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core::scoring::motif Namespace Reference

Classes

class  MotifHash
 
class  MotifHashManager
 
class  MotifHit
 
class  MotifHits
 
class  MotifHitStats
 
struct  MyHash
 
struct  MyPred
 
class  ResPairMotif
 
class  ResPairMotifMetaBinner
 
class  ResPairMotifQuery
 
class  ResPairMotifs
 
struct  RMSandEnergyCMP
 
struct  RPM_FilterStats
 
class  XformScore
 
struct  XformSummary
 
class  Xfrag
 
class  XfragSet
 
class  Xfres
 

Typedefs

typedef
utility::fixedsizearray1
< float, 20 > 
float20
 
typedef
utility::fixedsizearray1
< float, 9 > 
float9
 
typedef boost::unordered_set
< ResPairMotif, MyHash, MyPred
MotifSet
 
typedef
utility::pointer::shared_ptr
< XfragSet
XfragSetOP
 
typedef
utility::pointer::shared_ptr
< XfragSet const > 
XfragSetCOP
 
typedef
utility::pointer::weak_ptr
< XfragSet const > 
XfragSetCAP
 
typedef
utility::pointer::shared_ptr
< XformScore
XformScoreOP
 
typedef
utility::pointer::shared_ptr
< XformScore const > 
XformScoreCOP
 
typedef
utility::pointer::weak_ptr
< XformScore const > 
XformScoreCAP
 
typedef
utility::pointer::shared_ptr
< MotifHash
MotifHashOP
 
typedef
utility::pointer::shared_ptr
< MotifHash const > 
MotifHashCOP
 
typedef
utility::pointer::weak_ptr
< MotifHash const > 
MotifHashCAP
 
typedef
utility::pointer::shared_ptr
< MotifRotamerSetOperation > 
MotifRotamerSetOperationOP
 
typedef
utility::pointer::shared_ptr
< MotifRotamerSetOperation
const > 
MotifRotamerSetOperationCOP
 
typedef utility::vector1< RealReals
 
typedef utility::vector1< SizeSizes
 
typedef utility::vector1< int > Ints
 
typedef utility::vector1< float > Floats
 
typedef utility::vector1< boolBools
 
typedef numeric::xyzVector
< core::Real
Vec
 
typedef numeric::xyzMatrix
< core::Real
Mat
 
typedef numeric::xyzTransform
< core::Real
Xform
 
typedef std::map< std::string,
XformScore
XformScoreSringMap
 
typedef utility::vector1
< ResPairMotif const * > 
ResPairMotifPtrs
 
typedef boost::unordered_map
< ResPairMotifMetaBinner::Key,
XformScoreOP
XformScoreMap
 
typedef std::map< std::string,
ResPairMotifs
ResPairMotifsStringMap
 
typedef boost::unordered_map
< ResPairMotifMetaBinner::Key,
ResPairMotifs
ResPairMotifsMap
 
typedef std::map< std::string,
MotifHashOP
MotifHashStringMap
 

Enumerations

enum  RM_Type {
  RM_Type_NONE, RM_SC, RM_BB, RM_PH,
  RM_PO, NUM_RM_TYPES =RM_PO
}
 
enum  RPM_Type {
  RPM_Type_NONE, SC_SC, SC_BB, SC_PH,
  SC_PO, BB_BB, BB_PH, BB_PO,
  PH_PO, NUM_RPM_TYPES =PH_PO
}
 
enum  MotifMatchOverlapReq {
  NO_OVERLAP =1, SMALL_OVERLAP, MATCH_ROTAMER, MATCH_AA,
  MATCH_HYDROPHOBICITY, MATCH_ANY
}
 

