pentcb.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/smhybrid.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/keys/matdes.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/Tracer.hh>
#include <basic/database/open.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.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/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/make_symmetric_task.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/RotamerSampleOptions.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/func/XYZ_Func.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <numeric/conversions.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.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/symmetry/SetupForSymmetryMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/scoring/ImplicitFastClashCheck.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <apps/pilot/will/will_util.ihh>
#include <apps/pilot/will/mynamespaces.ihh>
#include <sys/stat.h>

Classes
struct	Hit

Macros
#define	CONTACT_D2   20.25
#define	CONTACT_TH   5
#define	NSS   8192

Typedefs
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat

Functions
Real const	sqr (Real const r)
Real	sigmoidish_neighbor (Real const &sqdist)
double	sicfast (vector1< Vec > &pa, vector1< Vec > &pb, vector1< Vec > &cba, vector1< Vec > &cbb, Real &cbcount, double BIN=1.8)
bool	cmp (Hit i, Hit j)
void	TEST (Pose const &init, Hit const &h, Real cbcount)
void	dock (Pose const init, std::string const &fn, vector1< xyzVector< double > > const &ssamp)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("pentcb")
static core::io::silent::SilentFileData	sfd

Macro Definition Documentation

CONTACT_D2

#define CONTACT_D2   20.25

CONTACT_TH

#define CONTACT_TH   5

NSS

#define NSS   8192

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

Vec

typedef numeric::xyzVector<Real> Vec

Function Documentation

cmp()

bool cmp	(	Hit	i,
		Hit	j
	)

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by dock().

dock()

void dock	(	Pose const	init,
		std::string const &	fn,
		vector1< xyzVector< double > > const &	ssamp
	)

References begin, cmp(), CONTACT_TH, utility::io::oc::cout, end, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, h, has, create_a3b_hbs::i, basic::init(), test.T008_Serialization::iss, subloop_histogram::iterator, min(), NSS, docking::R, rot, numeric::rotation_matrix_degrees(), sicfast(), subloop_histogram::size, predPRE::t, TEST(), and TR.

Referenced by main().

main()

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

References argv, dock(), basic::options::OptionKeys::in::file::dssp, test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, basic::init(), NSS, basic::database::open(), basic::options::option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::s, subloop_histogram::size, str(), basic::options::TR, trans_pose(), x, predPRE::y, and predPRE::z.

sicfast()

double sicfast	(	vector1< Vec > &	pa,
		vector1< Vec > &	pb,
		vector1< Vec > &	cba,
		vector1< Vec > &	cbb,
		Real &	cbcount,
		double	BIN = 1.8
	)

References BIN, 3d_histogram::dz, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, max(), min(), sigmoidish_neighbor(), xmn, xmx, ymn, and ymx.

Referenced by dock().

sigmoidish_neighbor()

Real sigmoidish_neighbor ( Real const &  sqdist )

inline

References CONTACT_D2, and sqr().

Referenced by sicfast(), and TEST().

sqr()

Real const sqr ( Real const  r )

inline

References create_a3b_hbs::r.

Referenced by sigmoidish_neighbor().

TEST()

void TEST	(	Pose const &	init,
		Hit const &	h,
		Real	cbcount
	)

References numeric::xyzVector< T >::distance_squared(), h, has, basic::init(), min(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, enumerate_junctions::q, docking::s, sigmoidish_neighbor(), str(), ObjexxFCL::string_of(), TR, utility_exit_with_message, xform_pose(), and xform_pose_rev().

Referenced by dock().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

TR

basic::Tracer TR("pentcb") ( "pentcb"  )

static

Referenced by dock(), and TEST().