#include <StrandPairing.hh>

Inheritance diagram for protocols::fldsgn::topology::StrandPairing:

Public Types
typedef std::string	String

typedef core::Size	Size

typedef core::Real	Real

typedef protocols::fldsgn::topology::SS_Info2_OP	SS_Info2_OP

typedef protocols::fldsgn::topology::SS_Info2_COP	SS_Info2_COP

Public Member Functions
	StrandPairing ()
	default constructor More...

	StrandPairing (core::Size const s1, core::Size const s2, core::Size const b1, core::Size const b2, core::Size const p, Real const rs, char const o)
	value constructor More...

	StrandPairing (core::Size const s1, core::Size const s2, Real const rs, char const o)
	value constructor More...

	StrandPairing (String const &spair)
	copy constructor More...

	~StrandPairing () override
	default destructor More...

StrandPairingOP	clone ()
	clone this object More...

core::Size	s1 () const
	the strand number of the 1st strand in strand pairing More...

core::Size	s2 () const
	the strand number of the 2nd strand in strand pairing More...

core::Size	begin1 () const
	the residue number of the beginning of 1st strand More...

core::Size	end1 () const
	the residue number of the end of 1st strand More...

core::Size	begin2 () const
	the residue number of the beginning of 2nd strand More...

core::Size	end2 () const
	the residue number of the end of 2nd strand More...

Real	rgstr_shift () const
	the number of register shift between the strands More...

utility::vector1< core::Size >	pleats1 () const
	the pleating at the begining of strand_pairing More...

utility::vector1< core::Size >	pleats2 () const
	the pleating at the end of strand_pairing More...

char	orient () const
	orientation, parallel or anti-parallel, of strand pairing More...

bool	has_bulge () const
	whether the strand pairing have bulge or not More...

bool	is_bulge (core::Size const resid) const
	whethe the given residue number is a bulge More...

String	name () const
	StrandPairing is descripbed as s1()-s2().orient().rgstr_shift() For example, 2-3.A.1 means 2nd and 3rd strands make anti-parallel strand_pairing with register shift 1. More...

bool	has_paired_residue (core::Size const res) const
	return residue pairing More...

core::Size	residue_pair (core::Size const res) const
	residue pair More...

bool	elongate (core::Size const r1, core::Size const r2, core::Size const p1, core::Size const p2)
	elongate strand pairings More...

bool	add_pair (core::Size const r1, core::Size const r2, char const orient, Real const rgstr)

core::Size	size1 () const
	the length of 1st strand More...

core::Size	size2 () const
	the length of 2nd strand More...

bool	is_parallel () const
	is parallel More...

bool	is_member (core::Size const res)
	whether input residue is included in this StrandPairinge or not More...

void	redefine_begin_end (SS_Info2_COP const ss_info, utility::vector1< String > const &abego)
	reset begin1_, begin2_, and end1_, end2_ based on ssinfo More...

Private Member Functions
void	initialize ()
	initialize StrandPairing More...

Private Attributes
core::Size	s1_
	Strand number of first strand in the strand pair. More...

core::Size	s2_
	Strand number of second strand in the strand pair. More...

core::Size	begin1_
	end resides of first and second strands More...

core::Size	end1_

core::Size	begin2_

core::Size	end2_

utility::vector1< core::Size >	pleats1_
	pleats of end residues More...

utility::vector1< core::Size >	pleats2_

Real	rgstr_shift_
	register shift between two strands More...

char	orient_
	two strands make a sheet by parallel, "P", anti parallel, "A", and if not defined, "N" More...

String	name_
	strand_pairing as in the style: s1_-s2_.orient_.rgstr_shift_ More...

std::map< core::Size, core::Size >	residue_pair_
	residue pair More...

std::set< core::Size >	bulges1_
	list of bulges in strand 1 More...

std::set< core::Size >	bulges2_
	list of bulges in strand 2 More...

Friends
std::ostream &	operator<< (std::ostream &out, const StrandPairing &sp)
	return strand pairing More...