Functions

static basic::Tracer TR ("core.scoring.motif")
 
template<typename T >
static T sqr (T const &x)
 
static Real uint16_to_real (uint16_t const &val, Real const &lb, Real const &ub)
 
static uint16_t real_to_uint16 (Real const &val, Real const &lb, Real const &ub)
 
static Real uint8_to_real (uint8_t const &val, Real const &lb, Real const &ub)
 
static uint8_t real_to_uint8 (Real const &val, Real const &lb, Real const &ub)
 
std::ostream & operator<< (std::ostream &out, RPM_FilterStats const &s)
 
ostream & operator<< (ostream &out, ResPairMotif const &x)
 
ostream & operator<< (ostream &out, RM_Type const &x)
 
ostream & operator<< (ostream &out, RPM_Type const &x)
 
bool write_motifs_binary (ostream &out, ResPairMotifs const &motifs)
 
bool write_motifs_binary (string const &fname_in, ResPairMotifs const &motifs)
 
bool read_motifs_binary (std::istream &in, ResPairMotifs &motifs)
 
bool read_motifs_binary (string const &fname, ResPairMotifs &motifs)
 
bool read_motifs_binary (vector1< string > const &fnames, ResPairMotifs &motifs)
 
void load_motifs (vector1< string > const &fnames, ResPairMotifs &motifs, ResPairMotifsStringMap *map)
 
void load_motifs (string const &fname, ResPairMotifs &motifs, ResPairMotifsStringMap *map)
 
std::ostream & operator<< (std::ostream &out, XformScoreMap const &x)
 
ostream & operator<< (ostream &out, MotifHit const &h)
 
ostream & operator<< (ostream &out, MotifHits const &h)
 
ostream & operator<< (ostream &out, MotifHash const &x)
 
std::ostream & operator<< (std::ostream &out, ResPairMotifQuery const &opt)
 
void filter_motifs (ResPairMotifs const &motifs_in, ResPairMotifs &motifs_out)
 
void filter_motifs (ResPairMotifs &motifs)
 
ostream & operator<< (ostream &out, XformScore const &xh)
 
ostream & operator<< (ostream &out, XformScoreSringMap const &x)
 
void fill_xform_score_from_file (XformScoreOP &xs, string const &datfile, Real const &wt=1.0)
 
void * preload_motif_data_pthread_wrapper (void *ptr)
 
void preload_motif_data (MotifHashManager &mhman)
 
std::istream & operator>> (std::istream &in, ResPairMotif &x)
 
bool read_motifs_binary (utility::vector1< std::string > const &fnames, ResPairMotifs &motifs)
 
std::istream & operator>> (std::istream &in, MotifHash &x)
 
void load_motifs (utility::vector1< std::string > const &fnames, ResPairMotifs &motifs, ResPairMotifsStringMap *map=nullptr)
 
static basic::Tracer TR ("core.scoring.motif.util")
 
void xform_pose (core::pose::Pose &pose, Xform const &s, Size sres=1, Size eres=0)
 
Mat random_rotation ()
 
std::string tag_from_pdb_fname (string const &fname0)
 
ostream & operator<< (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)
 
RM_Type rpm_type1 (RPM_Type const &type)
 
RM_Type rpm_type2 (RPM_Type const &type)
 
Xform get_residue_pair_xform (Pose const &pose1, Size ir, Pose const &pose2, Size jr, RPM_Type const &type)
 
Xform get_residue_pair_xform (Pose const &pose, Size ir, Size jr, RPM_Type const &type)
 
Real6 get_residue_pair_rt6 (Pose const &pose1, Size ir, Pose const &pose2, Size jr, RPM_Type const &type)
 
Real6 get_residue_pair_rt6 (Pose const &pose, Size ir, Size jr, RPM_Type const &type)
 
void set_residue_pair_xform (Xform const &x, Pose &pose, Size ir, Size jr, RPM_Type const &type)
 
Reals get_sasa (Pose const &pose, Real const &probesize)
 
Reals get_nbrs (Pose const &pose)
 
void HACK_dump_helix (Pose const &pose, string fname, int beg, int end)
 
int HACK_dump_helices (Pose const &pose, string tag, int nres, int minlen=10)
 
