motif_hash_stuff.cc File Reference

#include <protocols/motif_hash/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/ResidueFactory.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/util.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 <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/xyzStripeHashPose.hh>
#include <protocols/sic_dock/util.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/fixedsizearray1.hh>
#include <numeric/geometry/hashing/SixDHasher.hh>
#include <numeric/HomogeneousTransform.hh>
#include <protocols/sic_dock/read_biounit.hh>
#include <boost/unordered_set.hpp>

Classes
struct	protocols::motif_hash::MyHash
struct	protocols::motif_hash::MyPred

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

Macros
#define	MAX_UINT16   65535
#define	MAX_UINT8   255

Typedefs
typedef numeric::xyzVector < core::Real >	protocols::motif_hash::Vec
typedef numeric::xyzMatrix < core::Real >	protocols::motif_hash::Mat
typedef numeric::xyzTransform < core::Real >	protocols::motif_hash::Xform
typedef utility::fixedsizearray1 < float, 20 >	protocols::motif_hash::float20
typedef utility::fixedsizearray1 < float, 9 >	protocols::motif_hash::float9
typedef boost::unordered_set < ResPairMotif, MyHash, MyPred >	protocols::motif_hash::MotifSet

Functions
Mat	protocols::motif_hash::random_rotation ()
std::string	protocols::motif_hash::tag_from_pdb_fname (std::string const &fname0)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, Real6 const &r6)
Real	protocols::motif_hash::rt6_rt6_bb_dis2_explicit_stupid (Real6 const &x1, Real6 const &x2)
Real	protocols::motif_hash::rt6_rt6_dis2 (Real6 const &x1, Real6 const &x2, Real const lever)
Real	protocols::motif_hash::rt6_rt6_bb_dis2 (Real6 const &x1, Real6 const &x2)
Real6	protocols::motif_hash::inverse_rt6 (Real6 const &rt)
Real6	protocols::motif_hash::rt_to_real6 (core::kinematics::RT const &rt)
core::kinematics::RT	protocols::motif_hash::real6_to_rt (Real6 const &rt6)
Real6	protocols::motif_hash::get_residue_pair_rt6 (Pose const &pose1, Size ir, Pose const &pose2, Size jr)
Real6	protocols::motif_hash::get_residue_pair_rt6 (Pose const &pose, Size ir, Size jr)
void	protocols::motif_hash::set_residue_pair_rt (Real6 const &rt6, Pose &pose, Size ir, Size jr)
Real	protocols::motif_hash::uint16_to_real (uint16_t const &val, Real const &lb, Real const &ub)
uint16_t	protocols::motif_hash::real_to_uint16 (Real const &val, Real const &lb, Real const &ub)
Real	protocols::motif_hash::uint8_to_real (uint8_t const &val, Real const &lb, Real const &ub)
uint8_t	protocols::motif_hash::real_to_uint8 (Real const &val, Real const &lb, Real const &ub)
vector1< Real >	protocols::motif_hash::get_sasa (Pose const &pose, Real const &probesize)
vector1< Real >	protocols::motif_hash::get_nbrs (Pose const &pose)
void	protocols::motif_hash::HACK_dump_helix (core::pose::Pose const &pose, string fname, int beg, int end)
int	protocols::motif_hash::HACK_dump_helices (core::pose::Pose const &pose, string tag, int nres, int minlen=10)
utility::fixedsizearray1< Real, 6 >	protocols::motif_hash::get_bins (Real c, Real a)
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)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, ResPairMotif const &x)
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 (std::istream &in, ResPairMotifs &motifs)
bool	protocols::motif_hash::read_motifs_binary (std::string const &fname, ResPairMotifs &motifs)
bool	protocols::motif_hash::read_motifs_binary (vector1< string > const &fnames, ResPairMotifs &motifs)
void	protocols::motif_hash::load_motifs (vector1< string > const &fnames, ResPairMotifs &motifs)
void	protocols::motif_hash::load_motifs (string const &fname, ResPairMotifs &motifs)
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)
void	protocols::motif_hash::print_motifs (std::ostream &out)
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::filter_motifs (ResPairMotifs const &motifs_in, ResPairMotifs &motifs_out)
Real6 &	protocols::motif_hash::reframe_rt_centered (Real6 &rt)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, XformScore const &xh)
bool	protocols::motif_hash::gather_simplemotifs (ResPairMotifs &motifs, string const &tag, Pose const &pose, core::scoring::dssp::Dssp &dssp, Size const &ir, core::scoring::EnergyEdge const &edge, vector1< Real > const &occupancy, vector1< Real > const &bfactors, vector1< Real > const &rsd_sasa, vector1< Real > const &nbrs, int &nbad, int &nbadbfac, int &nbadocc, int &nbadiface, int &nbaddist)
void	protocols::motif_hash::harvest_motifs ()
XformScore *	protocols::motif_hash::get_xform_score_from_file (XformScore *xs, vector1< string > const &datfiles, XformScore *defaultval=NULL)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, MotifHit const &h)
std::ostream &	protocols::motif_hash::operator<< (std::ostream &out, MotifHits const &h)
int	protocols::motif_hash::base_dump_matching_motifs (Pose const &pose1, Pose const &pose2, std::ostream &out, int &count, bool print, MotifHits const &hits)

Variables
static basic::Tracer	protocols::motif_hash::TR ("protocols.motif_hash")

Macro Definition Documentation

#define MAX_UINT16   65535

Referenced by protocols::motif_hash::real_to_uint16(), and protocols::motif_hash::uint16_to_real().

#define MAX_UINT8   255

Referenced by protocols::motif_hash::real_to_uint8(), and protocols::motif_hash::uint8_to_real().