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core::scoring::motif Namespace Reference

Classes

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

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< Real > Reals
 
typedef utility::vector1< Size > Sizes
 
typedef utility::vector1< int > Ints
 
typedef utility::vector1< float > Floats
 
typedef utility::vector1< bool > Bools
 
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

◆ Bools

typedef utility::vector1< bool > core::scoring::motif::Bools

◆ float20

typedef utility::fixedsizearray1< float, 20 > core::scoring::motif::float20

◆ float9

typedef utility::fixedsizearray1< float, 9 > core::scoring::motif::float9

◆ Floats

typedef utility::vector1< float > core::scoring::motif::Floats

◆ Ints

typedef utility::vector1< int > core::scoring::motif::Ints

◆ Mat

typedef numeric::xyzMatrix< core::Real > core::scoring::motif::Mat

◆ MotifHashCAP

typedef utility::pointer::weak_ptr< MotifHash const > core::scoring::motif::MotifHashCAP

◆ MotifHashCOP

typedef utility::pointer::shared_ptr< MotifHash const > core::scoring::motif::MotifHashCOP

◆ MotifHashOP

typedef utility::pointer::shared_ptr< MotifHash > core::scoring::motif::MotifHashOP

◆ MotifHashStringMap

typedef std::map<std::string,MotifHashOP> core::scoring::motif::MotifHashStringMap

◆ MotifRotamerSetOperationCOP

typedef utility::pointer::shared_ptr<MotifRotamerSetOperation const> core::scoring::motif::MotifRotamerSetOperationCOP

◆ MotifRotamerSetOperationOP

typedef utility::pointer::shared_ptr<MotifRotamerSetOperation > core::scoring::motif::MotifRotamerSetOperationOP

◆ MotifSet

typedef boost::unordered_set<ResPairMotif,MyHash,MyPred> core::scoring::motif::MotifSet

◆ Reals

typedef utility::vector1< Real > core::scoring::motif::Reals

◆ ResPairMotifPtrs

typedef utility::vector1<ResPairMotif const*> core::scoring::motif::ResPairMotifPtrs

◆ ResPairMotifsMap

typedef boost::unordered_map<ResPairMotifMetaBinner::Key,ResPairMotifs> core::scoring::motif::ResPairMotifsMap

◆ ResPairMotifsStringMap

typedef std::map<std::string,ResPairMotifs> core::scoring::motif::ResPairMotifsStringMap

◆ Sizes

typedef utility::vector1< Size > core::scoring::motif::Sizes

◆ Vec

typedef numeric::xyzVector< core::Real > core::scoring::motif::Vec

◆ Xform

typedef numeric::xyzTransform< core::Real > core::scoring::motif::Xform

◆ XformScoreCAP

typedef utility::pointer::weak_ptr< XformScore const > core::scoring::motif::XformScoreCAP

◆ XformScoreCOP

typedef utility::pointer::shared_ptr< XformScore const > core::scoring::motif::XformScoreCOP

◆ XformScoreMap

typedef boost::unordered_map<ResPairMotifMetaBinner::Key,XformScoreOP> core::scoring::motif::XformScoreMap

◆ XformScoreOP

typedef utility::pointer::shared_ptr< XformScore > core::scoring::motif::XformScoreOP

◆ XformScoreSringMap

typedef std::map<std::string,XformScore> core::scoring::motif::XformScoreSringMap

◆ XfragSetCAP

typedef utility::pointer::weak_ptr< XfragSet const > core::scoring::motif::XfragSetCAP

◆ XfragSetCOP

typedef utility::pointer::shared_ptr< XfragSet const > core::scoring::motif::XfragSetCOP

◆ XfragSetOP

typedef utility::pointer::shared_ptr< XfragSet > core::scoring::motif::XfragSetOP

Enumeration Type Documentation

◆ MotifMatchOverlapReq

enum core::scoring::motif::MotifMatchOverlapReq
Enumerator
NO_OVERLAP 
SMALL_OVERLAP 
MATCH_ROTAMER 
MATCH_AA 
MATCH_HYDROPHOBICITY 
MATCH_ANY 

◆ RM_Type

enum core::scoring::motif::RM_Type
Enumerator
RM_Type_NONE 
RM_SC 
RM_BB 
RM_PH 
RM_PO 
NUM_RM_TYPES 

◆ RPM_Type

enum core::scoring::motif::RPM_Type
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

◆ aa_trustworthiness()

core::Real core::scoring::motif::aa_trustworthiness ( char  aa)

References protocols::cluster::calibur::aa.

