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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 > 		SizeList
 

Private Attributes

core::Size begin1_
 
core::Size end1_
 
core::Size begin2_
 
core::Size end2_
 
std::vector< core::Size > pairing1
 
std::vector< core::Size > pleating1
 
std::vector< core::Size > pairing2
 
bool antipar_
 

Friends

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
private

Constructor & Destructor Documentation

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

References antipar_, begin1_, begin2_, end1_, end2_, pairing1, pairing2, and pleating1.

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

Member Function Documentation

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

References antipar_.

Referenced by protocols::abinitio::AlternativePairings::add_pairing(), protocols::fldsgn::topology::calc_strand_pairing_set(), and protocols::abinitio::AlternativePairings::compatible().

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

References begin1_.

Referenced by protocols::fldsgn::topology::calc_strand_pairing_set(), and protocols::abinitio::AlternativePairings::compatible().

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

Referenced by protocols::abinitio::PairingStatEntry::contact_order().

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
inline

References end1_.

Referenced by protocols::fldsgn::topology::calc_strand_pairing_set(), and protocols::abinitio::AlternativePairings::compatible().

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

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

References antipar_, begin1_, end1_, core::scoring::dssp::Pairing::Orientation(), core::scoring::pair, pairing1, core::scoring::dssp::Pairing::Pleating(), pleating1, core::scoring::dssp::Pairing::Pos1(), and core::scoring::dssp::Pairing::Pos2().

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

References begin1_, begin2_, end1_, end2_, pairing1, and pairing2.

Referenced by protocols::fldsgn::topology::calc_strand_pairing_set(), and is_bulge().

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

Referenced by protocols::fldsgn::topology::calc_strand_pairing_set().

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

References antipar_, begin1_, and pairing1.

Referenced by protocols::abinitio::AlternativePairings::compatible().

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

References antipar_, begin1_, end1_, has_pairing(), core::scoring::dssp::Pairing::Orientation(), core::scoring::pair, pairing1, core::scoring::dssp::Pairing::Pleating(), pleating1, core::scoring::dssp::Pairing::Pos1(), and core::scoring::dssp::Pairing::Pos2().

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

References core::scoring::dssp::Pairing::is_anti(), core::scoring::dssp::Pairing::Pos1(), and core::scoring::dssp::Pairing::Pos2().

Referenced by has_common_pairing().

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

References boost::tuples::hash_value(), and protocols::kinmatch::str().

Referenced by protocols::abinitio::hash_value().

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 
)

References begin1_, begin2_, end1_, extend_to(), protocols::mean_field::max(), protocols::mean_field::min(), pairing1, pairing2, pleating1, and valid_ends().

Referenced by protocols::abinitio::PairingStatEntry::add_pairing().

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

References antipar_, begin1_, begin2_, end1_, end2_, extend_to(), pairing1, pairing2, pleating1, and tr().

Referenced by protocols::abinitio::PairingStatEntry::compatible(), core::scoring::dssp::StrandPairingSet::has_pairing(), protocols::abinitio::PairingStatEntry::operator!=(), protocols::abinitio::_MergableEntries::operator()(), and protocols::abinitio::PairingStatEntry::operator==().

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

References antipar_, begin1_, begin2_, end1_, end2_, pairing1, and core::scoring::dssp::tr().

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

References begin1_, begin2_, end1_, end2_, pairing1, pairing2, and pleating1.

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

References protocols::sparta::contains().

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

References begin1_, begin2_, end1_, end2_, pairing1, and pairing2.

Referenced by core::scoring::dssp::StrandPairingSet::add_pairing(), and protocols::abinitio::PairingStatEntry::show().

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

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

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

References begin1_, and end1_.

Referenced by protocols::abinitio::PairingStatEntry::size().

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

Member Data Documentation

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

Referenced by antiparallel(), get_all_register_and_bulges(), get_beta_pairs(), get_register(), has_common_pairing(), mergeable(), operator<(), core::scoring::dssp::operator<<(), core::scoring::dssp::operator>>(), StrandPairing(), and valid_ends().

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

Referenced by begin1(), contains(), get_all_register_and_bulges(), get_beta_pairs(), get_pair(), get_register(), has_common_pairing(), is_ladder(), merge(), mergeable(), operator<(), core::scoring::dssp::operator<<(), operator==(), core::scoring::dssp::operator>>(), range_check(), size(), and StrandPairing().

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

Referenced by contains(), get_pair(), is_ladder(), merge(), mergeable(), operator<(), core::scoring::dssp::operator<<(), operator==(), core::scoring::dssp::operator>>(), range_check(), and StrandPairing().

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

Referenced by contains(), end1(), get_beta_pairs(), get_pair(), has_common_pairing(), is_ladder(), merge(), mergeable(), operator<(), core::scoring::dssp::operator<<(), operator==(), core::scoring::dssp::operator>>(), range_check(), size(), and StrandPairing().

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

Referenced by contains(), get_pair(), is_ladder(), mergeable(), operator<(), core::scoring::dssp::operator<<(), operator==(), core::scoring::dssp::operator>>(), range_check(), and StrandPairing().

std::vector<core::Size> core::scoring::dssp::StrandPairing::pairing1
private

Referenced by get_all_register_and_bulges(), get_beta_pairs(), get_pair(), get_register(), has_common_pairing(), merge(), mergeable(), operator<(), core::scoring::dssp::operator<<(), operator==(), core::scoring::dssp::operator>>(), range_check(), StrandPairing(), and valid_ends().

std::vector<core::Size> core::scoring::dssp::StrandPairing::pairing2
private

Referenced by get_pair(), merge(), mergeable(), operator==(), core::scoring::dssp::operator>>(), range_check(), and StrandPairing().

std::vector<core::Size> core::scoring::dssp::StrandPairing::pleating1
private

Referenced by get_beta_pairs(), has_common_pairing(), merge(), mergeable(), core::scoring::dssp::operator<<(), operator==(), core::scoring::dssp::operator>>(), and StrandPairing().

core::Size core::scoring::dssp::StrandPairing::SMALL_BULGE_LIMIT
static
The documentation for this class was generated from the following files:
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