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core::scoring::dssp::StrandPairingSet Class Reference

#include <StrandPairing.hh>

Inheritance diagram for core::scoring::dssp::StrandPairingSet:
Inheritance graph
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Public Types

typedef
StrandPairings::const_iterator 
const_iterator
 

Public Member Functions

 StrandPairingSet ()
 
 StrandPairingSet (ObjexxFCL::FArray2_float const &hbonds, float threshold, core::pose::Pose const &)
 
 StrandPairingSet (core::pose::Pose const &, core::Real threshold=-0.5)
 Constructor for set of StrandPairing objects. More...
 
 StrandPairingSet (core::scoring::dssp::PairingList const &)
 
 ~StrandPairingSet () override
 
bool check_pleat () const
 
char dssp_state (core::Size res) const
 
char featurizer_state (core::Size res) const
 
bool paired (core::Size res1, core::Size res2, bool antiparallel) const
 
bool has_pairing (core::scoring::dssp::Pairing const &) const
 
bool has_pairing (StrandPairing const &) const
 
void get_beta_pairs (core::scoring::dssp::PairingList &) const
 
bool merge (const StrandPairingSet &other, bool domerge=false)
 
const_iterator begin () const
 
const_iterator end () const
 
Size size () const
 
StrandPairing const & strand_pairing (Size i) const
 
void push_back (StrandPairing const &sp)
 

Private Types

typedef utility::vector1
< StrandPairing
StrandPairings
 
typedef StrandPairings::iterator iterator
 

Private Member Functions

void add_pairing (core::Size res1, core::Size res2, bool antiparallel, core::Size pleating)
 Add a new pair of bonded residues to the set. More...
 
void add_pairing (core::scoring::dssp::Pairing const &pairing)
 
void selfmerge ()
 
void compute (ObjexxFCL::FArray2_float const &hbonds, float threshold, core::pose::Pose const &)
 

Private Attributes

StrandPairings pairings_
 

Friends

std::ostream & operator<< (std::ostream &out, const StrandPairingSet &sp)
 
std::istream & operator>> (std::istream &is, StrandPairingSet &sp)
 

Member Typedef Documentation

typedef StrandPairings::const_iterator core::scoring::dssp::StrandPairingSet::const_iterator
typedef StrandPairings::iterator core::scoring::dssp::StrandPairingSet::iterator
private

Constructor & Destructor Documentation

core::scoring::dssp::StrandPairingSet::StrandPairingSet ( )
inline
core::scoring::dssp::StrandPairingSet::StrandPairingSet ( ObjexxFCL::FArray2_float const &  hbonds,
float  threshold,
core::pose::Pose const &   
)
core::scoring::dssp::StrandPairingSet::StrandPairingSet ( core::pose::Pose const &  pose,
core::Real  threshold = -0.5 
)

Constructor for set of StrandPairing objects.

The incoming hbonds matrix is indexed by (acceptor residue, donor residue). Residues with energy less than threshold are considered paired, unless they are disallowed by the array called allowed (this was included to prevent helical residues from being considered paired, a problem which occasionally arose).

Parameters
par Global Read:
Global Write:
Remarks
References:
Author
bblum

References core::scoring::dssp::fill_hbond_bb_pair_score_dssp().

core::scoring::dssp::StrandPairingSet::StrandPairingSet ( core::scoring::dssp::PairingList const &  in_pairings)
core::scoring::dssp::StrandPairingSet::~StrandPairingSet ( )
overridedefault

Member Function Documentation

void core::scoring::dssp::StrandPairingSet::add_pairing ( core::Size  res1,
core::Size  res2,
bool  antiparallel,
core::Size  pleating 
)
private

Add a new pair of bonded residues to the set.

Look for a strand pairing to extend with the given pair of residues; if none exists, create a new one.

Parameters
par Global Read:
Global Write:
Remarks
References:
Author
bblum

References protocols::mean_field::add(), core::sequence::end, core::scoring::dssp::StrandPairing::range_check(), and tr().

void core::scoring::dssp::StrandPairingSet::add_pairing ( core::scoring::dssp::Pairing const &  pairing)
private
const_iterator core::scoring::dssp::StrandPairingSet::begin ( ) const
inline

References pairings_.

Referenced by protocols::abinitio::operator<<().

bool core::scoring::dssp::StrandPairingSet::check_pleat ( ) const
void core::scoring::dssp::StrandPairingSet::compute ( ObjexxFCL::FArray2_float const &  hbonds,
float  threshold,
core::pose::Pose const &   
)
private
char core::scoring::dssp::StrandPairingSet::dssp_state ( core::Size  res) const
const_iterator core::scoring::dssp::StrandPairingSet::end ( ) const
inline

References pairings_.

Referenced by protocols::abinitio::operator<<().

char core::scoring::dssp::StrandPairingSet::featurizer_state ( core::Size  res) const
void core::scoring::dssp::StrandPairingSet::get_beta_pairs ( core::scoring::dssp::PairingList beta_pairs) const
bool core::scoring::dssp::StrandPairingSet::has_pairing ( core::scoring::dssp::Pairing const &  p) const
bool core::scoring::dssp::StrandPairingSet::has_pairing ( StrandPairing const &  p) const
bool core::scoring::dssp::StrandPairingSet::merge ( const StrandPairingSet other,
bool  domerge = false 
)
bool core::scoring::dssp::StrandPairingSet::paired ( core::Size  res1,
core::Size  res2,
bool  antiparallel 
) const
void core::scoring::dssp::StrandPairingSet::push_back ( StrandPairing const &  sp)
inline

References pairings_.

Referenced by protocols::abinitio::operator>>().

void core::scoring::dssp::StrandPairingSet::selfmerge ( )
private

References core::sequence::end.

Size core::scoring::dssp::StrandPairingSet::size ( ) const
inline
StrandPairing const& core::scoring::dssp::StrandPairingSet::strand_pairing ( Size  i) const
inline

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const StrandPairingSet sp 
)
friend
std::istream& operator>> ( std::istream &  is,
StrandPairingSet sp 
)
friend

Member Data Documentation

StrandPairings core::scoring::dssp::StrandPairingSet::pairings_
private

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