Referenced by core::scoring::motif::ResPairMotif::filter().

◆ align_motif_pose()

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 
)

References align_motif_pose_super().

◆ align_motif_pose_break()

Real core::scoring::motif::align_motif_pose_break ( Pose &  ,
Pose const &  ,
Size const &  ,
Pose const &  ,
Size const &  ,
RPM_Type const &   
)

◆ align_motif_pose_by_one_frame()

Real core::scoring::motif::align_motif_pose_by_one_frame ( Pose &  ,
Pose const &  ,
Size const &  ,
Pose const &  ,
Size const &  ,
RPM_Type const &   
)

◆ align_motif_pose_NCAC_super()

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 
)

References BB_BB, core::id::AtomID::BOGUS_ATOM_ID(), core::kinematics::tree::distance_squared(), core::pose::initialize_atomid_map(), core::scoring::ref, core::pose::Pose::residue(), core::scoring::superimpose_pose(), and core::pose::Pose::xyz().

◆ align_motif_pose_super()

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 
)

References core::pose::Pose::append_residue_by_jump(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::motif::get_backbone_reference_frame_atomids(), core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), core::pose::motif::get_sidechain_reference_frame_atomids(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), RM_BB, RM_PH, RM_PO, RM_SC, core::scoring::rms, rpm_type1(), rpm_type2(), core::scoring::superimpose_pose(), and core::pose::Pose::xyz().

Referenced by align_motif_pose(), and core::scoring::motif::MotifHash::get_matching_motifs().

◆ angle_distance()

Real core::scoring::motif::angle_distance ( Real const &  a,
Real const &  b 
)
inline

References core::pose::motif::a(), protocols::match::upstream::b, and protocols::mean_field::min().

Referenced by core::scoring::motif::MotifHash::get_matching_motifs().

◆ fill_xform_score_from_file()

void core::scoring::motif::fill_xform_score_from_file ( XformScoreOP &  xs,
string const &  datfile,
Real const &  wt = 1.0 
)

References core::scoring::motif::XformScore::read_binary(), and TR().

Referenced by core::scoring::motif::MotifHashManager::init().

◆ filter_motifs() [1/2]

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

References filter_motifs().

◆ filter_motifs() [2/2]

void core::scoring::motif::filter_motifs ( ResPairMotifs const &  motifs_in,
ResPairMotifs &  motifs_out 
)

References TR().

Referenced by filter_motifs(), and load_motifs().

◆ get_bins()

static utility::fixedsizearray1< Real, 6 > core::scoring::motif::get_bins ( Real  c,
Real  a 
)

References core::pose::motif::a().

◆ get_motif_atom_mask()

core::id::AtomID_Mask core::scoring::motif::get_motif_atom_mask ( Pose const &  motif_pose,
RPM_Type const &  type,
bool  with_Hpol 
)

References core::pose::motif::get_backbone_reference_frame_atomids_with_downstream(), core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), core::pose::motif::get_sidechain_reference_frame_atomids(), core::pose::motif::get_sidechain_reference_frame_atomids_with_downstream(), core::pose::initialize_atomid_map(), RM_BB, RM_PH, RM_PO, RM_SC, rpm_type1(), and rpm_type2().

◆ get_nbrs()

Reals core::scoring::motif::get_nbrs ( Pose const &  pose)

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

◆ get_residue_pair_rt6() [1/2]

Real6 core::scoring::motif::get_residue_pair_rt6 ( Pose const &  pose,
Size  ir,
Size  jr,
RPM_Type const &  type 
)

References get_residue_pair_rt6().

