1.808803
#define	CYS_CB_SG_PERP   1.646237

Typedefs
typedef utility::vector1< core::Real >	Reals
typedef utility::vector1< core::Size >	Sizes
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat
typedef utility::vector1< Vec >	Vecs

Enumerations
enum	KRSQueryType { CEN , CEN_ANG , CEN_AXS , CEN_AXS_ORI }

Functions
Real const	sqr (Real const r)
Vec	xyz (Pose const &p, Size const &ia, Size const &ir)
Pose &	alapose (Pose &pose)
vector1< Size >	allifnone (vector1< Size > v, Size n)
void	dumpcgo (Vec v, string l)
void	xform_rsd_gl2 (Stub const &s, Residue &rsd)
core::pack::rotamer_set::RotamerSetOP	get_rotset (Pose &pose, Size icys)
void	run (std::string fname)
int	main (int argc, char *argv[])

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

Macro Definition Documentation

CYS_1oSIN_CB_SG_HG

#define CYS_1oSIN_CB_SG_HG   1.09875

CYS_CB_HG_DIS

#define CYS_CB_HG_DIS   2.911171

CYS_CB_SG_BLEN

#define CYS_CB_SG_BLEN   1.808803

CYS_CB_SG_PERP

#define CYS_CB_SG_PERP   1.646237

CYS_HG_SG_PRJLEN

#define CYS_HG_SG_PRJLEN   2.088496

CYS_HG_SG_X_DROP

#define CYS_HG_SG_X_DROP   0.0998

CYS_SG_CB_H

#define CYS_SG_CB_H   0.7494478

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

Reals

typedef utility::vector1<core::Real> Reals

Sizes

typedef utility::vector1<core::Size> Sizes

Vec

typedef numeric::xyzVector<Real> Vec

Vecs

typedef utility::vector1<Vec> Vecs

Enumeration Type Documentation

KRSQueryType

enum KRSQueryType

Enumerator
CEN
CEN_ANG
CEN_AXS
CEN_AXS_ORI

Function Documentation

alapose()

Pose& alapose

(

Pose &

pose

)

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

Referenced by main(), and run().

allifnone()

vector1<Size> allifnone	(	vector1< Size >	v,
		Size	n
	)

References create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

dumpcgo()

void dumpcgo	(	Vec	v,
		string	l
	)

References utility::io::oc::cerr, extract_by_sidechain_sasa_score::l, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

get_rotset()

core::pack::rotamer_set::RotamerSetOP get_rotset	(	Pose &	pose,
		Size	icys
	)

References beta_nonlocal::pose.

Referenced by run().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), basic::options::option, option, run(), and in::file::s().

run()

void run

(

std::string

fname

)

References alapose(), CEN_ANG, clash(), pyrosetta.io::create_score_function, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, get_rotset(), pyrosetta.distributed.io::get_score_function(), create_a3b_hbs::i, FunGroupTK::ifc(), basic::options::option, option, adapt_rotamers::ori, FunGroupTK::place_c(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), enumerate_junctions::q, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, str(), and TR.

Referenced by main().

sqr()

Real const sqr ( Real const  r )

inline

References create_a3b_hbs::r.

Referenced by KinFunGroupTK::place_c().

xform_rsd_gl2()

void xform_rsd_gl2	(	Stub const &	s,
		Residue &	rsd
	)

References create_a3b_hbs::i, and docking::s.

xyz()

Vec xyz ( Pose const &  p, Size const &  ia, Size const &  ir  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.

Variable Documentation

TR

basic::Tracer TR("IKFGDB") ( "IKFGDB"  )

static

Referenced by run().