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

#include <motif_hash_stuff.hh>

Inheritance diagram for core::scoring::motif::MotifHash:

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
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 ResPairMotif core::scoring::motif::MotifHash::Motif

typedef boost::unordered_multimap< Key, ResPairMotif , bin_index_hasher > core::scoring::motif::MotifHash::MotifMap

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

)

References bin_index(), cart_size_, and core::scoring::motif::ResPairMotif::rt().

Referenced by MotifHash().

void core::scoring::motif::MotifHash::add_motif	(	Motif const &	d,
		Key const &	key
	)

References key_set_, motif_umap_, core::scoring::motif::RPM_Type_NONE, core::scoring::motif::ResPairMotif::type(), and type_.

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().

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

References angle_resl_, cart_resl_, check_bounds(), hasher_, motif_umap_, and core::scoring::motif::ResPairMotif::rt().

Referenced by get_motif_summary().

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

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

References core::scoring::motif::XformSummary::best_motif, find_motifs_with_radius(), core::scoring::motif::XformSummary::num_by_cut, core::scoring::motif::ResPairMotif::score(), and core::scoring::motif::ResPairMotif::valid().

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

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_.

Referenced by type1(), and type2().

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().

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_

Referenced by find_motifs_with_radius(), and sanity_check().

core::Real const core::scoring::motif::MotifHash::cart_resl_

Referenced by find_motifs_with_radius(), and sanity_check().

core::Real 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().

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

• src/core/scoring/motif/motif_hash_stuff.hh
• src/core/scoring/motif/motif_hash_stuff.cc