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core::scoring::motif::MotifHash Class Reference

#include <motif_hash_stuff.hh>

Inheritance diagram for core::scoring::motif::MotifHash:
Inheritance graph
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Public Types

typedef ResPairMotif Motif
 
typedef boost::uint64_t Key
 
typedef
numeric::geometry::hashing::SixDCoordinateBinner 
SixDCoordinateBinner
 
typedef
numeric::geometry::hashing::bin_index_hasher 
bin_index_hasher
 
typedef
boost::unordered_multimap< Key,
ResPairMotif, bin_index_hasher
MotifMap
 
typedef boost::unordered_set< KeyKeySet
 
typedef
numeric::geometry::hashing::xyzStripeHashCOP 
ClashCheckerPtr
 

Public Member Functions

 MotifHash ()
 
 MotifHash (Real cart_resl, Real ang_resl)
 
 MotifHash (ResPairMotifs const &motifs)
 
void sanity_check () const
 
SixDCoordinateBinner const & hasher () const
 
SixDCoordinateBinnerhasher ()
 
RPM_Type type () const
 
RM_Type type1 () const
 
RM_Type type2 () const
 
bool check_bounds (Real6 const &rt6) const
 
void add_motif (Motif const &d)
 
void add_motif (Motif const &d, Key const &key)
 
void find_motifs (Key const &k, ResPairMotifs &results) const
 
void find_motifs (Real6 const &rt, ResPairMotifs &results) const
 
Size count_motifs (Real6 const &rt) const
 
Size count_motifs (Key const &k) const
 
void find_motifs_with_radius (Real6 const &rt, Real radius, utility::vector1< Motif > &results) const
 
XformSummary get_motif_summary (Real6 const &rt, Real radius, char ss1, char ss2, utility::vector1< Real > score_cuts, char aa1=0, char aa2=0) const
 
Size num_motifs ()
 
Real cart_size () const
 
Key bin_index (Real6 const &rt) const
 
Key bin_index (Motif const &m) const
 
int get_matching_motifs (ResPairMotifQuery const &opt, MotifHits &hits) const
 
int get_matching_motifs (ResPairMotifQuery const &opt, MotifHits &hits, MotifHits &newhits) const
 
MotifHits get_matching_motifs (ResPairMotifQuery const &opt) const
 
KeySet const & keys () const
 

Public Attributes

core::Real const cart_size_
 
core::Real const cart_resl_
 
core::Real const angle_resl_
 
SixDCoordinateBinner hasher_
 
MotifMap motif_umap_
 
KeySet key_set_
 
RPM_Type type_
 

Friends

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

Member Typedef Documentation

typedef numeric::geometry::hashing::bin_index_hasher core::scoring::motif::MotifHash::bin_index_hasher
typedef numeric::geometry::hashing::xyzStripeHashCOP core::scoring::motif::MotifHash::ClashCheckerPtr
typedef boost::uint64_t core::scoring::motif::MotifHash::Key
typedef boost::unordered_set<Key> core::scoring::motif::MotifHash::KeySet
typedef numeric::geometry::hashing::SixDCoordinateBinner core::scoring::motif::MotifHash::SixDCoordinateBinner

Constructor & Destructor Documentation

core::scoring::motif::MotifHash::MotifHash ( )

References sanity_check().

core::scoring::motif::MotifHash::MotifHash ( Real  cart_resl,
Real  ang_resl 
)

References sanity_check().

core::scoring::motif::MotifHash::MotifHash ( ResPairMotifs const &  motifs)

References add_motif(), and sanity_check().

Member Function Documentation

void core::scoring::motif::MotifHash::add_motif ( Motif const &  d)
void core::scoring::motif::MotifHash::add_motif ( Motif const &  d,
Key const &  key 
)
MotifHash::Key core::scoring::motif::MotifHash::bin_index ( Real6 const &  rt) const
MotifHash::Key core::scoring::motif::MotifHash::bin_index ( Motif const &  m) const
Real core::scoring::motif::MotifHash::cart_size ( ) const
inline

References cart_size_.

bool core::scoring::motif::MotifHash::check_bounds ( Real6 const &  rt6) const

References cart_size_.

Referenced by find_motifs_with_radius().

Size core::scoring::motif::MotifHash::count_motifs ( Real6 const &  rt) const

References bin_index().

Size core::scoring::motif::MotifHash::count_motifs ( Key const &  k) const

References motif_umap_.

void core::scoring::motif::MotifHash::find_motifs ( Key const &  k,
ResPairMotifs results 
) const

References motif_umap_, and protocols::sic_dock::range().