◆ get_residue_pair_rt6() [2/2]

Real6 core::scoring::motif::get_residue_pair_rt6 ( Pose const &  pose1,
Size  ir,
Pose const &  pose2,
Size  jr,
RPM_Type const &  type 
)

References get_residue_pair_xform().

Referenced by core::scoring::motif::MotifHash::get_matching_motifs(), and get_residue_pair_rt6().

◆ get_residue_pair_xform() [1/2]

Xform core::scoring::motif::get_residue_pair_xform ( Pose const &  pose,
Size  ir,
Size  jr,
RPM_Type const &  type 
)

References get_residue_pair_xform().

◆ get_residue_pair_xform() [2/2]

Xform core::scoring::motif::get_residue_pair_xform ( Pose const &  pose1,
Size  ir,
Pose const &  pose2,
Size  jr,
RPM_Type const &  type 
)

References core::pose::motif::get_backbone_reference_frame(), core::pose::motif::get_cterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_sidechain_reference_frame(), RM_BB, RM_PH, RM_PO, RM_SC, rpm_type1(), and rpm_type2().

Referenced by get_residue_pair_rt6(), and get_residue_pair_xform().

◆ get_sasa()

Reals core::scoring::motif::get_sasa ( Pose const &  pose,
Real const &  probesize 
)

References core::scoring::calc_per_atom_sasa(), and core::pose::Pose::size().

Referenced by core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::get_all_sasas().

◆ HACK_dump_helices()

int core::scoring::motif::HACK_dump_helices ( Pose const &  pose,
string  tag,
int  nres,
int  minlen = 10 
)

References core::pose::Pose::chain(), HACK_dump_helix(), protocols::hybridization::minlen, and core::pose::Pose::secstruct().

◆ HACK_dump_helix()

void core::scoring::motif::HACK_dump_helix ( Pose const &  pose,
string  fname,
int  beg,
int  end 
)

References core::io::pdb::dump_pdb_residue(), core::sequence::end, core::conformation::membrane::out, and core::pose::Pose::residue().

Referenced by HACK_dump_helices().

◆ inverse_rt6()

Real6 core::scoring::motif::inverse_rt6 ( Real6 const &  rt)

◆ load_motifs() [1/3]

void core::scoring::motif::load_motifs ( string const &  fname,
ResPairMotifs &  motifs,
ResPairMotifsStringMap *  map 
)

References load_motifs().

◆ load_motifs() [2/3]

void core::scoring::motif::load_motifs ( utility::vector1< std::string > const &  fnames,
ResPairMotifs &  motifs,
ResPairMotifsStringMap *  map = nullptr 
)

◆ load_motifs() [3/3]

void core::scoring::motif::load_motifs ( vector1< string > const &  fnames,
ResPairMotifs &  motifs,
ResPairMotifsStringMap *  map 
)

References core::scoring::motif::ResPairMotifs::add_reverse_motifs(), filter_motifs(), core::scoring::motif::ResPairMotifs::filter_structurally_similar_motifs(), read_motifs_binary(), and TR().

Referenced by load_motifs().

◆ operator<<() [1/14]

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
MotifHash const &  x 
)

◆ operator<<() [2/14]

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
MotifHit const &  h 
)

References core::chemical::element::F, core::chemical::element::I, core::scoring::motif::MotifHit::motif, core::conformation::membrane::out, core::scoring::motif::MotifHit::residue1, core::scoring::motif::MotifHit::residue2, core::scoring::motif::MotifHit::score1, and core::scoring::motif::MotifHit::score2.

◆ operator<<() [3/14]

ostream& core::scoring::motif::operator<< ( std::ostream &  out,
MotifHits const &  h 
)

◆ operator<<() [4/14]

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
Real6 const &  r6 
)

References core::conformation::membrane::out.

◆ operator<<() [5/14]

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
ResPairMotif const &  x 
)

◆ operator<<() [6/14]

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
RM_Type const &  x 
)

References core::chemical::element::I, core::conformation::membrane::out, RM_BB, RM_PH, RM_PO, RM_SC, and RM_Type_NONE.

