Rosetta Protocols  2014.35
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protocols::motif_hash::MotifHash Class Reference

#include <motif_hash_stuff.hh>

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_map
< Key, float, bin_index_hasher > 		ScoreMap
 
typedef boost::unordered_set< Key > KeySet
 
typedef
protocols::sic_dock::xyzStripeHashPoseCAP 		ClashChecker
 

Public Member Functions

 MotifHash ()
 
 MotifHash (Real cart_size, Real cart_resl, Real ang_resl)
 
 MotifHash (ResPairMotifs const &motifs)
 
SixDCoordinateBinner const & hasher () const
 
SixDCoordinateBinner & hasher ()
 
void add_motif (Motif const &d)
 
void add_motif (Motif const &d, Key const &key)
 
void add_motif_shift (Motif const &d, Real6 const &shift)
 
void set_score (Key const &k, float const &score)
 
void find_motifs (Key const &k, ResPairMotifs &results) const
 
void find_motifs (Real6 const &rt, ResPairMotifs &results) const
 
int count_motifs (Real6 const &rt) const
 
int count_motifs (Key const &k) const
 
void find_motifs_with_radius (Real6 const &rt, Real radius, vector1< Motif > &results) const
 
float motif_score (Real6 const &rt) const
 
void generate_scoring_hash ()
 
Size num_motifs ()
 
Real cart_size () const
 
Key bin_index (Real6 const &rt) const
 
Key bin_index (Motif const &m) const
 
int dump_matching_motifs (Pose const &pose1, Pose const &pose2, Real radius, std::ostream &out, int &count, ClashChecker clash_check=NULL, bool print=false) const
 
int dump_matching_motifs (Pose const &pose1, Pose const &pose2, std::ostream &out, int &count, ClashChecker clash_check=NULL, bool print=false) const
 
int print_matching_motifs (Pose const &pose1, Pose const &pose2, std::ostream &out, ClashChecker clash_check=NULL) const
 
int stat_matching_motifs (Pose const &pose1, Pose const &pose2, std::map< std::string, Real > &stats, ClashChecker clash_check=NULL, Real radius=0.0) const
 
int get_matching_motifs (Pose const &pose1, Pose const &pose2, MotifHits &hits, ClashChecker clash_check=NULL, Real radius=0.0) const
 
int get_matching_motifs (Pose const &pose1, Pose const &pose2, Bools const &useres1, Bools const &useres2, MotifHits &hits, ClashChecker clash_check=NULL, Real radius=0.0) const
 
int get_matching_motifs (Pose const &pose, core::pack::task::PackerTaskCOP ptask, MotifHits &hits, ClashChecker clash_check=NULL, Real radius=0.0) const
 
MotifRotamerSetOperationCOP get_matching_motifs_rotsetop (Pose const &pose, core::pack::task::PackerTaskCOP ptask=NULL, Real radius=0.6, ClashChecker clash_check=NULL) const
 
KeySet::const_iterator begin ()
 
KeySet::const_iterator end ()
 
KeySet const & key_set () const
 

Public Attributes

double const cart_size_
 
double const cart_resl_
 
double const angle_resl_
 
SixDCoordinateBinner hasher_
 
MotifMap motif_hash_
 
ScoreMap score_hash_
 
KeySet key_set_
 

Friends

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

Member Typedef Documentation

typedef numeric::geometry::hashing::bin_index_hasher protocols::motif_hash::MotifHash::bin_index_hasher
typedef protocols::sic_dock::xyzStripeHashPoseCAP protocols::motif_hash::MotifHash::ClashChecker
typedef boost::uint64_t protocols::motif_hash::MotifHash::Key
typedef boost::unordered_set<Key> protocols::motif_hash::MotifHash::KeySet
typedef ResPairMotif protocols::motif_hash::MotifHash::Motif
typedef boost::unordered_multimap< Key, ResPairMotif , bin_index_hasher > protocols::motif_hash::MotifHash::MotifMap
typedef boost::unordered_map< Key, float , bin_index_hasher > protocols::motif_hash::MotifHash::ScoreMap
typedef numeric::geometry::hashing::SixDCoordinateBinner protocols::motif_hash::MotifHash::SixDCoordinateBinner

Constructor & Destructor Documentation

protocols::motif_hash::MotifHash::MotifHash ( )

References hash_angle_resl, hash_cart_resl, hash_cart_size, mh, option, and options.

protocols::motif_hash::MotifHash::MotifHash ( Real  cart_size,
Real  cart_resl,
Real  ang_resl 
)
protocols::motif_hash::MotifHash::MotifHash ( ResPairMotifs const &  motifs)

References add_motif(), hash_angle_resl, hash_cart_resl, hash_cart_size, mh, option, and options.