Real6 get_bins (Real c, Real a)
 
core::id::AtomID_Mask get_motif_atom_mask (Pose const &motif_pose, RPM_Type const &type, bool with_Hpol)
 
Real align_motif_pose_NCAC_super (Pose &motif_pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr, RPM_Type const &type)
 
Real align_motif_pose_break (Pose &, Pose const &, Size const &, Pose const &, Size const &, RPM_Type const &)
 
Real align_motif_pose_by_one_frame (Pose &, Pose const &, Size const &, Pose const &, Size const &, RPM_Type const &)
 
Real align_motif_pose_super (Pose &motif_pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr, RPM_Type const &type)
 
Real align_motif_pose (Pose &motif_pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr, RPM_Type const &type)
 
core::Real aa_trustworthiness (char aa)
 
Real angle_distance (Real const &a, Real const &b)
 
static basic::Tracer TR ("core.scoring.motif")
 
static Real uint16_to_real (uint16_t const &val, Real const &lb, Real const &ub)
 
static uint16_t real_to_uint16 (Real const &val, Real const &lb, Real const &ub)
 
static Real uint8_to_real (uint8_t const &val, Real const &lb, Real const &ub)
 
static uint8_t real_to_uint8 (Real const &val, Real const &lb, Real const &ub)
 
ostream & operator<< (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 (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)
 
ostream & operator<< (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 (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 (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)
 
bool read_xfres_binary (std::string const &fname, utility::vector1< Xfres > &Xfres)
 
bool read_xfres_binary (std::istream &in, utility::vector1< Xfres > &Xfres)
 
bool write_xfres_binary (std::ostream &out, utility::vector1< Xfres > const &Xfres)
 
bool write_xfres_binary (std::string const &fname, utility::vector1< Xfres > const &Xfres)
 
bool read_xfres_binary (utility::vector1< std::string > const &fnames, utility::vector1< Xfres > &Xfres)
 
bool read_xfrag_binary (std::string const &fname, utility::vector1< Xfrag > &xfrag)
 
bool read_xfrag_binary (std::istream &in, utility::vector1< Xfrag > &xfrag)
 
bool write_xfrag_binary (std::ostream &out, utility::vector1< Xfrag > const &xfrag)
 
bool write_xfrag_binary (std::string const &fname, utility::vector1< Xfrag > const &xfrag)
 
bool read_xfrag_binary (utility::vector1< std::string > const &fnames, utility::vector1< Xfrag > &xfrag)
 
bool read_xfrag_binary (std::string const &fname, utility::vector1< Xfrag > &xfrag, utility::vector1< Xfres > &xfres)
 
bool read_xfrag_binary (std::istream &in, utility::vector1< Xfrag > &xfrag, utility::vector1< Xfres > &xfres)
 
bool write_xfrag_binary (std::ostream &out, utility::vector1< Xfrag > const &xfrag, utility::vector1< Xfres > const &xfres)
 
bool write_xfrag_binary (std::string const &fname, utility::vector1< Xfrag > const &xfrag, utility::vector1< Xfres > const &xfres)
 
bool read_xfrag_binary (utility::vector1< std::string > const &fnames, utility::vector1< Xfrag > &xfrag, utility::vector1< Xfres > &xfres)
 

Variables

const numeric::Real MOTIF_HASH_CART_SIZE = 16.0
 
const uint64_t MOTIF_VERSION = 2
 
static const numeric::Xforms XsI = numeric::Xforms(1,numeric::Xform::identity())
 