Referenced by find_motifs().

void core::scoring::motif::MotifHash::find_motifs ( Real6 const &  rt,
ResPairMotifs results 
) const

References bin_index(), and find_motifs().

void core::scoring::motif::MotifHash::find_motifs_with_radius ( Real6 const &  rt,
Real  radius,
utility::vector1< Motif > &  results 
) const
int core::scoring::motif::MotifHash::get_matching_motifs ( ResPairMotifQuery const &  opt,
MotifHits hits 
) const
int core::scoring::motif::MotifHash::get_matching_motifs ( ResPairMotifQuery const &  opt,
MotifHits hits,
MotifHits newhits 
) const

References core::scoring::motif::align_motif_pose_super(), core::scoring::motif::angle_distance(), core::scoring::motif::ResPairMotifQuery::auto_clash_, core::pose::Pose::chain(), core::conformation::Residue::chi(), core::scoring::motif::MotifHit::chi_rmsd_, core::scoring::motif::ResPairMotifQuery::clash_check(), core::pose::symmetry::get_component_of_residue(), core::pose::symmetry::get_jump_name_to_subunits(), core::scoring::motif::get_residue_pair_rt6(), core::scoring::motif::ResPairMotifQuery::interface_only(), core::pose::symmetry::is_multicomponent(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::scoring::motif::ResPairMotifQuery::match_aa1(), core::scoring::motif::ResPairMotifQuery::match_aa2(), core::scoring::motif::ResPairMotifQuery::match_chi_rmsd(), core::scoring::motif::ResPairMotifQuery::match_radius(), core::scoring::motif::ResPairMotifQuery::match_ss1(), core::scoring::motif::ResPairMotifQuery::max_ca_dis2(), core::scoring::motif::MotifHit::mpose(), core::conformation::Residue::name1(), core::conformation::Residue::nchi(), core::conformation::Residue::nheavyatoms(), core::scoring::motif::NO_OVERLAP, core::scoring::motif::MotifHits::num_hits1(), core::scoring::motif::MotifHits::num_hits2(), core::scoring::motif::ResPairMotifQuery::overlap1(), core::scoring::motif::ResPairMotifQuery::overlap2(), core::scoring::motif::ResPairMotifQuery::pose1(), core::scoring::motif::ResPairMotifQuery::pose1_, core::scoring::motif::ResPairMotifQuery::pose2(), core::scoring::motif::ResPairMotifQuery::pose2_, core::pose::PoseCoordPickMode_BB, core::scoring::motif::MotifHits::push_back(), core::pose::Pose::residue(), core::scoring::motif::RM_BB, core::scoring::motif::RM_PH, core::scoring::motif::RM_PO, core::scoring::motif::RM_SC, core::scoring::motif::MotifHit::rms, core::scoring::motif::RPM_Type_NONE, core::pose::Pose::secstruct(), core::pose::Pose::size(), core::scoring::motif::sqr(), core::pose::symmetry::sym_dof_names(), core::pose::symmetry::symmetry_info(), core::scoring::motif::ResPairMotifQuery::useres1(), core::scoring::motif::ResPairMotifQuery::useres1_, core::scoring::motif::ResPairMotifQuery::useres2(), core::scoring::motif::ResPairMotifQuery::useres2_, and core::pose::Pose::xyz().

MotifHits core::scoring::motif::MotifHash::get_matching_motifs ( ResPairMotifQuery const &  opt) const
XformSummary core::scoring::motif::MotifHash::get_motif_summary ( Real6 const &  rt,
Real  radius,
char  ss1,
char  ss2,
utility::vector1< Real score_cuts,
char  aa1 = 0,
char  aa2 = 0 
) const
SixDCoordinateBinner const& core::scoring::motif::MotifHash::hasher ( ) const
inline

References hasher_.

SixDCoordinateBinner& core::scoring::motif::MotifHash::hasher ( )
inline

References hasher_.

KeySet const& core::scoring::motif::MotifHash::keys ( ) const
inline

References key_set_.

Size core::scoring::motif::MotifHash::num_motifs ( )
inline

References motif_umap_.

void core::scoring::motif::MotifHash::sanity_check ( ) const
RPM_Type core::scoring::motif::MotifHash::type ( ) const

References core::scoring::motif::RPM_Type_NONE, and type_.

Referenced by type1(), and type2().

RM_Type core::scoring::motif::MotifHash::type1 ( ) const
RM_Type core::scoring::motif::MotifHash::type2 ( ) const

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
MotifHash const &  x 
)
friend

Member Data Documentation

core::Real const core::scoring::motif::MotifHash::angle_resl_
core::Real const core::scoring::motif::MotifHash::cart_resl_
core::Real const core::scoring::motif::MotifHash::cart_size_
SixDCoordinateBinner core::scoring::motif::MotifHash::hasher_
KeySet core::scoring::motif::MotifHash::key_set_

Referenced by add_motif(), and keys().

MotifMap core::scoring::motif::MotifHash::motif_umap_
RPM_Type core::scoring::motif::MotifHash::type_

Referenced by add_motif(), and type().


The documentation for this class was generated from the following files: