#include <StrandPairing.hh>

Collaboration diagram for core::scoring::dssp::StrandPairing:

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	pleat_weird

bool	antipar

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

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

Detailed Description

Definition at line 53 of file StrandPairing.hh.

Member Typedef Documentation

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

private

Definition at line 54 of file StrandPairing.hh.

Constructor & Destructor Documentation

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

Definition at line 689 of file StrandPairing.cc.

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

Definition at line 679 of file StrandPairing.cc.

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

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

Definition at line 692 of file StrandPairing.cc.

Member Function Documentation

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

Definition at line 989 of file StrandPairing.cc.

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

Definition at line 68 of file StrandPairing.hh.

References begin1_.

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

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

Definition at line 266 of file StrandPairing.cc.

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

Definition at line 274 of file StrandPairing.cc.

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

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

Definition at line 968 of file StrandPairing.cc.

References begin1_, begin2_, end1_, and end2_.

Referenced by is_bulge().

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

inline

Definition at line 72 of file StrandPairing.hh.

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.

StrandPairing::extend

Detailed:: 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