Typedef Documentation

typedef utility::vector1< bool > core::scoring::motif::Bools
typedef utility::fixedsizearray1< float, 20 > core::scoring::motif::float20
typedef utility::fixedsizearray1< float, 9 > core::scoring::motif::float9
typedef utility::vector1< float > core::scoring::motif::Floats
typedef utility::vector1< int > core::scoring::motif::Ints
typedef numeric::xyzMatrix< core::Real > core::scoring::motif::Mat
typedef utility::pointer::weak_ptr< MotifHash const > core::scoring::motif::MotifHashCAP
typedef utility::pointer::shared_ptr< MotifHash const > core::scoring::motif::MotifHashCOP
typedef utility::pointer::shared_ptr< MotifHash > core::scoring::motif::MotifHashOP
typedef utility::pointer::shared_ptr<MotifRotamerSetOperation const> core::scoring::motif::MotifRotamerSetOperationCOP
typedef utility::pointer::shared_ptr<MotifRotamerSetOperation > core::scoring::motif::MotifRotamerSetOperationOP
typedef utility::vector1< Real > core::scoring::motif::Reals
typedef utility::vector1<ResPairMotif const*> core::scoring::motif::ResPairMotifPtrs
typedef utility::vector1< Size > core::scoring::motif::Sizes
typedef numeric::xyzVector< core::Real > core::scoring::motif::Vec
typedef numeric::xyzTransform< core::Real > core::scoring::motif::Xform
typedef utility::pointer::weak_ptr< XformScore const > core::scoring::motif::XformScoreCAP
typedef utility::pointer::shared_ptr< XformScore const > core::scoring::motif::XformScoreCOP
typedef utility::pointer::shared_ptr< XformScore > core::scoring::motif::XformScoreOP
typedef utility::pointer::weak_ptr< XfragSet const > core::scoring::motif::XfragSetCAP
typedef utility::pointer::shared_ptr< XfragSet const > core::scoring::motif::XfragSetCOP
typedef utility::pointer::shared_ptr< XfragSet > core::scoring::motif::XfragSetOP

Enumeration Type Documentation

Enumerator
NO_OVERLAP 
SMALL_OVERLAP 
MATCH_ROTAMER 
MATCH_AA 
MATCH_HYDROPHOBICITY 
MATCH_ANY 
Enumerator
RM_Type_NONE 
RM_SC 
RM_BB 
RM_PH 
RM_PO 
NUM_RM_TYPES 
Enumerator
RPM_Type_NONE 
SC_SC 
SC_BB 
SC_PH 
SC_PO 
BB_BB 
BB_PH 
BB_PO 
PH_PO 
NUM_RPM_TYPES 

Function Documentation

core::Real core::scoring::motif::aa_trustworthiness ( char  aa)
Real core::scoring::motif::align_motif_pose ( Pose motif_pose,
Pose const &  paln1,
Size const &  ir,
Pose const &  paln2,
Size const &  jr,
RPM_Type const &  type 
)
Real core::scoring::motif::align_motif_pose_break ( Pose ,
Pose const &  ,
Size const &  ,
Pose const &  ,
Size const &  ,
RPM_Type const &   
)
Real core::scoring::motif::align_motif_pose_by_one_frame ( Pose ,
Pose const &  ,
Size const &  ,
Pose const &  ,
Size const &  ,
RPM_Type const &   
)
Real core::scoring::motif::align_motif_pose_NCAC_super ( Pose motif_pose,
Pose const &  paln1,
Size const &  ir,
Pose const &  paln2,
Size const &  jr,
RPM_Type const &  type 
)
Real core::scoring::motif::align_motif_pose_super ( Pose motif_pose,
Pose const &  paln1,
Size const &  ir,
Pose const &  paln2,
Size const &  jr,
RPM_Type const &  type 
)
Real core::scoring::motif::angle_distance ( Real const &  a,
Real const &  b 
)
inline
void core::scoring::motif::fill_xform_score_from_file ( XformScoreOP &  xs,
string const &  datfile,
Real const &  wt = 1.0 
)
void core::scoring::motif::filter_motifs ( ResPairMotifs const &  motifs_in,
ResPairMotifs &  motifs_out 
)

Referenced by filter_motifs(), and load_motifs().

void core::scoring::motif::filter_motifs ( ResPairMotifs &  motifs)

References filter_motifs().