Member Function Documentation

void protocols::motif_hash::MotifHash::add_motif ( Motif const &  d)

References bin_index(), cart_size_, key, and protocols::motif_hash::ResPairMotif::rt().

Referenced by add_motif_shift(), and MotifHash().

void protocols::motif_hash::MotifHash::add_motif ( Motif const &  d,
Key const &  key 
)

References key_set_, and motif_hash_.

void protocols::motif_hash::MotifHash::add_motif_shift ( Motif const &  d,
Real6 const &  shift 
)

References add_motif(), angle_resl_, bin_index(), cart_resl_, cart_size_, key, and protocols::motif_hash::ResPairMotif::rt().

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

KeySet::const_iterator protocols::motif_hash::MotifHash::begin ( )
inline

References key_set_.

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

MotifHash::Key protocols::motif_hash::MotifHash::bin_index ( Real6 const &  rt) const

References numeric::geometry::hashing::SixDCoordinateBinner::bin_index(), and hasher_.

Referenced by add_motif(), add_motif_shift(), bin_index(), count_motifs(), find_motifs(), and motif_score().

MotifHash::Key protocols::motif_hash::MotifHash::bin_index ( Motif const &  m) const

References bin_index(), and protocols::motif_hash::ResPairMotif::rt().

Real protocols::motif_hash::MotifHash::cart_size ( ) const
inline

References cart_size_.

Referenced by protocols::motif_hash::dump_matching_motifs().

int protocols::motif_hash::MotifHash::count_motifs ( Real6 const &  rt) const

References bin_index().

int protocols::motif_hash::MotifHash::count_motifs ( Key const &  k) const

References c, motif_hash_, and protocols::sic_dock::range().

int protocols::motif_hash::MotifHash::dump_matching_motifs ( Pose const &  pose1,
Pose const &  pose2,
Real  radius,
std::ostream &  out,
int &  count,
ClashChecker  clash_check = NULL,
bool  print = false 
) const

References protocols::motif_hash::base_dump_matching_motifs().

int protocols::motif_hash::MotifHash::dump_matching_motifs ( Pose const &  pose1,
Pose const &  pose2,
std::ostream &  out,
int &  count,
ClashChecker  clash_check = NULL,
bool  print = false 
) const

References protocols::motif_hash::base_dump_matching_motifs().

KeySet::const_iterator protocols::motif_hash::MotifHash::end ( )
inline

References key_set_.

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

void protocols::motif_hash::MotifHash::find_motifs ( Key const &  k,
ResPairMotifs &  results 
) const

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

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs(), and find_motifs().

void protocols::motif_hash::MotifHash::find_motifs ( Real6 const &  rt,
ResPairMotifs &  results 
) const

References bin_index(), and find_motifs().

void protocols::motif_hash::MotifHash::find_motifs_with_radius ( Real6 const &  rt,
Real  radius,
vector1< Motif > &  results 
) const

References angle_resl_, cart_resl_, degrees(), numeric::xyzTransform< class >::from_euler_angles_deg(), hasher_, key, motif_hash_, numeric::xyzTransform< class >::R, numeric::geometry::hashing::SixDCoordinateBinner::radial_bin_index(), protocols::motif_hash::ResPairMotif::rt(), protocols::cartesian::sqr(), numeric::xyzMatrix< class >::transposed(), numeric::xyzMatrix< class >::xx(), numeric::xyzMatrix< class >::yy(), and numeric::xyzMatrix< class >::zz().

void protocols::motif_hash::MotifHash::generate_scoring_hash ( )

References utility_exit_with_message.

int protocols::motif_hash::MotifHash::get_matching_motifs ( Pose const &  pose1,
Pose const &  pose2,
MotifHits &  hits,
ClashChecker  clash_check = NULL,
Real  radius = 0.0 
) const

References core::pose::Pose::n_residue().

