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::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

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
	)

References antipar_, begin1_, begin2_, end1_, end2_, pairing1_, pairing2_, and pleating1_.

~StrandPairing()

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

default

Member Function Documentation

antiparallel()

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().

begin1()

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().

check_pleat()

bool core::scoring::dssp::StrandPairing::check_pleat

(

)

const

contact_order()

core::Size core::scoring::dssp::StrandPairing::contact_order

(

)

const

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

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

References end1_.

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

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

References antipar_, begin1_, end1_, core::scoring::pair, pairing1_, and pleating1_.

Referenced by protocols::abinitio::TemplateJumpSetup::create_jump_sample().

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

References begin1_, begin2_, end1_, end2_, pairing1_, and pairing2_.

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

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

References pleating1_.

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

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

References antipar_, begin1_, and pairing1_.

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

has_common_pairing()

bool core::scoring::dssp::StrandPairing::has_common_pairing

(

StrandPairing const &

other

)

const

References antipar_, begin1_, end1_, has_pairing(), core::scoring::pair, pairing1_, and pleating1_.

has_pairing()

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().

hash_value()

std::size_t core::scoring::dssp::StrandPairing::hash_value

(

)

const

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

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
	)

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().

mergeable()

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==().

operator<()

Size core::scoring::dssp::StrandPairing::operator<

(

const StrandPairing &

rhs

)

const

References antipar_, begin1_, begin2_, end1_, end2_, pairing1_, and core::scoring::dssp::tr().

operator==()

Size core::scoring::dssp::StrandPairing::operator==

(

const StrandPairing &

rhs

)

const

References begin1_, begin2_, end1_, end2_, pairing1_, pairing2_, and pleating1_.

paired()

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

References protocols::sparta::contains().

range_check()

bool core::scoring::dssp::StrandPairing::range_check

(

)

const

References begin1_, begin2_, end1_, end2_, pairing1_, and pairing2_.

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

show_internals()

void core::scoring::dssp::StrandPairing::show_internals

(

std::ostream &

out

)

const

References core::conformation::membrane::out.

size()

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

inline

References begin1_, and end1_.

Referenced by protocols::abinitio::TemplateJumpSetup::create_jump_sample(), and protocols::abinitio::PairingStatEntry::size().

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

Referenced by antiparallel(), get_all_register_and_bulges(), get_beta_pairs(), get_register(), has_common_pairing(), mergeable(), operator<(), StrandPairing(), and valid_ends().

begin1_

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<(), operator==(), range_check(), size(), and StrandPairing().

begin2_

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

private

Referenced by contains(), get_begin2(), get_pair(), is_ladder(), merge(), mergeable(), operator<(), operator==(), range_check(), and StrandPairing().

BIG_BULGE_LIMIT

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

static

end1_

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<(), operator==(), range_check(), size(), and StrandPairing().

end2_

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

private

Referenced by contains(), get_end2(), get_pair(), is_ladder(), mergeable(), operator<(), operator==(), range_check(), and StrandPairing().

pairing1_

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

private

Referenced by get_all_register_and_bulges(), get_beta_pairs(), get_pair(), get_pairing1_(), get_register(), has_common_pairing(), merge(), mergeable(), operator<(), operator==(), range_check(), StrandPairing(), and valid_ends().

pairing2_

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

private

Referenced by get_pair(), get_pairing2_(), merge(), mergeable(), operator==(), range_check(), and StrandPairing().

pleating1_

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

private

Referenced by get_beta_pairs(), get_pleating(), has_common_pairing(), merge(), mergeable(), operator==(), and StrandPairing().

SMALL_BULGE_LIMIT

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

static

---

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

• src/core/scoring/dssp/StrandPairing.hh
• src/core/scoring/dssp/StrandPairing.cc