static utility::fixedsizearray1< Real, 6 > core::scoring::motif::get_bins ( Real  c,
Real  a 
)
core::id::AtomID_Mask core::scoring::motif::get_motif_atom_mask ( Pose const &  motif_pose,
RPM_Type const &  type,
bool  with_Hpol 
)
Reals core::scoring::motif::get_nbrs ( Pose const &  pose)
Real6 core::scoring::motif::get_residue_pair_rt6 ( Pose const &  pose1,
Size  ir,
Pose const &  pose2,
Size  jr,
RPM_Type const &  type 
)
Real6 core::scoring::motif::get_residue_pair_rt6 ( Pose const &  pose,
Size  ir,
Size  jr,
RPM_Type const &  type 
)
Xform core::scoring::motif::get_residue_pair_xform ( Pose const &  pose1,
Size  ir,
Pose const &  pose2,
Size  jr,
RPM_Type const &  type 
)
Xform core::scoring::motif::get_residue_pair_xform ( Pose const &  pose,
Size  ir,
Size  jr,
RPM_Type const &  type 
)
Reals core::scoring::motif::get_sasa ( Pose const &  pose,
Real const &  probesize 
)
int core::scoring::motif::HACK_dump_helices ( Pose const &  pose,
string  tag,
int  nres,
int  minlen = 10 
)
void core::scoring::motif::HACK_dump_helix ( Pose const &  pose,
string  fname,
int  beg,
int  end 
)
Real6 core::scoring::motif::inverse_rt6 ( Real6 const &  rt)
void core::scoring::motif::load_motifs ( utility::vector1< std::string > const &  fnames,
ResPairMotifs &  motifs,
ResPairMotifsStringMap *  map = nullptr 
)
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 
)

References load_motifs().

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
Real6 const &  r6 
)
std::ostream & core::scoring::motif::operator<< ( ostream &  out,
Xfres const &  x 
)
std::ostream & core::scoring::motif::operator<< ( ostream &  out,
Xfrag const &  x 
)
std::ostream& core::scoring::motif::operator<< ( std::ostream &  out,
RPM_FilterStats const &  s 
)

