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

#include <StrandPairing.hh>

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

Collaboration 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 &)
virtual	~StrandPairingSet ()
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)

Detailed Description

Definition at line 130 of file StrandPairing.hh.

Member Typedef Documentation

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

Definition at line 134 of file StrandPairing.hh.

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

private

Definition at line 132 of file StrandPairing.hh.

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

private

Definition at line 131 of file StrandPairing.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 136 of file StrandPairing.hh.

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.

StrandPairingSet::StrandPairingSet

Detailed:

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:

Authors

bblum

Last Modified:

Definition at line 90 of file StrandPairing.cc.

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

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

(

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

in_pairings)

Definition at line 101 of file StrandPairing.cc.

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

virtual

Definition at line 676 of file StrandPairing.cc.

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.

StrandPairingSet::add_pairing

Detailed:

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:

Authors

bblum

Last Modified:

Definition at line 193 of file StrandPairing.cc.

References core::scoring::dssp::StrandPairing::range_check(), and tr().

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

private

Definition at line 108 of file StrandPairing.cc.

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

Definition at line 155 of file StrandPairing.hh.

References pairings_.

Referenced by protocols::abinitio::PairingStatistics::add_topology(), and protocols::abinitio::operator<<().

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

(

)

const

Definition at line 256 of file StrandPairing.cc.

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

private

Definition at line 112 of file StrandPairing.cc.

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

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

(

core::Size

res)

const

Definition at line 596 of file StrandPairing.cc.

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

inline

Definition at line 156 of file StrandPairing.hh.

References pairings_.

Referenced by protocols::abinitio::PairingStatistics::add_topology(), and protocols::abinitio::operator<<().

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

(

core::Size

res)

const

Definition at line 610 of file StrandPairing.cc.

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

(

core::scoring::dssp::PairingList &

beta_pairs)

const

Definition at line 669 of file StrandPairing.cc.

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

Definition at line 635 of file StrandPairing.cc.

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

Definition at line 639 of file StrandPairing.cc.

References core::scoring::dssp::StrandPairing::mergeable().

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

Definition at line 225 of file StrandPairing.cc.

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

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

Definition at line 656 of file StrandPairing.cc.

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

inline

Definition at line 164 of file StrandPairing.hh.

References pairings_.

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

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

private

Definition at line 244 of file StrandPairing.cc.

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

inline

Definition at line 157 of file StrandPairing.hh.

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

Definition at line 159 of file StrandPairing.hh.

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

Definition at line 162 of file StrandPairing.cc.

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

friend

Definition at line 143 of file StrandPairing.cc.

Member Data Documentation

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

private

Definition at line 173 of file StrandPairing.hh.

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