◆ operator<<() [7/14]

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
RPM_Type const &  x 
)

References BB_BB, BB_PH, BB_PO, core::chemical::element::I, core::conformation::membrane::out, PH_PO, RPM_Type_NONE, SC_BB, SC_PH, SC_PO, and SC_SC.

◆ operator<<() [8/14]

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
XformScore const &  xh 
)

◆ operator<<() [9/14]

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
XformScoreSringMap const &  x 
)

References core::conformation::membrane::out.

◆ operator<<() [10/14]

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
Xfrag const &  x 
)

References core::scoring::motif::Xfrag::bfac(), core::scoring::motif::Xfrag::burial(), core::scoring::motif::Xfrag::ex1(), core::scoring::motif::Xfrag::ex2(), core::scoring::motif::Xfrag::ex3(), core::scoring::motif::Xfrag::ex4(), core::chemical::element::F, core::chemical::element::I, core::conformation::membrane::out, core::scoring::motif::Xfrag::position(), core::scoring::motif::Xfrag::rt6(), core::scoring::motif::Xfrag::size(), and core::scoring::motif::Xfrag::sscomp().

◆ operator<<() [11/14]

std::ostream & core::scoring::motif::operator<< ( ostream &  out,
Xfres const &  x 
)

◆ operator<<() [12/14]

std::ostream& core::scoring::motif::operator<< ( std::ostream &  out,
ResPairMotifQuery const &  opt 
)

◆ operator<<() [13/14]

std::ostream& core::scoring::motif::operator<< ( std::ostream &  out,
RPM_FilterStats const &  s 
)

◆ operator<<() [14/14]

std::ostream & core::scoring::motif::operator<< ( std::ostream &  out,
XformScoreMap const &  x 
)

References core::scoring::motif::ResPairMotifMetaBinner::hash_to_labal(), and core::conformation::membrane::out.

◆ operator>>() [1/4]

std::istream& core::scoring::motif::operator>> ( std::istream &  in,
MotifHash &  x 
)

◆ operator>>() [2/4]

std::istream& core::scoring::motif::operator>> ( std::istream &  in,
ResPairMotif &  x 
)

◆ operator>>() [3/4]

std::istream & core::scoring::motif::operator>> ( std::istream &  in,
Xfrag &  x 
)

References core::scoring::motif::Xfrag::bfac(), core::scoring::motif::Xfrag::burial(), core::scoring::motif::Xfrag::ex1(), core::scoring::motif::Xfrag::ex2(), core::scoring::motif::Xfrag::ex3(), core::scoring::motif::Xfrag::ex4(), core::conformation::membrane::in, core::scoring::motif::Xfrag::position(), core::scoring::motif::Xfrag::size(), and core::scoring::motif::Xfrag::sscomp().

◆ operator>>() [4/4]

std::istream & core::scoring::motif::operator>> ( std::istream &  in,
Xfres &  x 
)

References core::scoring::motif::Xfres::aa(), core::scoring::motif::Xfres::chi1(), core::scoring::motif::Xfres::chi2(), core::scoring::motif::Xfres::chi3(), core::scoring::motif::Xfres::chi4(), core::conformation::membrane::in, core::scoring::motif::Xfres::omg(), core::scoring::motif::Xfres::phi(), core::scoring::motif::Xfres::psi(), and core::scoring::motif::Xfres::ss().

◆ preload_motif_data()

void core::scoring::motif::preload_motif_data ( MotifHashManager &  mhman)

Referenced by preload_motif_data_pthread_wrapper().

◆ preload_motif_data_pthread_wrapper()

void* core::scoring::motif::preload_motif_data_pthread_wrapper ( void *  ptr)

References preload_motif_data(), and TR().

Referenced by core::scoring::motif::MotifHashManager::init().

◆ random_rotation()

Mat core::scoring::motif::random_rotation ( )

References core::pose::motif::a(), and protocols::match::upstream::b.

Referenced by core::energy_methods::parcs_ccs(), and protocols::ligand_docking::ga_ligand_dock::LigandAligner::randomize_lig().