Member Typedef Documentation

◆ Real

typedef core::Real protocols::fldsgn::topology::StrandPairing::Real

◆ Size

typedef core::Size protocols::fldsgn::topology::StrandPairing::Size

◆ SS_Info2_COP

typedef protocols::fldsgn::topology::SS_Info2_COP protocols::fldsgn::topology::StrandPairing::SS_Info2_COP

◆ SS_Info2_OP

typedef protocols::fldsgn::topology::SS_Info2_OP protocols::fldsgn::topology::StrandPairing::SS_Info2_OP

◆ String

typedef std::string protocols::fldsgn::topology::StrandPairing::String

Constructor & Destructor Documentation

◆ StrandPairing() [1/4]

protocols::fldsgn::topology::StrandPairing::StrandPairing ( )

default constructor

◆ StrandPairing() [2/4]

protocols::fldsgn::topology::StrandPairing::StrandPairing	(	core::Size const	s1,
		core::Size const	s2,
		core::Size const	b1,
		core::Size const	b2,
		core::Size const	p,
		Real const	rs,
		char const	o
	)

value constructor

References initialize(), pleats1_, pleats2_, residue_pair_, s1(), and s2().

◆ StrandPairing() [3/4]

protocols::fldsgn::topology::StrandPairing::StrandPairing	(	core::Size const	s1,
		core::Size const	s2,
		Real const	rs,
		char const	o
	)

value constructor

References initialize(), s1(), and s2().

◆ StrandPairing() [4/4]

protocols::fldsgn::topology::StrandPairing::StrandPairing ( String const & spair )

copy constructor

value constructor

References orient_, rgstr_shift_, s1_, and s2_.

◆ ~StrandPairing()

protocols::fldsgn::topology::StrandPairing::~StrandPairing ( )

overridedefault

default destructor

Member Function Documentation

◆ add_pair()

bool protocols::fldsgn::topology::StrandPairing::add_pair	(	core::Size const	r1,
		core::Size const	r2,
		char const	orient,
		Real const	rgstr
	)

References begin1_, begin2_, end1_, end2_, orient(), orient_, protocols::hybridization::r1, protocols::hybridization::r2, residue_pair_, and rgstr_shift_.

◆ begin1()

core::Size protocols::fldsgn::topology::StrandPairing::begin1 ( ) const

inline

the residue number of the beginning of 1st strand

References begin1_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute_paired_residues().

◆ begin2()

core::Size protocols::fldsgn::topology::StrandPairing::begin2 ( ) const

inline

the residue number of the beginning of 2nd strand

References begin2_.

◆ clone()

StrandPairingOP protocols::fldsgn::topology::StrandPairing::clone ( )

clone this object

◆ elongate()

bool protocols::fldsgn::topology::StrandPairing::elongate	(	core::Size const	r1,
		core::Size const	r2,
		core::Size const	p1,
		core::Size const	p2
	)

elongate strand pairings

References begin1_, begin2_, end1_, end2_, orient_, pleats1_, pleats2_, protocols::hybridization::r1, protocols::hybridization::r2, and residue_pair_.

Referenced by redefine_begin_end().

◆ end1()

core::Size protocols::fldsgn::topology::StrandPairing::end1 ( ) const

inline

the residue number of the end of 1st strand

References end1_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute_paired_residues().

◆ end2()

core::Size protocols::fldsgn::topology::StrandPairing::end2 ( ) const

inline

the residue number of the end of 2nd strand

References end2_.

◆ has_bulge()

bool protocols::fldsgn::topology::StrandPairing::has_bulge ( ) const

inline

whether the strand pairing have bulge or not

References bulges1_, and bulges2_.

◆ has_paired_residue()

bool protocols::fldsgn::topology::StrandPairing::has_paired_residue ( core::Size const res ) const

return residue pairing

References residue_pair_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute_paired_residues().

◆ initialize()

void protocols::fldsgn::topology::StrandPairing::initialize ( )

private

initialize StrandPairing

References name_, orient_, rgstr_shift_, s1_, s2_, and core::id::to_string().

Referenced by StrandPairing().

◆ is_bulge()

bool protocols::fldsgn::topology::StrandPairing::is_bulge ( core::Size const resid ) const

inline

whethe the given residue number is a bulge

References bulges1_, and bulges2_.

