core::scoring::dssp::StrandPairingSet Class Reference

#include <StrandPairing.hh>

Inheritance diagram for core::scoring::dssp::StrandPairingSet:

Public Types
typedef StrandPairings::const_iterator	const_iterator

Public Member Functions
	StrandPairingSet ()
	StrandPairingSet (ObjexxFCL::FArray2_float const &hbonds, float threshold, core::pose::Pose const &)
	StrandPairingSet (core::pose::Pose const &, core::Real threshold=-0.5)
	Constructor for set of StrandPairing objects. More...
	StrandPairingSet (core::scoring::dssp::PairingList const &)
	~StrandPairingSet () override
bool	check_pleat () const
char	dssp_state (core::Size res) const
char	featurizer_state (core::Size res) const
bool	paired (core::Size res1, core::Size res2, bool antiparallel) const
bool	has_pairing (core::scoring::dssp::Pairing const &) const
bool	has_pairing (StrandPairing const &) const
void	get_beta_pairs (core::scoring::dssp::PairingList &) const
bool	merge (const StrandPairingSet &other, bool domerge=false)
const_iterator	begin () const
const_iterator	end () const
Size	size () const
StrandPairing const &	strand_pairing (Size i) const
void	push_back (StrandPairing const &sp)

Private Types
typedef utility::vector1 < StrandPairing >	StrandPairings
typedef StrandPairings::iterator	iterator

Private Member Functions
void	add_pairing (core::Size res1, core::Size res2, bool antiparallel, core::Size pleating)
	Add a new pair of bonded residues to the set. More...
void	add_pairing (core::scoring::dssp::Pairing const &pairing)
void	selfmerge ()
void	compute (ObjexxFCL::FArray2_float const &hbonds, float threshold, core::pose::Pose const &)

Private Attributes
StrandPairings	pairings_

Friends
std::ostream &	operator<< (std::ostream &out, const StrandPairingSet &sp)
std::istream &	operator>> (std::istream &is, StrandPairingSet &sp)

Member Typedef Documentation

typedef StrandPairings::const_iterator core::scoring::dssp::StrandPairingSet::const_iterator

typedef StrandPairings::iterator core::scoring::dssp::StrandPairingSet::iterator

private

typedef utility::vector1< StrandPairing > core::scoring::dssp::StrandPairingSet::StrandPairings

private

Constructor & Destructor Documentation

core::scoring::dssp::StrandPairingSet::StrandPairingSet ( )

inline

core::scoring::dssp::StrandPairingSet::StrandPairingSet	(	ObjexxFCL::FArray2_float const &	hbonds,
		float	threshold,
		core::pose::Pose const &
	)

core::scoring::dssp::StrandPairingSet::StrandPairingSet	(	core::pose::Pose const &	pose,
		core::Real	threshold = -0.5
	)

Constructor for set of StrandPairing objects.

The incoming hbonds matrix is indexed by (acceptor residue, donor residue). Residues with energy less than threshold are considered paired, unless they are disallowed by the array called allowed (this was included to prevent helical residues from being considered paired, a problem which occasionally arose).

Parameters

par Global Read:

Global Write:

Remarks

References:

Author

bblum

References core::scoring::dssp::fill_hbond_bb_pair_score_dssp().

core::scoring::dssp::StrandPairingSet::StrandPairingSet

(

core::scoring::dssp::PairingList const &

in_pairings

)

core::scoring::dssp::StrandPairingSet::~StrandPairingSet ( )

overridedefault

Member Function Documentation

void core::scoring::dssp::StrandPairingSet::add_pairing ( core::Size  res1, core::Size  res2, bool  antiparallel, core::Size  pleating  )

private

Add a new pair of bonded residues to the set.

Look for a strand pairing to extend with the given pair of residues; if none exists, create a new one.

Parameters

par Global Read:

Global Write:

Remarks

References:

Author

bblum

References protocols::mean_field::add(), core::sequence::end, core::scoring::dssp::StrandPairing::range_check(), and tr().

void core::scoring::dssp::StrandPairingSet::add_pairing ( core::scoring::dssp::Pairing const &  pairing )

private

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

const_iterator core::scoring::dssp::StrandPairingSet::begin ( ) const

inline

References pairings_.

Referenced by protocols::abinitio::operator<<().

bool core::scoring::dssp::StrandPairingSet::check_pleat

(

)

const

void core::scoring::dssp::StrandPairingSet::compute ( ObjexxFCL::FArray2_float const &  hbonds, float  threshold, core::pose::Pose const &    )

private

References core::scoring::dssp::get_pleating(), and core::pose::Pose::size().

char core::scoring::dssp::StrandPairingSet::dssp_state

(

core::Size

res

)

const

const_iterator core::scoring::dssp::StrandPairingSet::end ( ) const

inline

References pairings_.

Referenced by protocols::abinitio::operator<<().

char core::scoring::dssp::StrandPairingSet::featurizer_state

(

core::Size

res

)

const

void core::scoring::dssp::StrandPairingSet::get_beta_pairs

(

core::scoring::dssp::PairingList &

beta_pairs

)

const

Referenced by protocols::abinitio::PairingStatistics::compute(), and protocols::abinitio::Template::Template().

bool core::scoring::dssp::StrandPairingSet::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 protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), and protocols::abinitio::PairingStatistics::is_native_pairing().

bool core::scoring::dssp::StrandPairingSet::has_pairing

(

StrandPairing const &

p

)

const

References core::sequence::end, and core::scoring::dssp::StrandPairing::mergeable().

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

References core::kinematics::FoldTree::begin(), core::sequence::end, and pairings_.

bool core::scoring::dssp::StrandPairingSet::paired	(	core::Size	res1,
		core::Size	res2,
		bool	antiparallel
	)		const

void core::scoring::dssp::StrandPairingSet::push_back ( StrandPairing const &  sp )

inline

References pairings_.

Referenced by protocols::abinitio::operator>>().

void core::scoring::dssp::StrandPairingSet::selfmerge ( )

private

References core::sequence::end.

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

inline

References pairings_.

Referenced by protocols::fldsgn::topology::calc_strand_pairing_set(), and protocols::abinitio::operator<<().

StrandPairing const& core::scoring::dssp::StrandPairingSet::strand_pairing ( Size  i ) const

inline

References pairings_.

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

Friends And Related Function Documentation

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

friend

std::istream& operator>> ( std::istream &  is, StrandPairingSet &  sp  )

friend

Member Data Documentation

StrandPairings core::scoring::dssp::StrandPairingSet::pairings_

private

Referenced by begin(), end(), merge(), core::scoring::dssp::operator<<(), core::scoring::dssp::operator>>(), push_back(), size(), and strand_pairing().

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

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