References core::scoring::motif::RPM_FilterStats::F_aa1, core::scoring::motif::RPM_FilterStats::F_aa2, core::scoring::motif::RPM_FilterStats::F_coorderr, core::scoring::motif::RPM_FilterStats::F_dssp1, core::scoring::motif::RPM_FilterStats::F_dssp2, core::scoring::motif::RPM_FilterStats::F_faatr, core::scoring::motif::RPM_FilterStats::F_faatr_or_hb, core::scoring::motif::RPM_FilterStats::F_faatr_or_hbbb, core::scoring::motif::RPM_FilterStats::F_hb_bb, core::scoring::motif::RPM_FilterStats::F_hb_bb_sc, core::scoring::motif::RPM_FilterStats::F_hb_sc, core::scoring::motif::RPM_FilterStats::F_lig, core::scoring::motif::RPM_FilterStats::F_max_seqsep, core::scoring::motif::RPM_FilterStats::F_maxdist2, core::scoring::motif::RPM_FilterStats::F_mindist2, core::scoring::motif::RPM_FilterStats::F_no_hb_bb, core::scoring::motif::RPM_FilterStats::F_nodisulf, core::scoring::motif::RPM_FilterStats::F_noloops, core::scoring::motif::RPM_FilterStats::F_not_restype, core::scoring::motif::RPM_FilterStats::F_not_restype_one, core::scoring::motif::RPM_FilterStats::F_oneloop, core::scoring::motif::RPM_FilterStats::F_pdb, core::scoring::motif::RPM_FilterStats::F_restype, core::scoring::motif::RPM_FilterStats::F_restype1, core::scoring::motif::RPM_FilterStats::F_restype2, core::scoring::motif::RPM_FilterStats::F_restype_one, core::scoring::motif::RPM_FilterStats::F_score, core::scoring::motif::RPM_FilterStats::F_seqsep, core::scoring::motif::RPM_FilterStats::F_ss1, core::scoring::motif::RPM_FilterStats::F_ss2, core::scoring::motif::RPM_FilterStats::F_type_BB_BB, core::scoring::motif::RPM_FilterStats::F_type_BB_PH, core::scoring::motif::RPM_FilterStats::F_type_BB_PO, core::scoring::motif::RPM_FilterStats::F_type_PH_PO, core::scoring::motif::RPM_FilterStats::F_type_SC_BB, core::scoring::motif::RPM_FilterStats::F_type_SC_PH, core::scoring::motif::RPM_FilterStats::F_type_SC_PO, core::scoring::motif::RPM_FilterStats::F_type_SC_SC, core::scoring::motif::RPM_FilterStats::F_uniformfrag, core::chemical::element::I, core::conformation::membrane::out, core::scoring::motif::RPM_FilterStats::P_aa1, core::scoring::motif::RPM_FilterStats::P_aa2, core::scoring::motif::RPM_FilterStats::P_coorderr, core::scoring::motif::RPM_FilterStats::P_dssp1, core::scoring::motif::RPM_FilterStats::P_dssp2, core::scoring::motif::RPM_FilterStats::P_faatr, core::scoring::motif::RPM_FilterStats::P_faatr_or_hb, core::scoring::motif::RPM_FilterStats::P_faatr_or_hbbb, core::scoring::motif::RPM_FilterStats::P_hb_bb, core::scoring::motif::RPM_FilterStats::P_hb_bb_sc, core::scoring::motif::RPM_FilterStats::P_hb_sc, core::scoring::motif::RPM_FilterStats::P_lig, core::scoring::motif::RPM_FilterStats::P_max_seqsep, core::scoring::motif::RPM_FilterStats::P_maxdist2, core::scoring::motif::RPM_FilterStats::P_mindist2, core::scoring::motif::RPM_FilterStats::P_no_hb_bb, core::scoring::motif::RPM_FilterStats::P_nodisulf, core::scoring::motif::RPM_FilterStats::P_noloops, core::scoring::motif::RPM_FilterStats::P_not_restype, core::scoring::motif::RPM_FilterStats::P_not_restype_one, core::scoring::motif::RPM_FilterStats::P_oneloop, core::scoring::motif::RPM_FilterStats::P_pdb, core::scoring::motif::RPM_FilterStats::P_restype, core::scoring::motif::RPM_FilterStats::P_restype1, core::scoring::motif::RPM_FilterStats::P_restype2, core::scoring::motif::RPM_FilterStats::P_restype_one, core::scoring::motif::RPM_FilterStats::P_score, core::scoring::motif::RPM_FilterStats::P_seqsep, core::scoring::motif::RPM_FilterStats::P_ss1, core::scoring::motif::RPM_FilterStats::P_ss2, core::scoring::motif::RPM_FilterStats::P_type_BB_BB, core::scoring::motif::RPM_FilterStats::P_type_BB_PH, core::scoring::motif::RPM_FilterStats::P_type_BB_PO, core::scoring::motif::RPM_FilterStats::P_type_PH_PO, core::scoring::motif::RPM_FilterStats::P_type_SC_BB, core::scoring::motif::RPM_FilterStats::P_type_SC_PH, core::scoring::motif::RPM_FilterStats::P_type_SC_PO, core::scoring::motif::RPM_FilterStats::P_type_SC_SC, and core::scoring::motif::RPM_FilterStats::P_uniformfrag.

