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core::scoring::dssp::StrandPairing Class Reference

#include <StrandPairing.hh>

Public Member Functions

 StrandPairing ()
 StrandPairing (core::Size res1, core::Size res2, bool antiparallel, core::Size pleating)
 ~StrandPairing ()
core::Size operator== (const StrandPairing &rhs) const
core::Size operator< (const StrandPairing &rhs) const
core::Size size () const
core::Size begin1 () const
core::Size end1 () const
bool range_check () const
core::Size contact_order () const
core::Size get_register () const
void get_all_register_and_bulges (SizeList &regs, SizeList &bulges) const
std::size_t hash_value () const
bool contains (core::Size res) const
bool is_bulge (core::Size res) const
bool is_ladder () const
core::Size get_pair (core::Size res) const
bool check_pleat () const
core::Size get_pleating (core::Size res) const
bool extend (core::Size res, core::Size res2, bool antiparallel, core::Size pleating)
 If possible, extend this pairing by the given residues. More...
void extend_to (core::Size res)
bool antiparallel () const
bool has_pairing (core::scoring::dssp::Pairing const &) const
bool has_common_pairing (StrandPairing const &other) const
bool paired (core::Size res1, core::Size res2, bool anti) const
void get_beta_pairs (core::scoring::dssp::PairingList &) const
bool merge (StrandPairing const &other, bool domerge=false)
bool mergeable (StrandPairing const &other) const
void show_internals (std::ostream &out) const
bool valid_ends () const

Static Public Attributes

static core::Size BIG_BULGE_LIMIT
static core::Size SMALL_BULGE_LIMIT

Private Types

typedef utility::vector1
< core::Size

Private Attributes

core::Size begin1_
core::Size end1_
core::Size begin2_
core::Size end2_
std::vector< core::Sizepairing1
std::vector< core::Sizepleating1
std::vector< core::Sizepairing2
bool antipar_


std::ostream & operator<< (std::ostream &out, StrandPairing const &sp)
std::istream & operator>> (std::istream &in, StrandPairing &sp)

Member Typedef Documentation

typedef utility::vector1< core::Size > core::scoring::dssp::StrandPairing::SizeList

Constructor & Destructor Documentation

core::scoring::dssp::StrandPairing::StrandPairing ( )
core::scoring::dssp::StrandPairing::StrandPairing ( core::Size  res1,
core::Size  res2,
bool  antiparallel,
core::Size  pleating 
core::scoring::dssp::StrandPairing::~StrandPairing ( )

Member Function Documentation

bool core::scoring::dssp::StrandPairing::antiparallel ( ) const
core::Size core::scoring::dssp::StrandPairing::begin1 ( ) const
bool core::scoring::dssp::StrandPairing::check_pleat ( ) const
core::Size core::scoring::dssp::StrandPairing::contact_order ( ) const
bool core::scoring::dssp::StrandPairing::contains ( core::Size  res) const

References begin1_, begin2_, end1_, and end2_.

Referenced by is_bulge().

core::Size core::scoring::dssp::StrandPairing::end1 ( ) const
bool core::scoring::dssp::StrandPairing::extend ( core::Size  res,
core::Size  res2,
bool  antiparallel,
core::Size  pleating 

If possible, extend this pairing by the given residues.

If one of res1 or res2 is within 2 residues of the beginning or end of one of the strands of the pairing, and the other is within 5 residues, extend the pairing. This is the dssp definition of allowable beta bulges. Return true if the pairing was extended.

par Global Read:
Global Write:

References protocols::mean_field::max(), protocols::mean_field::min(), and tr().

void core::scoring::dssp::StrandPairing::extend_to ( core::Size  res)

References protocols::loops::extend.

Referenced by merge(), and mergeable().

void core::scoring::dssp::StrandPairing::get_all_register_and_bulges ( SizeList regs,
SizeList bulges 
) const

References antipar_, begin1_, and pairing1.

Referenced by core::scoring::dssp::operator<<().

void core::scoring::dssp::StrandPairing::get_beta_pairs ( core::scoring::dssp::PairingList beta_pairs) const
Size core::scoring::dssp::StrandPairing::get_pair ( core::Size  res) const
Size core::scoring::dssp::StrandPairing::get_pleating ( core::Size  res) const
Size core::scoring::dssp::StrandPairing::get_register ( ) const
bool core::scoring::dssp::StrandPairing::has_common_pairing ( StrandPairing const &  other) const
bool core::scoring::dssp::StrandPairing::has_pairing ( core::scoring::dssp::Pairing const &  p) const
std::size_t core::scoring::dssp::StrandPairing::hash_value ( ) const
bool core::scoring::dssp::StrandPairing::is_bulge ( core::Size  res) const

References contains(), and get_pair().

bool core::scoring::dssp::StrandPairing::is_ladder ( ) const

References begin1_, begin2_, end1_, and end2_.

bool core::scoring::dssp::StrandPairing::merge ( StrandPairing const &  other,
bool  domerge = false 
bool core::scoring::dssp::StrandPairing::mergeable ( StrandPairing const &  other) const
Size core::scoring::dssp::StrandPairing::operator< ( const StrandPairing rhs) const
Size core::scoring::dssp::StrandPairing::operator== ( const StrandPairing rhs) const
bool core::scoring::dssp::StrandPairing::paired ( core::Size  res1,
core::Size  res2,
bool  anti 
) const
bool core::scoring::dssp::StrandPairing::range_check ( ) const
void core::scoring::dssp::StrandPairing::show_internals ( std::ostream &  out) const
core::Size core::scoring::dssp::StrandPairing::size ( ) const
bool core::scoring::dssp::StrandPairing::valid_ends ( ) const

References antipar_, and pairing1.

Referenced by merge().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
StrandPairing const &  sp 
std::istream& operator>> ( std::istream &  in,
StrandPairing sp 

Member Data Documentation

bool core::scoring::dssp::StrandPairing::antipar_
core::Size core::scoring::dssp::StrandPairing::begin1_
core::Size core::scoring::dssp::StrandPairing::begin2_
core::Size core::scoring::dssp::StrandPairing::BIG_BULGE_LIMIT
core::Size core::scoring::dssp::StrandPairing::end1_
core::Size core::scoring::dssp::StrandPairing::end2_
std::vector<core::Size> core::scoring::dssp::StrandPairing::pairing1
std::vector<core::Size> core::scoring::dssp::StrandPairing::pairing2
std::vector<core::Size> core::scoring::dssp::StrandPairing::pleating1
core::Size core::scoring::dssp::StrandPairing::SMALL_BULGE_LIMIT

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