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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
 
core::Size get_begin2 () const
 
core::Size get_end2 () const
 
std::vector< core::Size > const & get_pairing1_ () const
 
std::vector< core::Size > const & get_pairing2_ () const
 
std::vector< core::Size > const & get_pleating () 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::SizeSizeList
 

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_
 

Friends

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

Member Typedef Documentation

◆ SizeList

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

Constructor & Destructor Documentation

◆ StrandPairing() [1/2]

core::scoring::dssp::StrandPairing::StrandPairing ( )

◆ StrandPairing() [2/2]

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

◆ ~StrandPairing()

core::scoring::dssp::StrandPairing::~StrandPairing ( )
default

Member Function Documentation

◆ antiparallel()

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

◆ begin1()

core::Size core::scoring::dssp::StrandPairing::begin1 ( ) const
inline

◆ check_pleat()

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

◆ contact_order()

core::Size core::scoring::dssp::StrandPairing::contact_order ( ) const

◆ contains()

bool core::scoring::dssp::StrandPairing::contains ( core::Size  res) const

References begin1_, begin2_, end1_, and end2_.

Referenced by is_bulge().

◆ end1()

core::Size core::scoring::dssp::StrandPairing::end1 ( ) const
inline

◆ extend()

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.

Parameters

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

◆ extend_to()

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

References protocols::loops::extend.

Referenced by merge(), and mergeable().

◆ get_all_register_and_bulges()

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

References antipar_, begin1_, and pairing1_.

◆ get_begin2()

core::Size core::scoring::dssp::StrandPairing::get_begin2 ( ) const
inline

References begin2_.

◆ get_beta_pairs()

void core::scoring::dssp::StrandPairing::get_beta_pairs ( core::scoring::dssp::PairingList beta_pairs) const

◆ get_end2()

core::Size core::scoring::dssp::StrandPairing::get_end2 ( ) const
inline

References end2_.

◆ get_pair()

Size core::scoring::dssp::StrandPairing::get_pair ( core::Size  res) const

◆ get_pairing1_()

std::vector<core::Size> const& core::scoring::dssp::StrandPairing::get_pairing1_ ( ) const
inline

References pairing1_.

◆ get_pairing2_()

std::vector<core::Size> const& core::scoring::dssp::StrandPairing::get_pairing2_ ( ) const
inline

References pairing2_.

◆ get_pleating() [1/2]

std::vector<core::Size> const& core::scoring::dssp::StrandPairing::get_pleating ( ) const
inline

◆ get_pleating() [2/2]

Size core::scoring::dssp::StrandPairing::get_pleating ( core::Size  res) const

◆ get_register()

Size core::scoring::dssp::StrandPairing::get_register ( ) const

◆ has_common_pairing()

bool core::scoring::dssp::StrandPairing::has_common_pairing ( StrandPairing const &  other) const

◆ has_pairing()

bool core::scoring::dssp::StrandPairing::has_pairing ( core::scoring::dssp::Pairing const &  p) const

◆ hash_value()

std::size_t core::scoring::dssp::StrandPairing::hash_value ( ) const

◆ is_bulge()

bool core::scoring::dssp::StrandPairing::is_bulge ( core::Size  res) const

References contains(), and get_pair().

◆ is_ladder()

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

References begin1_, begin2_, end1_, and end2_.

◆ merge()

bool core::scoring::dssp::StrandPairing::merge ( StrandPairing const &  other,
bool  domerge = false 
)

◆ mergeable()

bool core::scoring::dssp::StrandPairing::mergeable ( StrandPairing const &  other) const

◆ operator<()

Size core::scoring::dssp::StrandPairing::operator< ( const StrandPairing rhs) const

◆ operator==()

Size core::scoring::dssp::StrandPairing::operator== ( const StrandPairing rhs) const

◆ paired()

bool core::scoring::dssp::StrandPairing::paired ( core::Size  res1,
core::Size  res2,
bool  anti 
) const

◆ range_check()

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

◆ show_internals()

void core::scoring::dssp::StrandPairing::show_internals ( std::ostream &  out) const

◆ size()

core::Size core::scoring::dssp::StrandPairing::size ( ) const
inline

◆ valid_ends()

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

References antipar_, and pairing1_.

Referenced by merge().

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<< ( std::ostream &  out,
StrandPairing const &  sp 
)
friend

◆ operator>>

std::istream& operator>> ( std::istream &  in,
StrandPairing sp 
)
friend

Member Data Documentation

◆ antipar_

bool core::scoring::dssp::StrandPairing::antipar_
private

◆ begin1_

core::Size core::scoring::dssp::StrandPairing::begin1_
private

◆ begin2_

core::Size core::scoring::dssp::StrandPairing::begin2_
private

◆ BIG_BULGE_LIMIT

core::Size core::scoring::dssp::StrandPairing::BIG_BULGE_LIMIT
static

◆ end1_

core::Size core::scoring::dssp::StrandPairing::end1_
private

◆ end2_

core::Size core::scoring::dssp::StrandPairing::end2_
private

◆ pairing1_

std::vector<core::Size> core::scoring::dssp::StrandPairing::pairing1_
private

◆ pairing2_

std::vector<core::Size> core::scoring::dssp::StrandPairing::pairing2_
private

◆ pleating1_

std::vector<core::Size> core::scoring::dssp::StrandPairing::pleating1_
private

◆ SMALL_BULGE_LIMIT

core::Size core::scoring::dssp::StrandPairing::SMALL_BULGE_LIMIT
static

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