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motif_hash_stuff.cc File Reference
#include <core/scoring/motif/motif_hash_stuff.hh>
#include <core/scoring/motif/util.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/chemical/ResidueTypeSet.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.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/motif/reference_frames.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/util.hh>
#include <core/io/pdb/pdb_writer.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 <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 <utility/string_constants.hh>
#include <numeric/xyzTransform.hh>
#include <numeric/geometry/hashing/SixDHasher.hh>
#include <boost/unordered_set.hpp>
#include <boost/foreach.hpp>
#include <bitset>

Classes

struct  core::scoring::motif::MyHash
 
struct  core::scoring::motif::MyPred
 
struct  core::scoring::motif::RMSandEnergyCMP
 

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
 

Typedefs

typedef
utility::fixedsizearray1
< float, 20 > 
core::scoring::motif::float20
 
typedef
utility::fixedsizearray1
< float, 9 > 
core::scoring::motif::float9
 
typedef boost::unordered_set
< ResPairMotif, MyHash, MyPred > 
core::scoring::motif::MotifSet
 

Functions

static basic::Tracer core::scoring::motif::TR ("core.scoring.motif")
 
template<typename T >
static T core::scoring::motif::sqr (T const &x)
 
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)
 
std::ostream & core::scoring::motif::operator<< (std::ostream &out, RPM_FilterStats const &s)
 
ostream & core::scoring::motif::operator<< (ostream &out, ResPairMotif const &x)
 
ostream & core::scoring::motif::operator<< (ostream &out, RM_Type const &x)
 
ostream & core::scoring::motif::operator<< (ostream &out, RPM_Type const &x)
 
bool core::scoring::motif::write_motifs_binary (ostream &out, ResPairMotifs const &motifs)
 
bool core::scoring::motif::write_motifs_binary (string const &fname_in, ResPairMotifs const &motifs)
 
bool core::scoring::motif::read_motifs_binary (std::istream &in, ResPairMotifs &motifs)
 
bool core::scoring::motif::read_motifs_binary (string const &fname, ResPairMotifs &motifs)
 
bool core::scoring::motif::read_motifs_binary (vector1< string > const &fnames, ResPairMotifs &motifs)
 
void core::scoring::motif::load_motifs (vector1< string > const &fnames, ResPairMotifs &motifs, ResPairMotifsStringMap *map)
 
void core::scoring::motif::load_motifs (string const &fname, ResPairMotifs &motifs, ResPairMotifsStringMap *map)
 
std::ostream & core::scoring::motif::operator<< (std::ostream &out, XformScoreMap const &x)
 
ostream & core::scoring::motif::operator<< (ostream &out, MotifHit const &h)
 
ostream & core::scoring::motif::operator<< (ostream &out, MotifHits const &h)
 
ostream & core::scoring::motif::operator<< (ostream &out, MotifHash const &x)
 
std::ostream & core::scoring::motif::operator<< (std::ostream &out, ResPairMotifQuery const &opt)
 
void core::scoring::motif::filter_motifs (ResPairMotifs const &motifs_in, ResPairMotifs &motifs_out)
 
void core::scoring::motif::filter_motifs (ResPairMotifs &motifs)
 
ostream & core::scoring::motif::operator<< (ostream &out, XformScore const &xh)
 
ostream & core::scoring::motif::operator<< (ostream &out, XformScoreSringMap const &x)
 
void core::scoring::motif::fill_xform_score_from_file (XformScoreOP &xs, string const &datfile, Real const &wt=1.0)
 
void * core::scoring::motif::preload_motif_data_pthread_wrapper (void *ptr)
 
void core::scoring::motif::preload_motif_data (MotifHashManager &mhman)
 

Variables

const numeric::Real core::scoring::motif::MOTIF_HASH_CART_SIZE = 16.0
 
const uint64_t core::scoring::motif::MOTIF_VERSION = 2
 

Macro Definition Documentation

#define MAX_UINT16   65535
#define MAX_UINT8   255