◆ read_motifs_binary() [1/4]

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

References core::conformation::membrane::in, and MOTIF_VERSION.

Referenced by load_motifs(), and read_motifs_binary().

◆ read_motifs_binary() [2/4]

bool core::scoring::motif::read_motifs_binary ( string const &  fname,
ResPairMotifs &  motifs 
)

References core::conformation::membrane::in, and read_motifs_binary().

◆ read_motifs_binary() [3/4]

bool core::scoring::motif::read_motifs_binary ( utility::vector1< std::string > const &  fnames,
ResPairMotifs &  motifs 
)

◆ read_motifs_binary() [4/4]

bool core::scoring::motif::read_motifs_binary ( vector1< string > const &  fnames,
ResPairMotifs &  motifs 
)

References read_motifs_binary(), and TR().

◆ read_xfrag_binary() [1/12]

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

◆ read_xfrag_binary() [2/12]

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

◆ read_xfrag_binary() [3/12]

bool core::scoring::motif::read_xfrag_binary ( std::istream &  in,
vector1< Xfrag > &  xfrag 
)

References core::conformation::membrane::in.

◆ read_xfrag_binary() [4/12]

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

References core::conformation::membrane::in, read_xfrag_binary(), and read_xfres_binary().

◆ read_xfrag_binary() [5/12]

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

◆ read_xfrag_binary() [6/12]

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

◆ read_xfrag_binary() [7/12]

bool core::scoring::motif::read_xfrag_binary ( string const &  fname,
vector1< Xfrag > &  xfrag 
)

References core::conformation::membrane::in, and TR().

Referenced by read_xfrag_binary().

◆ read_xfrag_binary() [8/12]

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

References core::conformation::membrane::in, read_xfrag_binary(), and TR().

◆ read_xfrag_binary() [9/12]

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

◆ read_xfrag_binary() [10/12]

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

◆ read_xfrag_binary() [11/12]

bool core::scoring::motif::read_xfrag_binary ( vector1< string > const &  fnames,
vector1< Xfrag > &  xfrag 
)

References read_xfrag_binary(), and TR().

◆ read_xfrag_binary() [12/12]

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

References read_xfrag_binary(), and TR().

◆ read_xfres_binary() [1/6]

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

◆ read_xfres_binary() [2/6]

bool core::scoring::motif::read_xfres_binary ( std::istream &  in,
vector1< Xfres > &  xfres 
)

References core::conformation::membrane::in.

◆ read_xfres_binary() [3/6]

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

◆ read_xfres_binary() [4/6]

bool core::scoring::motif::read_xfres_binary ( string const &  fname,
vector1< Xfres > &  xfres 
)

References core::conformation::membrane::in, and TR().

Referenced by read_xfrag_binary(), and read_xfres_binary().

◆ read_xfres_binary() [5/6]

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

◆ read_xfres_binary() [6/6]

bool core::scoring::motif::read_xfres_binary ( vector1< string > const &  fnames,
vector1< Xfres > &  xfres 
)

References read_xfres_binary(), and TR().

◆ real6_to_rt()

core::kinematics::RT core::scoring::motif::real6_to_rt ( Real6 const &  rt6)

References protocols::hybridization::t.

◆ real_to_uint16() [1/2]

static uint16_t core::scoring::motif::real_to_uint16 ( Real const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic

References protocols::mean_field::max(), MAX_UINT16, protocols::mean_field::min(), and protocols::hybridization::val.

Referenced by core::scoring::motif::Xfres::omg(), core::scoring::motif::Xfres::phi(), core::scoring::motif::Xfres::psi(), core::scoring::motif::ResPairMotif::rt(), and core::scoring::motif::Xfrag::rt6().

◆ real_to_uint16() [2/2]

static uint16_t core::scoring::motif::real_to_uint16 ( Real const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic

References protocols::mean_field::max(), MAX_UINT16, protocols::mean_field::min(), and protocols::hybridization::val.