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
ResPairMotif const &  x 
)
std::ostream & core::scoring::motif::operator<< ( ostream &  out,
RM_Type const &  x 
)
std::ostream & core::scoring::motif::operator<< ( ostream &  out,
RPM_Type const &  x 
)
std::ostream & core::scoring::motif::operator<< ( std::ostream &  out,
XformScoreMap const &  x 
)
std::ostream & core::scoring::motif::operator<< ( ostream &  out,
MotifHit const &  h 
)
ostream& core::scoring::motif::operator<< ( std::ostream &  out,
MotifHits const &  h 
)
std::ostream & core::scoring::motif::operator<< ( ostream &  out,
MotifHash const &  x 
)
std::ostream& core::scoring::motif::operator<< ( std::ostream &  out,
ResPairMotifQuery const &  opt 
)
std::ostream & core::scoring::motif::operator<< ( ostream &  out,
XformScore const &  xh 
)
std::ostream & core::scoring::motif::operator<< ( ostream &  out,
XformScoreSringMap const &  x 
)
std::istream & core::scoring::motif::operator>> ( std::istream &  in,
Xfres &  x 
)
std::istream& core::scoring::motif::operator>> ( std::istream &  in,
ResPairMotif &  x 
)
std::istream & core::scoring::motif::operator>> ( std::istream &  in,
Xfrag &  x 
)
std::istream& core::scoring::motif::operator>> ( std::istream &  in,
MotifHash &  x 
)
void core::scoring::motif::preload_motif_data ( MotifHashManager &  mhman)
void* core::scoring::motif::preload_motif_data_pthread_wrapper ( void *  ptr)
Mat core::scoring::motif::random_rotation ( )
bool core::scoring::motif::read_motifs_binary ( utility::vector1< std::string > const &  fnames,
ResPairMotifs &  motifs 
)

References read_motifs_binary().

bool core::scoring::motif::read_motifs_binary ( std::istream &  in,
ResPairMotifs &  motifs 
)

References MOTIF_VERSION.

Referenced by load_motifs(), and read_motifs_binary().

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 
)

References read_motifs_binary().

bool core::scoring::motif::read_xfrag_binary ( std::string const &  fname,
utility::vector1< Xfrag > &  xfrag 
)
bool core::scoring::motif::read_xfrag_binary ( std::istream &  in,
utility::vector1< Xfrag > &  xfrag 
)
bool core::scoring::motif::read_xfrag_binary ( utility::vector1< std::string > const &  fnames,
utility::vector1< Xfrag > &  xfrag 
)

References read_xfrag_binary().

bool core::scoring::motif::read_xfrag_binary ( std::string const &  fname,
utility::vector1< Xfrag > &  xfrag,
utility::vector1< Xfres > &  xfres 
)
bool core::scoring::motif::read_xfrag_binary ( std::istream &  in,
utility::vector1< Xfrag > &  xfrag,
utility::vector1< Xfres > &  xfres 
)
bool core::scoring::motif::read_xfrag_binary ( utility::vector1< std::string > const &  fnames,
utility::vector1< Xfrag > &  xfrag,
utility::vector1< Xfres > &  xfres 
)

References read_xfrag_binary().

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::read_xfrag_binary ( vector1< string > const &  fnames,
vector1< Xfrag > &  xfrag 
)

References read_xfrag_binary().

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::read_xfrag_binary ( vector1< string > const &  fnames,
vector1< Xfrag > &  xfrag,
vector1< Xfres > &  xfres 
)

References read_xfrag_binary().

bool core::scoring::motif::read_xfres_binary ( std::string const &  fname,
utility::vector1< Xfres > &  Xfres 
)
bool core::scoring::motif::read_xfres_binary ( std::istream &  in,
utility::vector1< Xfres > &  Xfres 
)
bool core::scoring::motif::read_xfres_binary ( utility::vector1< std::string > const &  fnames,
utility::vector1< Xfres > &  Xfres 
)

References read_xfres_binary().