int protocols::motif_hash::MotifHash::get_matching_motifs ( Pose const &  pose1,
Pose const &  pose2,
Bools const &  useres1,
Bools const &  useres2,
MotifHits &  hits,
ClashChecker  clash_check = NULL,
Real  radius = 0.0 
) const

References protocols::motif_hash::align_motif_pose_super(), BB, protocols::motif_hash::XformScore::cart_size(), numeric::xyzVector< class >::distance_squared(), protocols::motif_hash::get_residue_pair_rt6(), motifs, protocols::sic_dock::NCO, core::pose::Pose::secstruct(), ss1, ss2, core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

int protocols::motif_hash::MotifHash::get_matching_motifs ( Pose const &  pose,
core::pack::task::PackerTaskCOP  ptask,
MotifHits &  hits,
ClashChecker  clash_check = NULL,
Real  radius = 0.0 
) const
MotifRotamerSetOperationCOP protocols::motif_hash::MotifHash::get_matching_motifs_rotsetop ( Pose const &  pose,
core::pack::task::PackerTaskCOP  ptask = NULL,
Real  radius = 0.6,
ClashChecker  clash_check = NULL 
) const

References core::pack::task::TaskFactory::create_packer_task().

SixDCoordinateBinner const& protocols::motif_hash::MotifHash::hasher ( ) const
inline

References hasher_.

Referenced by protocols::motif_hash::dump_matching_motifs().

SixDCoordinateBinner& protocols::motif_hash::MotifHash::hasher ( )
inline

References hasher_.

KeySet const& protocols::motif_hash::MotifHash::key_set ( ) const
inline

References key_set_.

float protocols::motif_hash::MotifHash::motif_score ( Real6 const &  rt) const

References bin_index().

Size protocols::motif_hash::MotifHash::num_motifs ( )
inline

References motif_hash_.

int protocols::motif_hash::MotifHash::print_matching_motifs ( Pose const &  pose1,
Pose const &  pose2,
std::ostream &  out,
ClashChecker  clash_check = NULL 
) const
void protocols::motif_hash::MotifHash::set_score ( Key const &  k,
float const &  score 
)

References score_hash_.

int protocols::motif_hash::MotifHash::stat_matching_motifs ( Pose const &  pose1,
Pose const &  pose2,
std::map< std::string, Real > &  stats,
ClashChecker  clash_check = NULL,
Real  radius = 0.0 
) const

References aa1, protocols::motif_hash::ResPairMotif::aa1(), aa2, protocols::motif_hash::ResPairMotif::aa2(), protocols::motif_hash::ResPairMotif::dssp1(), protocols::motif_hash::ResPairMotif::dssp2(), protocols::motif_hash::get_residue_pair_rt6(), protocols::motif_hash::MotifHit::motif, core::conformation::Residue::name1(), core::pose::Pose::residue(), protocols::motif_hash::MotifHit::residue1, protocols::motif_hash::MotifHit::residue2, protocols::motif_hash::ResPairMotif::rt(), protocols::motif_hash::rt6_rt6_bb_dis2(), score, core::pose::Pose::secstruct(), ss1, protocols::motif_hash::ResPairMotif::ss1(), ss2, and protocols::motif_hash::ResPairMotif::ss2().

Friends And Related Function Documentation

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

Member Data Documentation

double const protocols::motif_hash::MotifHash::angle_resl_

Referenced by add_motif_shift(), and find_motifs_with_radius().

double const protocols::motif_hash::MotifHash::cart_resl_

Referenced by add_motif_shift(), and find_motifs_with_radius().

double const protocols::motif_hash::MotifHash::cart_size_

Referenced by add_motif(), add_motif_shift(), and cart_size().

SixDCoordinateBinner protocols::motif_hash::MotifHash::hasher_

Referenced by bin_index(), find_motifs_with_radius(), hasher(), and protocols::motif_hash::operator<<().

KeySet protocols::motif_hash::MotifHash::key_set_

Referenced by add_motif(), begin(), end(), and key_set().

MotifMap protocols::motif_hash::MotifHash::motif_hash_

Referenced by add_motif(), count_motifs(), protocols::motif_hash::dump_matching_motifs(), find_motifs(), find_motifs_with_radius(), num_motifs(), and protocols::motif_hash::operator<<().

ScoreMap protocols::motif_hash::MotifHash::score_hash_

Referenced by set_score().

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