◆ is_member()

bool protocols::fldsgn::topology::StrandPairing::is_member ( core::Size const res )

whether input residue is included in this StrandPairinge or not

References begin1_, begin2_, end1_, and end2_.

◆ is_parallel()

bool protocols::fldsgn::topology::StrandPairing::is_parallel ( ) const

is parallel

return length of 2nd strand

References orient_.

Referenced by redefine_begin_end().

◆ name()

String protocols::fldsgn::topology::StrandPairing::name ( ) const

inline

StrandPairing is descripbed as s1()-s2().orient().rgstr_shift() For example, 2-3.A.1 means 2nd and 3rd strands make anti-parallel strand_pairing with register shift 1.

References name_.

Referenced by protocols::fldsgn::topology::StrandPairingSet::finalize(), and protocols::fldsgn::topology::StrandPairingSet::name_wo_rgstr().

◆ orient()

char protocols::fldsgn::topology::StrandPairing::orient ( ) const

inline

orientation, parallel or anti-parallel, of strand pairing

References orient_.

Referenced by add_pair(), and protocols::fldsgn::filters::SheetTopologyFilter::compute().

◆ pleats1()

utility::vector1< core::Size > protocols::fldsgn::topology::StrandPairing::pleats1 ( ) const

inline

the pleating at the begining of strand_pairing

References pleats1_.

◆ pleats2()

utility::vector1< core::Size > protocols::fldsgn::topology::StrandPairing::pleats2 ( ) const

inline

the pleating at the end of strand_pairing

References pleats2_.

◆ redefine_begin_end()

void protocols::fldsgn::topology::StrandPairing::redefine_begin_end	(	SS_Info2_COP const	ss_info,
		utility::vector1< String > const &	abego
	)

reset begin1_, begin2_, and end1_, end2_ based on ssinfo

reset begin1_, end1_, begin2_, end2_ based on ssinfo

Detailed: abego is used for obtaining bulge information if it is non-empty

Detailed: abego is used for determining proper pairings in bulges

References core::scoring::abego, bulges1_, bulges2_, protocols::fldsgn::topology::compute_bulges(), elongate(), is_parallel(), rgstr_shift_, s1_, s2_, size1(), size2(), and protocols::fldsgn::TR().

◆ residue_pair()

StrandPairing::Size protocols::fldsgn::topology::StrandPairing::residue_pair ( core::Size const res ) const

residue pair

return residue pairing

References residue_pair_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute_paired_residues().

◆ rgstr_shift()

Real protocols::fldsgn::topology::StrandPairing::rgstr_shift ( ) const

inline

the number of register shift between the strands

References rgstr_shift_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute_paired_residues().

◆ s1()

core::Size protocols::fldsgn::topology::StrandPairing::s1 ( ) const

inline

the strand number of the 1st strand in strand pairing

References s1_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute_paired_residues(), protocols::fldsgn::topology::SheetSet::initialize(), and StrandPairing().

◆ s2()

core::Size protocols::fldsgn::topology::StrandPairing::s2 ( ) const

inline

the strand number of the 2nd strand in strand pairing

References s2_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute_paired_residues(), protocols::fldsgn::topology::StrandPairingSet::finalize(), protocols::fldsgn::topology::SheetSet::initialize(), and StrandPairing().

◆ size1()

StrandPairing::Size protocols::fldsgn::topology::StrandPairing::size1 ( ) const

the length of 1st strand

return length of 1st strand

References begin1_, and end1_.

Referenced by redefine_begin_end().

◆ size2()

StrandPairing::Size protocols::fldsgn::topology::StrandPairing::size2 ( ) const

the length of 2nd strand

return length of 2nd strand

References begin2_, and end2_.

Referenced by redefine_begin_end().

Friends And Related Function Documentation

◆ operator<<

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

friend

return strand pairing

Member Data Documentation

◆ begin1_

core::Size protocols::fldsgn::topology::StrandPairing::begin1_

private

end resides of first and second strands

Referenced by add_pair(), begin1(), elongate(), is_member(), and size1().