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::read_xfres_binary ( vector1< string > const &  fnames,
vector1< Xfres > &  xfres 
)

References read_xfres_binary().

core::kinematics::RT core::scoring::motif::real6_to_rt ( Real6 const &  rt6)
static uint16_t core::scoring::motif::real_to_uint16 ( Real const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic
static uint16_t core::scoring::motif::real_to_uint16 ( Real const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic
static uint8_t core::scoring::motif::real_to_uint8 ( Real const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic
static uint8_t core::scoring::motif::real_to_uint8 ( Real const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic
RM_Type core::scoring::motif::rpm_type1 ( RPM_Type const &  type)
RM_Type core::scoring::motif::rpm_type2 ( RPM_Type const &  type)
Real core::scoring::motif::rt6_rt6_bb_dis2 ( Real6 const &  x1,
Real6 const &  x2 
)

References rt6_rt6_dis2().

Real core::scoring::motif::rt6_rt6_bb_dis2_explicit_stupid ( Real6 const &  x1,
Real6 const &  x2 
)
Real core::scoring::motif::rt6_rt6_dis2 ( Real6 const &  x1,
Real6 const &  x2,
Real const &  lever 
)

Referenced by rt6_rt6_bb_dis2().

Real6 core::scoring::motif::rt_to_real6 ( core::kinematics::RT const &  rt)
void core::scoring::motif::set_residue_pair_xform ( Xform const &  x,
Pose pose,
Size  ir,
Size  jr,
RPM_Type const &  type 
)
template<typename T >
static T core::scoring::motif::sqr ( T const &  x)
inlinestatic
std::string core::scoring::motif::tag_from_pdb_fname ( string const &  fname0)
static basic::Tracer core::scoring::motif::TR ( "core.scoring.motif"  )
static
static basic::Tracer core::scoring::motif::TR ( "core.scoring.motif"  )
static
static basic::Tracer core::scoring::motif::TR ( "core.scoring.motif.util"  )
static
static Real core::scoring::motif::uint16_to_real ( uint16_t const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic
static Real core::scoring::motif::uint16_to_real ( uint16_t const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic
static Real core::scoring::motif::uint8_to_real ( uint8_t const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic
static Real core::scoring::motif::uint8_to_real ( uint8_t const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic
bool core::scoring::motif::write_motifs_binary ( ostream &  out,
ResPairMotifs const &  motifs 
)

References MOTIF_VERSION.

Referenced by write_motifs_binary().

bool core::scoring::motif::write_motifs_binary ( string const &  fname_in,
ResPairMotifs const &  motifs 
)
bool core::scoring::motif::write_xfrag_binary ( std::ostream &  out,
utility::vector1< Xfrag > const &  xfrag 
)

Referenced by write_xfrag_binary().

bool core::scoring::motif::write_xfrag_binary ( std::string const &  fname,
utility::vector1< Xfrag > const &  xfrag 
)
bool core::scoring::motif::write_xfrag_binary ( std::ostream &  out,
utility::vector1< Xfrag > const &  xfrag,
utility::vector1< Xfres > const &  xfres 
)
bool core::scoring::motif::write_xfrag_binary ( std::string const &  fname,
utility::vector1< Xfrag > const &  xfrag,
utility::vector1< Xfres > const &  xfres 
)
bool core::scoring::motif::write_xfrag_binary ( ostream &  out,
vector1< Xfrag > const &  xfrag 
)

Referenced by write_xfrag_binary().

bool core::scoring::motif::write_xfrag_binary ( string const &  fname,
vector1< Xfrag > const &  xfrag 
)
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::write_xfres_binary ( std::ostream &  out,
utility::vector1< Xfres > const &  Xfres 
)
bool core::scoring::motif::write_xfres_binary ( std::string const &  fname,
utility::vector1< Xfres > const &  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 
)
void core::scoring::motif::xform_pose ( core::pose::Pose pose,
Xform const &  s,
Size  sres = 1,
Size  eres = 0 
)

Variable Documentation

const numeric::Real core::scoring::motif::MOTIF_HASH_CART_SIZE = 16.0
const uint64_t core::scoring::motif::MOTIF_VERSION = 2
const numeric::Xforms core::scoring::motif::XsI = numeric::Xforms(1,numeric::Xform::identity())
static