◆ real_to_uint8() [1/2]

static uint8_t core::scoring::motif::real_to_uint8 ( Real const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic

References protocols::mean_field::max(), MAX_UINT8, protocols::mean_field::min(), and protocols::hybridization::val.

Referenced by core::scoring::motif::Xfrag::bfac(), core::scoring::motif::ResPairMotif::bfac1(), core::scoring::motif::ResPairMotif::bfac2(), core::scoring::motif::Xfrag::burial(), core::scoring::motif::Xfres::chi1(), core::scoring::motif::Xfres::chi2(), core::scoring::motif::Xfres::chi3(), core::scoring::motif::Xfres::chi4(), core::scoring::motif::Xfrag::ex1(), core::scoring::motif::Xfrag::ex2(), core::scoring::motif::Xfrag::ex3(), core::scoring::motif::Xfrag::ex4(), core::scoring::motif::ResPairMotif::fa_atr(), core::scoring::motif::ResPairMotif::fa_atr_bb(), core::scoring::motif::ResPairMotif::fa_atr_sc_bb(), core::scoring::motif::ResPairMotif::hb_bb(), core::scoring::motif::ResPairMotif::hb_bb_sc(), core::scoring::motif::ResPairMotif::hb_sc(), core::scoring::motif::ResPairMotif::nbrs1(), core::scoring::motif::ResPairMotif::nbrs2(), and core::scoring::motif::ResPairMotif::ResPairMotif().

◆ real_to_uint8() [2/2]

static uint8_t core::scoring::motif::real_to_uint8 ( Real const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic

References protocols::mean_field::max(), MAX_UINT8, protocols::mean_field::min(), and protocols::hybridization::val.

◆ rpm_type1()

RM_Type core::scoring::motif::rpm_type1 ( RPM_Type const &  type)

References BB_BB, BB_PH, BB_PO, PH_PO, RM_BB, RM_PH, RM_SC, RPM_Type_NONE, SC_BB, SC_PH, SC_PO, and SC_SC.

Referenced by align_motif_pose_super(), get_motif_atom_mask(), get_residue_pair_xform(), set_residue_pair_xform(), core::scoring::motif::ResPairMotif::type1(), and core::scoring::motif::MotifHash::type1().

◆ rpm_type2()

RM_Type core::scoring::motif::rpm_type2 ( RPM_Type const &  type)

References BB_BB, BB_PH, BB_PO, PH_PO, RM_BB, RM_PH, RM_PO, RM_SC, RPM_Type_NONE, SC_BB, SC_PH, SC_PO, and SC_SC.

Referenced by align_motif_pose_super(), get_motif_atom_mask(), get_residue_pair_xform(), set_residue_pair_xform(), core::scoring::motif::ResPairMotif::type2(), and core::scoring::motif::MotifHash::type2().

◆ rt6_rt6_bb_dis2()

Real core::scoring::motif::rt6_rt6_bb_dis2 ( Real6 const &  x1,
Real6 const &  x2 
)

References rt6_rt6_dis2().

◆ rt6_rt6_bb_dis2_explicit_stupid()

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

References core::chemical::element::C, protocols::frag_picker::CA, protocols::frag_picker::CB, core::kinematics::tree::distance_squared(), core::chemical::element::N, and core::chemical::element::O.

◆ rt6_rt6_dis2()

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

Referenced by rt6_rt6_bb_dis2().

◆ rt_to_real6()

Real6 core::scoring::motif::rt_to_real6 ( core::kinematics::RT const &  rt)

References core::kinematics::RT::get_rotation(), and core::kinematics::RT::get_translation().

◆ set_residue_pair_xform()

void core::scoring::motif::set_residue_pair_xform ( Xform const &  x,
Pose &  pose,
Size  ir,
Size  jr,
RPM_Type const &  type 
)

References core::pose::motif::get_backbone_reference_frame(), core::pose::motif::get_cterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_sidechain_reference_frame(), RM_BB, RM_PH, RM_PO, RM_SC, rpm_type1(), rpm_type2(), and xform_pose().

Referenced by core::scoring::motif::ResPairMotif::fill_pose_with_motif().

