Rosetta Protocols  2014.35
Classes | Typedefs | Functions | Variables
protocols::motif_hash Namespace Reference

Classes

class  MotifHash
 
class  MotifHashManager
 
struct  MotifHit
 
class  MotifHits
 
class  MotifRotamerSetOperation
 
struct  MyHash
 
struct  MyPred
 
class  ResPairMotif
 
class  ResPairMotifs
 
class  XformScore
 
class  Xfrag
 
class  XfragSet
 
class  Xfres
 

Typedefs

typedef numeric::xyzVector
< core::Real
Vec
 
typedef numeric::xyzMatrix
< core::Real
Mat
 
typedef numeric::xyzTransform
< core::Real
Xform
 
typedef
utility::fixedsizearray1
< float, 20 > 
float20
 
typedef
utility::fixedsizearray1
< float, 9 > 
float9
 
typedef boost::unordered_set
< ResPairMotif, MyHash, MyPred
MotifSet
 
typedef
utility::pointer::owning_ptr
< XfragSet
XfragSetOP
 
typedef
utility::pointer::owning_ptr
< XfragSet const > 
XfragSetCOP
 
typedef
utility::pointer::access_ptr
< XfragSet const > 
XfragSetCAP
 
typedef
utility::pointer::owning_ptr
< XformScore
XformScoreOP
 
typedef
utility::pointer::owning_ptr
< XformScore const > 
XformScoreCOP
 
typedef
utility::pointer::access_ptr
< XformScore const > 
XformScoreCAP
 
typedef
utility::pointer::owning_ptr
< MotifHash
MotifHashOP
 
typedef
utility::pointer::owning_ptr
< MotifHash const > 
MotifHashCOP
 
typedef
utility::pointer::access_ptr
< MotifHash const > 
MotifHashCAP
 
typedef utility::vector1< boolBools
 
typedef
utility::pointer::owning_ptr
< MotifRotamerSetOperation
MotifRotamerSetOperationOP
 
typedef
utility::pointer::owning_ptr
< MotifRotamerSetOperation
const > 
MotifRotamerSetOperationCOP
 

Functions

Mat random_rotation ()
 
std::string tag_from_pdb_fname (std::string const &fname0)
 
std::ostream & operator<< (std::ostream &out, Real6 const &r6)
 
Real rt6_rt6_bb_dis2_explicit_stupid (Real6 const &x1, Real6 const &x2)
 
Real rt6_rt6_dis2 (Real6 const &x1, Real6 const &x2, Real const lever)
 
Real rt6_rt6_bb_dis2 (Real6 const &x1, Real6 const &x2)
 
Real6 inverse_rt6 (Real6 const &rt)
 
Real6 rt_to_real6 (core::kinematics::RT const &rt)
 
core::kinematics::RT real6_to_rt (Real6 const &rt6)
 
Real6 get_residue_pair_rt6 (Pose const &pose1, Size ir, Pose const &pose2, Size jr)
 
Real6 get_residue_pair_rt6 (Pose const &pose, Size ir, Size jr)
 
void set_residue_pair_rt (Real6 const &rt6, Pose &pose, Size ir, Size jr)
 
Real uint16_to_real (uint16_t const &val, Real const &lb, Real const &ub)
 
uint16_t real_to_uint16 (Real const &val, Real const &lb, Real const &ub)
 
Real uint8_to_real (uint8_t const &val, Real const &lb, Real const &ub)
 
uint8_t real_to_uint8 (Real const &val, Real const &lb, Real const &ub)
 
vector1< Realget_sasa (Pose const &pose, Real const &probesize)
 
vector1< Realget_nbrs (Pose const &pose)
 
void HACK_dump_helix (core::pose::Pose const &pose, string fname, int beg, int end)
 
int HACK_dump_helices (core::pose::Pose const &pose, string tag, int nres, int minlen=10)
 
utility::fixedsizearray1< Real, 6 > get_bins (Real c, Real a)
 
Real align_motif_pose_super (Pose &pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr)
 
