motif_hash_stuff.hh File Reference

#include <protocols/motif_hash/motif_hash_stuff.fwd.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/option_macros.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/symmetry/util.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/util.hh>
#include <core/pack/task/PackerTask.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/packing/compute_holes_score.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <devel/init.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 <protocols/sic_dock/RigidScore.hh>
#include <protocols/sic_dock/SICFast.hh>
#include <protocols/sic_dock/util.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/fixedsizearray1.hh>
#include <core/pack/rotamer_set/RotamerSetOperation.hh>
#include <numeric/geometry/hashing/SixDHasher.hh>
#include <numeric/HomogeneousTransform.hh>
#include <boost/unordered_map.hpp>

Classes
class	protocols::motif_hash::XformScore
class	protocols::motif_hash::ResPairMotif
class	protocols::motif_hash::ResPairMotifs
class	protocols::motif_hash::Xfres
class	protocols::motif_hash::Xfrag
class	protocols::motif_hash::XfragSet
class	protocols::motif_hash::MotifHash
class	protocols::motif_hash::MotifHashManager
struct	protocols::motif_hash::MotifHit
class	protocols::motif_hash::MotifHits
class	protocols::motif_hash::MotifRotamerSetOperation

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::motif_hash

Typedefs
typedef utility::vector1< bool >	protocols::motif_hash::Bools
typedef utility::pointer::owning_ptr < MotifRotamerSetOperation >	protocols::motif_hash::MotifRotamerSetOperationOP
typedef utility::pointer::owning_ptr < MotifRotamerSetOperation const >	protocols::motif_hash::MotifRotamerSetOperationCOP

Functions
Real	protocols::motif_hash::align_motif_pose_super (Pose &pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr)
Real	protocols::motif_hash::align_motif_pose_break (Pose &pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr)
static float	protocols::motif_hash::fasterlog (float x)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, XformScore const &xh)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, ResPairMotif const &x)
std::istream &	protocols::motif_hash::operator>> (std::istream &in, ResPairMotif &x)
bool	protocols::motif_hash::read_motifs_binary (std::string const &fname, ResPairMotifs &motifs)
bool	protocols::motif_hash::read_motifs_binary (std::istream &in, ResPairMotifs &motifs)
bool	protocols::motif_hash::write_motifs_binary (std::ostream &out, ResPairMotifs const &motifs)
bool	protocols::motif_hash::write_motifs_binary (std::string const &fname, ResPairMotifs const &motifs)
bool	protocols::motif_hash::read_motifs_binary (vector1< string > const &fnames, ResPairMotifs &motifs)
void	protocols::motif_hash::filter_motifs (ResPairMotifs const &motifs_in, ResPairMotifs &motifs_out)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, Xfres const &x)
std::istream &	protocols::motif_hash::operator>> (std::istream &in, Xfres &x)
bool	protocols::motif_hash::read_xfres_binary (string const &fname, vector1< Xfres > &xfres)
bool	protocols::motif_hash::read_xfres_binary (std::istream &in, vector1< Xfres > &xfres)
bool	protocols::motif_hash::write_xfres_binary (std::ostream &out, vector1< Xfres > const &xfres)
bool	protocols::motif_hash::write_xfres_binary (string const &fname, vector1< Xfres > const &xfres)
bool	protocols::motif_hash::read_xfres_binary (vector1< string > const &fnames, vector1< Xfres > &xfres)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, Xfrag const &x)
std::istream &	protocols::motif_hash::operator>> (std::istream &in, Xfrag &x)
bool	protocols::motif_hash::read_xfrag_binary (string const &fname, vector1< Xfrag > &xfrag)
bool	protocols::motif_hash::read_xfrag_binary (std::istream &in, vector1< Xfrag > &xfrag)
bool	protocols::motif_hash::write_xfrag_binary (std::ostream &out, vector1< Xfrag > const &xfrag)
bool	protocols::motif_hash::write_xfrag_binary (string const &fname, vector1< Xfrag > const &xfrag)
bool	protocols::motif_hash::read_xfrag_binary (vector1< string > const &fnames, vector1< Xfrag > &xfrag)
bool	protocols::motif_hash::read_xfrag_binary (string const &fname, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
bool	protocols::motif_hash::read_xfrag_binary (std::istream &in, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
bool	protocols::motif_hash::write_xfrag_binary (std::ostream &out, vector1< Xfrag > const &xfrag, vector1< Xfres > const &xfres)
bool	protocols::motif_hash::write_xfrag_binary (string const &fname, vector1< Xfrag > const &xfrag, vector1< Xfres > const &xfres)
bool	protocols::motif_hash::read_xfrag_binary (vector1< string > const &fnames, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, MotifHash const &x)
std::istream &	protocols::motif_hash::operator>> (std::istream &in, MotifHash &x)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, MotifHit const &h)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, MotifHits const &h)
void	protocols::motif_hash::merge_motifs ()
void	protocols::motif_hash::dump_motif_pdbs ()
void	protocols::motif_hash::harvest_scores ()
void	protocols::motif_hash::print_scores ()
void	protocols::motif_hash::dump_matching_motifs ()
void	protocols::motif_hash::harvest_motifs ()
void	protocols::motif_hash::print_motifs (std::ostream &out)