◆ sqr()

template<typename T >
static T core::scoring::motif::sqr ( T const &  x)
inlinestatic

Referenced by core::scoring::motif::MotifHash::get_matching_motifs(), and core::scoring::motif::RMSandEnergyCMP::operator()().

◆ tag_from_pdb_fname()

std::string core::scoring::motif::tag_from_pdb_fname ( string const &  fname0)

◆ TR() [1/3]

static basic::Tracer core::scoring::motif::TR ( "core.scoring.motif"  )
static

Referenced by core::scoring::motif::MotifHashManager::add_motif_set_name(), core::scoring::motif::ResPairMotifs::add_reverse_motifs(), fill_xform_score_from_file(), filter_motifs(), core::scoring::motif::MotifHashManager::get_matching_motifs(), core::scoring::motif::MotifHash::get_matching_motifs(), core::scoring::motif::MotifHashManager::init(), load_motifs(), preload_motif_data_pthread_wrapper(), core::scoring::motif::XformScore::read_binary(), read_motifs_binary(), read_xfrag_binary(), read_xfres_binary(), write_motifs_binary(), write_xfrag_binary(), and write_xfres_binary().

◆ TR() [2/3]

static basic::Tracer core::scoring::motif::TR ( "core.scoring.motif"  )
static

◆ TR() [3/3]

static basic::Tracer core::scoring::motif::TR ( "core.scoring.motif.util"  )
static

◆ uint16_to_real() [1/2]

static Real core::scoring::motif::uint16_to_real ( uint16_t const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic

References protocols::mean_field::max(), MAX_UINT16, protocols::mean_field::min(), and protocols::hybridization::val.

Referenced by core::scoring::motif::ResPairMotif::dist2(), core::scoring::motif::ResPairMotif::filter(), core::scoring::motif::Xfres::omg(), core::scoring::motif::Xfres::phi(), core::scoring::motif::Xfres::psi(), core::scoring::motif::ResPairMotif::rt(), and core::scoring::motif::Xfrag::rt6().

◆ uint16_to_real() [2/2]

static Real core::scoring::motif::uint16_to_real ( uint16_t const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic

References protocols::mean_field::max(), MAX_UINT16, protocols::mean_field::min(), and protocols::hybridization::val.

◆ uint8_to_real() [1/2]

static Real core::scoring::motif::uint8_to_real ( uint8_t const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic

References protocols::mean_field::max(), MAX_UINT8, protocols::mean_field::min(), and protocols::hybridization::val.

Referenced by core::scoring::motif::Xfrag::bfac(), core::scoring::motif::ResPairMotif::bfac1(), core::scoring::motif::ResPairMotif::bfac2(), core::scoring::motif::Xfrag::burial(), core::scoring::motif::Xfres::chi1(), core::scoring::motif::ResPairMotif::chi11(), core::scoring::motif::ResPairMotif::chi12(), core::scoring::motif::ResPairMotif::chi13(), core::scoring::motif::ResPairMotif::chi14(), core::scoring::motif::Xfres::chi2(), core::scoring::motif::ResPairMotif::chi21(), core::scoring::motif::ResPairMotif::chi22(), core::scoring::motif::ResPairMotif::chi23(), core::scoring::motif::ResPairMotif::chi24(), core::scoring::motif::Xfres::chi3(), core::scoring::motif::Xfres::chi4(), core::scoring::motif::Xfrag::ex1(), core::scoring::motif::Xfrag::ex2(), core::scoring::motif::Xfrag::ex3(), core::scoring::motif::Xfrag::ex4(), core::scoring::motif::ResPairMotif::fa_atr(), core::scoring::motif::ResPairMotif::fa_atr_bb(), core::scoring::motif::ResPairMotif::fa_atr_sc_bb(), core::scoring::motif::ResPairMotif::fill_pose_with_motif(), core::scoring::motif::ResPairMotif::hb_bb(), core::scoring::motif::ResPairMotif::hb_bb_sc(), core::scoring::motif::ResPairMotif::hb_sc(), core::scoring::motif::ResPairMotif::nbrs1(), and core::scoring::motif::ResPairMotif::nbrs2().