Real align_motif_pose_break (Pose &pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr)
 
std::ostream & operator<< (std::ostream &out, ResPairMotif const &x)
 
bool write_motifs_binary (std::ostream &out, ResPairMotifs const &motifs)
 
bool write_motifs_binary (std::string const &fname, ResPairMotifs const &motifs)
 
bool read_motifs_binary (std::istream &in, ResPairMotifs &motifs)
 
bool read_motifs_binary (std::string const &fname, ResPairMotifs &motifs)
 
bool read_motifs_binary (vector1< string > const &fnames, ResPairMotifs &motifs)
 
void load_motifs (vector1< string > const &fnames, ResPairMotifs &motifs)
 
void load_motifs (string const &fname, ResPairMotifs &motifs)
 
std::ostream & operator<< (std::ostream &out, Xfres const &x)
 
std::istream & operator>> (std::istream &in, Xfres &x)
 
bool read_xfres_binary (string const &fname, vector1< Xfres > &xfres)
 
bool read_xfres_binary (std::istream &in, vector1< Xfres > &xfres)
 
bool write_xfres_binary (std::ostream &out, vector1< Xfres > const &xfres)
 
bool write_xfres_binary (string const &fname, vector1< Xfres > const &xfres)
 
bool read_xfres_binary (vector1< string > const &fnames, vector1< Xfres > &xfres)
 
std::ostream & operator<< (std::ostream &out, Xfrag const &x)
 
std::istream & operator>> (std::istream &in, Xfrag &x)
 
bool read_xfrag_binary (string const &fname, vector1< Xfrag > &xfrag)
 
bool read_xfrag_binary (std::istream &in, vector1< Xfrag > &xfrag)
 
bool write_xfrag_binary (std::ostream &out, vector1< Xfrag > const &xfrag)
 
bool write_xfrag_binary (string const &fname, vector1< Xfrag > const &xfrag)
 
bool read_xfrag_binary (vector1< string > const &fnames, vector1< Xfrag > &xfrag)
 
bool read_xfrag_binary (string const &fname, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
 
bool read_xfrag_binary (std::istream &in, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
 
bool write_xfrag_binary (std::ostream &out, vector1< Xfrag > const &xfrag, vector1< Xfres > const &xfres)
 
bool write_xfrag_binary (string const &fname, vector1< Xfrag > const &xfrag, vector1< Xfres > const &xfres)
 
bool read_xfrag_binary (vector1< string > const &fnames, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
 
std::ostream & operator<< (std::ostream &out, MotifHash const &x)
 
void print_motifs (std::ostream &out)
 
void merge_motifs ()
 
void dump_motif_pdbs ()
 
void harvest_scores ()
 
void print_scores ()
 
void dump_matching_motifs ()
 
void filter_motifs (ResPairMotifs const &motifs_in, ResPairMotifs &motifs_out)
 
Real6reframe_rt_centered (Real6 &rt)
 
std::ostream & operator<< (std::ostream &out, XformScore const &xh)
 
bool 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 harvest_motifs ()
 
XformScoreget_xform_score_from_file (XformScore *xs, vector1< string > const &datfiles, XformScore *defaultval=NULL)
 
std::ostream & operator<< (std::ostream &out, MotifHit const &h)
 
std::ostream & operator<< (std::ostream &out, MotifHits const &h)
 
int base_dump_matching_motifs (Pose const &pose1, Pose const &pose2, std::ostream &out, int &count, bool print, MotifHits const &hits)
 
static float fasterlog (float x)
 
std::istream & operator>> (std::istream &in, ResPairMotif &x)
 
std::istream & operator>> (std::istream &in, MotifHash &x)
 

Variables

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

Typedef Documentation

Function Documentation

Real protocols::motif_hash::align_motif_pose_break ( Pose pose,
Pose const &  paln1,
Size const &  ir,
Pose const &  paln2,
Size const &  jr 
)
Real protocols::motif_hash::align_motif_pose_super ( Pose pose,
Pose const &  paln1,
Size const &  ir,
Pose const &  paln2,
Size const &  jr 
)
int protocols::motif_hash::base_dump_matching_motifs ( Pose const &  pose1,
Pose const &  pose2,
std::ostream &  out,
int count,
bool  print,
MotifHits const &  hits 
)
void protocols::motif_hash::dump_matching_motifs ( )
void protocols::motif_hash::dump_motif_pdbs ( )
static float protocols::motif_hash::fasterlog ( float  x)
inlinestatic
void protocols::motif_hash::filter_motifs ( ResPairMotifs const &  motifs_in,
ResPairMotifs &  motifs_out 
)

Referenced by load_motifs().

