xfrags.cc File Reference

#include <core/scoring/motif/xfrags.hh>
#include <core/scoring/motif/motif_hash_stuff.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/Tracer.hh>
#include <basic/database/open.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/mh.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/pymol_chains.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/pose/xyzStripeHashPose.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreTypeManager.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/dssp/StrandPairing.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.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 <numeric/xyzVector.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/fixedsizearray1.hh>
#include <numeric/xyzTransform.hh>
#include <numeric/geometry/hashing/SixDHasher.hh>
#include <boost/unordered_set.hpp>
#include <boost/foreach.hpp>
#include <bitset>
#include <pthread.h>

Namespaces
	core
	A class for reading in the atom type properties.
	core::scoring
	core::scoring::motif

Macros
#define	MAX_UINT16   65535
#define	MAX_UINT8   255
#define	XFORM_SCORE_FILE_VERSION   1

Functions
Real6	core::scoring::motif::get_bins (Real c, Real a)
static Real	core::scoring::motif::uint16_to_real (uint16_t const &val, Real const &lb, Real const &ub)
static uint16_t	core::scoring::motif::real_to_uint16 (Real const &val, Real const &lb, Real const &ub)
static Real	core::scoring::motif::uint8_to_real (uint8_t const &val, Real const &lb, Real const &ub)
static uint8_t	core::scoring::motif::real_to_uint8 (Real const &val, Real const &lb, Real const &ub)
ostream &	core::scoring::motif::operator<< (ostream &out, Xfres const &x)
std::istream &	core::scoring::motif::operator>> (std::istream &in, Xfres &x)
bool	core::scoring::motif::read_xfres_binary (string const &fname, vector1< Xfres > &xfres)
bool	core::scoring::motif::read_xfres_binary (std::istream &in, vector1< Xfres > &xfres)
bool	core::scoring::motif::write_xfres_binary (ostream &out, vector1< Xfres > const &xfres)
bool	core::scoring::motif::write_xfres_binary (string const &fname, vector1< Xfres > const &xfres)
bool	core::scoring::motif::read_xfres_binary (vector1< string > const &fnames, vector1< Xfres > &xfres)
ostream &	core::scoring::motif::operator<< (ostream &out, Xfrag const &x)
std::istream &	core::scoring::motif::operator>> (std::istream &in, Xfrag &x)
bool	core::scoring::motif::read_xfrag_binary (string const &fname, vector1< Xfrag > &xfrag)
bool	core::scoring::motif::read_xfrag_binary (std::istream &in, vector1< Xfrag > &xfrag)
bool	core::scoring::motif::write_xfrag_binary (ostream &out, vector1< Xfrag > const &xfrag)
bool	core::scoring::motif::write_xfrag_binary (string const &fname, vector1< Xfrag > const &xfrag)
bool	core::scoring::motif::read_xfrag_binary (vector1< string > const &fnames, vector1< Xfrag > &xfrag)
bool	core::scoring::motif::read_xfrag_binary (string const &fname, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
bool	core::scoring::motif::read_xfrag_binary (std::istream &in, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
bool	core::scoring::motif::write_xfrag_binary (ostream &out, vector1< Xfrag > const &xfrag, vector1< Xfres > const &xfres)
bool	core::scoring::motif::write_xfrag_binary (string const &fname, vector1< Xfrag > const &xfrag, vector1< Xfres > const &xfres)
bool	core::scoring::motif::read_xfrag_binary (vector1< string > const &fnames, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)

Variables
static basic::Tracer	core::scoring::motif::TR ("core.scoring.motif")

Macro Definition Documentation

#define MAX_UINT16   65535

Referenced by core::scoring::motif::real_to_uint16(), and core::scoring::motif::uint16_to_real().

#define MAX_UINT8   255

Referenced by core::scoring::motif::real_to_uint8(), and core::scoring::motif::uint8_to_real().

#define XFORM_SCORE_FILE_VERSION   1