◆ uint8_to_real() [2/2]

static Real core::scoring::motif::uint8_to_real ( uint8_t const &  val,
Real const &  lb,
Real const &  ub 
)
inlinestatic

References protocols::mean_field::max(), MAX_UINT8, protocols::mean_field::min(), and protocols::hybridization::val.

◆ write_motifs_binary() [1/2]

bool core::scoring::motif::write_motifs_binary ( ostream &  out,
ResPairMotifs const &  motifs 
)

References MOTIF_VERSION, and core::conformation::membrane::out.

Referenced by write_motifs_binary().

◆ write_motifs_binary() [2/2]

bool core::scoring::motif::write_motifs_binary ( string const &  fname_in,
ResPairMotifs const &  motifs 
)

References core::conformation::membrane::out, TR(), and write_motifs_binary().

◆ write_xfrag_binary() [1/8]

bool core::scoring::motif::write_xfrag_binary ( ostream &  out,
vector1< Xfrag > const &  xfrag 
)

References core::conformation::membrane::out.

Referenced by write_xfrag_binary().

◆ write_xfrag_binary() [2/8]

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

References core::conformation::membrane::out, write_xfrag_binary(), and write_xfres_binary().

◆ write_xfrag_binary() [3/8]

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

◆ write_xfrag_binary() [4/8]

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

◆ write_xfrag_binary() [5/8]

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

◆ write_xfrag_binary() [6/8]

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

◆ write_xfrag_binary() [7/8]

bool core::scoring::motif::write_xfrag_binary ( string const &  fname,
vector1< Xfrag > const &  xfrag 
)

References core::conformation::membrane::out, TR(), and write_xfrag_binary().

◆ write_xfrag_binary() [8/8]

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

References core::conformation::membrane::out, TR(), and write_xfrag_binary().

◆ write_xfres_binary() [1/4]

bool core::scoring::motif::write_xfres_binary ( ostream &  out,
vector1< Xfres > const &  xfres 
)

References core::conformation::membrane::out.

Referenced by write_xfrag_binary(), and write_xfres_binary().

◆ write_xfres_binary() [2/4]

bool core::scoring::motif::write_xfres_binary ( std::ostream &  out,
utility::vector1< Xfres > const &  Xfres 
)

◆ write_xfres_binary() [3/4]

bool core::scoring::motif::write_xfres_binary ( std::string const &  fname,
utility::vector1< Xfres > const &  Xfres 
)

◆ write_xfres_binary() [4/4]

bool core::scoring::motif::write_xfres_binary ( string const &  fname,
vector1< Xfres > const &  xfres 
)

References core::conformation::membrane::out, TR(), and write_xfres_binary().

◆ xform_pose()

void core::scoring::motif::xform_pose ( core::pose::Pose &  pose,
Xform const &  s,
Size  sres = 1,
Size  eres = 0 
)

References core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::pose::Pose::xyz().

Referenced by set_residue_pair_xform().

Variable Documentation

◆ MOTIF_HASH_CART_SIZE

const numeric::Real core::scoring::motif::MOTIF_HASH_CART_SIZE = 16.0
extern

Referenced by core::scoring::motif::ResPairMotif::dist2(), core::scoring::motif::ResPairMotif::filter(), core::scoring::motif::ResPairMotifQuery::init(), core::scoring::motif::ResPairMotif::rt(), core::scoring::motif::Xfrag::rt6(), core::scoring::motif::XformScore::sanity_check(), and core::scoring::motif::MotifHash::sanity_check().

◆ MOTIF_VERSION

const uint64_t core::scoring::motif::MOTIF_VERSION = 2
extern

Referenced by core::scoring::motif::XformScore::read_binary(), read_motifs_binary(), core::scoring::motif::XformScore::write_binary(), and write_motifs_binary().

◆ XsI

const numeric::Xforms core::scoring::motif::XsI = numeric::Xforms(1,numeric::Xform::identity())
static
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