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 
)
utility::fixedsizearray1<Real,6> protocols::motif_hash::get_bins ( Real  c,
Real  a 
)
vector1<Real> protocols::motif_hash::get_nbrs ( Pose const &  pose)
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 
)
vector1<Real> protocols::motif_hash::get_sasa ( Pose const &  pose,
Real const &  probesize 
)
XformScore* protocols::motif_hash::get_xform_score_from_file ( XformScore *  xs,
vector1< string > const &  datfiles,
XformScore *  defaultval = NULL 
)
int protocols::motif_hash::HACK_dump_helices ( core::pose::Pose const &  pose,
string  tag,
int  nres,
int  minlen = 10 
)
void protocols::motif_hash::HACK_dump_helix ( core::pose::Pose const &  pose,
string  fname,
int  beg,
int  end 
)
void protocols::motif_hash::harvest_motifs ( )
void protocols::motif_hash::harvest_scores ( )
Real6 protocols::motif_hash::inverse_rt6 ( Real6 const &  rt)
void protocols::motif_hash::load_motifs ( vector1< string > const &  fnames,
ResPairMotifs &  motifs 
)
void protocols::motif_hash::load_motifs ( string const &  fname,
ResPairMotifs &  motifs 
)

References load_motifs().

void protocols::motif_hash::merge_motifs ( )
std::ostream& protocols::motif_hash::operator<< ( std::ostream &  out,
Real6 const &  r6 
)
std::ostream & protocols::motif_hash::operator<< ( std::ostream &  out,
ResPairMotif const &  x 
)
std::ostream & protocols::motif_hash::operator<< ( std::ostream &  out,
Xfres const &  x 
)
std::ostream & protocols::motif_hash::operator<< ( std::ostream &  out,
Xfrag const &  x 
)
std::ostream & protocols::motif_hash::operator<< ( std::ostream &  out,
MotifHash const &  x 
)
std::ostream & protocols::motif_hash::operator<< ( std::ostream &  out,
XformScore const &  xh 
)
std::ostream & protocols::motif_hash::operator<< ( std::ostream &  out,
MotifHit const &  h 
)
std::ostream & protocols::motif_hash::operator<< ( std::ostream &  out,
MotifHits const &  h 
)
std::istream& protocols::motif_hash::operator>> ( std::istream &  in,
ResPairMotif &  x 
)
std::istream& protocols::motif_hash::operator>> ( std::istream &  in,
MotifHash &  x 
)
std::istream & protocols::motif_hash::operator>> ( std::istream &  in,
Xfres &  x 
)
std::istream & protocols::motif_hash::operator>> ( std::istream &  in,
Xfrag &  x 
)
void protocols::motif_hash::print_motifs ( std::ostream &  out)
void protocols::motif_hash::print_scores ( )
Mat protocols::motif_hash::random_rotation ( )
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 
)
bool protocols::motif_hash::read_xfrag_binary ( string const &  fname,
vector1< Xfrag > &  xfrag 
)

References utility::io::izstream::good(), and in.

Referenced by read_xfrag_binary().

bool protocols::motif_hash::read_xfrag_binary ( std::istream &  in,
vector1< Xfrag > &  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::read_xfrag_binary ( vector1< string > const &  fnames,
vector1< Xfrag > &  xfrag,
vector1< Xfres > &  xfres 
)
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::read_xfres_binary ( vector1< string > const &  fnames,
vector1< Xfres > &  xfres 
)
core::kinematics::RT protocols::motif_hash::real6_to_rt ( Real6 const &  rt6)
uint16_t protocols::motif_hash::real_to_uint16 ( Real 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 
)
Real6& protocols::motif_hash::reframe_rt_centered ( Real6 rt)
Real protocols::motif_hash::rt6_rt6_bb_dis2 ( Real6 const &  x1,
Real6 const &  x2 
)
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 
)
Real6 protocols::motif_hash::rt_to_real6 ( core::kinematics::RT const &  rt)
void protocols::motif_hash::set_residue_pair_rt ( Real6 const &  rt6,
Pose pose,
Size  ir,
Size  jr 
)
std::string protocols::motif_hash::tag_from_pdb_fname ( std::string const &  fname0)

References utility::file_basename().

Referenced by harvest_motifs().

Real protocols::motif_hash::uint16_to_real ( uint16_t 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 
)
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::write_xfrag_binary ( std::ostream &  out,
vector1< Xfrag > const &  xfrag 
)

References cout.

Referenced by write_xfrag_binary().

bool protocols::motif_hash::write_xfrag_binary ( string const &  fname,
vector1< Xfrag > const &  xfrag 
)
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::write_xfres_binary ( std::ostream &  out,
vector1< Xfres > const &  xfres 
)

References cout.

Referenced by write_xfrag_binary(), and write_xfres_binary().

bool protocols::motif_hash::write_xfres_binary ( string const &  fname,
vector1< Xfres > const &  xfres 
)

Variable Documentation

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