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Rosetta
2019.12
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#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_set< Key > | KeySet |
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 |
SixDCoordinateBinner & | hasher () |
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 |
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 | |
double const | cart_size_ |
double const | cart_resl_ |
double const | angle_resl_ |
SixDCoordinateBinner | hasher_ |
MotifMap | motif_umap_ |
KeySet | key_set_ |
RPM_Type | type_ |
Friends | |
std::ostream & | operator<< (std::ostream &out, MotifHash const &x) |
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 boost::unordered_multimap< Key, ResPairMotif , bin_index_hasher > core::scoring::motif::MotifHash::MotifMap |
typedef numeric::geometry::hashing::SixDCoordinateBinner core::scoring::motif::MotifHash::SixDCoordinateBinner |
core::scoring::motif::MotifHash::MotifHash | ( | ) |
References sanity_check().
References sanity_check().
core::scoring::motif::MotifHash::MotifHash | ( | ResPairMotifs const & | motifs | ) |
References add_motif(), and sanity_check().
void core::scoring::motif::MotifHash::add_motif | ( | Motif const & | d | ) |
References bin_index(), cart_size_, and core::scoring::motif::ResPairMotif::rt().
Referenced by MotifHash().
MotifHash::Key core::scoring::motif::MotifHash::bin_index | ( | Real6 const & | rt | ) | const |
References hasher_, and protocols::mean_field::max().
Referenced by add_motif(), bin_index(), count_motifs(), and find_motifs().
MotifHash::Key core::scoring::motif::MotifHash::bin_index | ( | Motif const & | m | ) | const |
References bin_index(), and core::scoring::motif::ResPairMotif::rt().
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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().
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 |
References angle_resl_, cart_resl_, check_bounds(), hasher_, motif_umap_, and core::scoring::motif::ResPairMotif::rt().
int core::scoring::motif::MotifHash::get_matching_motifs | ( | ResPairMotifQuery const & | opt, |
MotifHits & | hits | ||
) | const |
Referenced by protocols::matdes::SchemePlaceMotifsMover::apply().
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 |
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inline |
References hasher_.
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inline |
References hasher_.
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inline |
References motif_umap_.
void core::scoring::motif::MotifHash::sanity_check | ( | ) | const |
References angle_resl_, cart_resl_, cart_size_, and core::scoring::motif::MOTIF_HASH_CART_SIZE.
Referenced by MotifHash().
RPM_Type core::scoring::motif::MotifHash::type | ( | ) | const |
References core::scoring::motif::RPM_Type_NONE, and type_.
RM_Type core::scoring::motif::MotifHash::type1 | ( | ) | const |
References core::scoring::motif::rpm_type1(), and type().
RM_Type core::scoring::motif::MotifHash::type2 | ( | ) | const |
References core::scoring::motif::rpm_type2(), and type().
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friend |
double const core::scoring::motif::MotifHash::angle_resl_ |
Referenced by find_motifs_with_radius(), and sanity_check().
double const core::scoring::motif::MotifHash::cart_resl_ |
Referenced by find_motifs_with_radius(), and sanity_check().
double const core::scoring::motif::MotifHash::cart_size_ |
Referenced by add_motif(), cart_size(), check_bounds(), and sanity_check().
SixDCoordinateBinner core::scoring::motif::MotifHash::hasher_ |
Referenced by bin_index(), find_motifs_with_radius(), hasher(), and core::scoring::motif::operator<<().
KeySet core::scoring::motif::MotifHash::key_set_ |
Referenced by add_motif(), and keys().
MotifMap core::scoring::motif::MotifHash::motif_umap_ |
Referenced by add_motif(), count_motifs(), find_motifs(), find_motifs_with_radius(), num_motifs(), and core::scoring::motif::operator<<().
RPM_Type core::scoring::motif::MotifHash::type_ |
Referenced by add_motif(), and type().