◆ begin2_

core::Size protocols::fldsgn::topology::StrandPairing::begin2_

private

Referenced by add_pair(), begin2(), elongate(), is_member(), and size2().

◆ bulges1_

std::set< core::Size > protocols::fldsgn::topology::StrandPairing::bulges1_

private

list of bulges in strand 1

Referenced by has_bulge(), is_bulge(), and redefine_begin_end().

◆ bulges2_

std::set< core::Size > protocols::fldsgn::topology::StrandPairing::bulges2_

private

list of bulges in strand 2

Referenced by has_bulge(), is_bulge(), and redefine_begin_end().

◆ end1_

core::Size protocols::fldsgn::topology::StrandPairing::end1_

private

Referenced by add_pair(), elongate(), end1(), is_member(), and size1().

◆ end2_

core::Size protocols::fldsgn::topology::StrandPairing::end2_

private

Referenced by add_pair(), elongate(), end2(), is_member(), and size2().

◆ name_

String protocols::fldsgn::topology::StrandPairing::name_

private

strand_pairing as in the style: s1_-s2_.orient_.rgstr_shift_

Referenced by initialize(), and name().

◆ orient_

char protocols::fldsgn::topology::StrandPairing::orient_

private

two strands make a sheet by parallel, "P", anti parallel, "A", and if not defined, "N"

Referenced by add_pair(), elongate(), initialize(), is_parallel(), orient(), and StrandPairing().

◆ pleats1_

utility::vector1< core::Size > protocols::fldsgn::topology::StrandPairing::pleats1_

private

pleats of end residues

Referenced by elongate(), pleats1(), and StrandPairing().

◆ pleats2_

utility::vector1< core::Size > protocols::fldsgn::topology::StrandPairing::pleats2_

private

Referenced by elongate(), pleats2(), and StrandPairing().

◆ residue_pair_

std::map< core::Size, core::Size > protocols::fldsgn::topology::StrandPairing::residue_pair_

private

residue pair

Referenced by add_pair(), elongate(), has_paired_residue(), residue_pair(), and StrandPairing().

◆ rgstr_shift_

Real protocols::fldsgn::topology::StrandPairing::rgstr_shift_

private

register shift between two strands

Referenced by add_pair(), initialize(), redefine_begin_end(), rgstr_shift(), and StrandPairing().

◆ s1_

core::Size protocols::fldsgn::topology::StrandPairing::s1_

private

Strand number of first strand in the strand pair.

Referenced by initialize(), redefine_begin_end(), s1(), and StrandPairing().

◆ s2_

core::Size protocols::fldsgn::topology::StrandPairing::s2_

private

Strand number of second strand in the strand pair.

Referenced by initialize(), redefine_begin_end(), s2(), and StrandPairing().

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

src/protocols/fldsgn/topology/StrandPairing.hh
src/protocols/fldsgn/topology/StrandPairing.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Member Typedef Documentation

◆ Real

◆ Size

◆ SS_Info2_COP

◆ SS_Info2_OP

◆ String

Constructor & Destructor Documentation

◆ StrandPairing() [1/4]

◆ StrandPairing() [2/4]

◆ StrandPairing() [3/4]

◆ StrandPairing() [4/4]

◆ ~StrandPairing()

Member Function Documentation

◆ add_pair()

◆ begin1()

◆ begin2()

◆ clone()

◆ elongate()

◆ end1()

◆ end2()

◆ has_bulge()

◆ has_paired_residue()

◆ initialize()

◆ is_bulge()

◆ is_member()

◆ is_parallel()

◆ name()

◆ orient()

◆ pleats1()

◆ pleats2()

◆ redefine_begin_end()

◆ residue_pair()

◆ rgstr_shift()

◆ s1()

◆ s2()

◆ size1()

◆ size2()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ begin1_

◆ begin2_

◆ bulges1_

◆ bulges2_

◆ end1_

◆ end2_

◆ name_

◆ orient_

◆ pleats1_

◆ pleats2_

◆ residue_pair_

◆ rgstr_shift_

◆ s1_

◆ s2_