#include <StrandPairing.hh>

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

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

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

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

	StrandPairing (StrandPairing const &sp)
	copy constructor More...

virtual	~StrandPairing ()
	default destructor More...

StrandPairingOP	clone ()
	clone this object More...

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

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

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

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

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

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< Size >	pleats1 () const
	the pleating at the begining of strand_pairing More...

utility::vector1< 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...

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...

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

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

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

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

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

bool	is_parallel () const
	is parallel More...

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

void	redefine_begin_end (SS_Info2_COP const ss_info)
	reset begin1_, begin2_, and end1_, end2_ based on ssinfo More...

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

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

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

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

Size	end1_

Size	begin2_

Size	end2_

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

utility::vector1< 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...

bool	has_bulge_

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

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

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

Detailed Description

Definition at line 37 of file StrandPairing.hh.

Member Typedef Documentation

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

Definition at line 42 of file StrandPairing.hh.

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

Definition at line 41 of file StrandPairing.hh.

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

Definition at line 44 of file StrandPairing.hh.

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

Definition at line 43 of file StrandPairing.hh.

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

Definition at line 40 of file StrandPairing.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 48 of file StrandPairing.cc.

Referenced by clone().

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

value constructor

Definition at line 63 of file StrandPairing.cc.

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

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

value constructor

Definition at line 93 of file StrandPairing.cc.

References initialize().

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

copy constructor

value constructor

Definition at line 115 of file StrandPairing.cc.

References name_, orient_, rgstr_shift_, s1_, and s2_.

protocols::fldsgn::topology::StrandPairing::StrandPairing ( StrandPairing const & sp)

copy constructor

Definition at line 148 of file StrandPairing.cc.

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

virtual

default destructor

Definition at line 167 of file StrandPairing.cc.

Member Function Documentation

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

Definition at line 235 of file StrandPairing.cc.

References begin1_, begin2_, end1_, end2_, has_bulge_, orient_, residue_pair_, rgstr_shift_, size1(), and size2().

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

inline

the residue number of the beginning of 1st strand

Definition at line 98 of file StrandPairing.hh.

References begin1_.

Referenced by protocols::fldsgn::topology::operator<<().

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

inline

the residue number of the beginning of 2nd strand

Definition at line 104 of file StrandPairing.hh.

References begin2_.

Referenced by protocols::fldsgn::topology::operator<<().

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

clone this object

Definition at line 172 of file StrandPairing.cc.

References StrandPairing().

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

elongate strand pairings

Definition at line 189 of file StrandPairing.cc.

References begin1_, begin2_, end1_, end2_, has_bulge_, orient_, pleats1_, pleats2_, residue_pair_, size1(), and size2().

Referenced by redefine_begin_end().

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

inline

the residue number of the end of 1st strand

Definition at line 101 of file StrandPairing.hh.

References end1_.

Referenced by protocols::fldsgn::topology::operator<<().

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

inline

the residue number of the end of 2nd strand

Definition at line 107 of file StrandPairing.hh.

References end2_.

Referenced by protocols::fldsgn::topology::operator<<().

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

inline

whether the strand pairing have bulge or not

Definition at line 122 of file StrandPairing.hh.

References has_bulge_.

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

private

initialize StrandPairing

Definition at line 140 of file StrandPairing.cc.

References name_, orient_, rgstr_shift_, s1_, and s2_.

Referenced by StrandPairing().

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

whether input residue is included in this StrandPairinge or not

Definition at line 301 of file StrandPairing.cc.

References begin1_, begin2_, end1_, and end2_.

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

is parallel

return length of 2nd strand

Definition at line 291 of file StrandPairing.cc.

References orient_.

Referenced by redefine_begin_end().

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.

Definition at line 126 of file StrandPairing.hh.

References name_.

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

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

inline

orientation, parallel or anti-parallel, of strand pairing

Definition at line 119 of file StrandPairing.hh.

References orient_.

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

inline

the pleating at the begining of strand_pairing

Definition at line 113 of file StrandPairing.hh.

References pleats1_.

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

inline

the pleating at the end of strand_pairing

Definition at line 116 of file StrandPairing.hh.

References pleats2_.

void protocols::fldsgn::topology::StrandPairing::redefine_begin_end ( SS_Info2_COP const ss_info)

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

reset begin1_, end1_, begin2_, end2_ based on ssinfo

Definition at line 329 of file StrandPairing.cc.

References elongate(), is_parallel(), rgstr_shift_, s1_, s2_, and protocols::fldsgn::TR().

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

residue pair

return residue pairing

Definition at line 321 of file StrandPairing.cc.

References begin1_, begin2_, end1_, end2_, and residue_pair_.

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

inline

the number of register shift between the strands

Definition at line 110 of file StrandPairing.hh.

References rgstr_shift_.

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

inline

the strand number of the 1st strand in strand pairing

Definition at line 92 of file StrandPairing.hh.

References s1_.

Referenced by protocols::fldsgn::topology::SheetSet::initialize().

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

inline

the strand number of the 2nd strand in strand pairing

Definition at line 95 of file StrandPairing.hh.

References s2_.

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

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

the length of 1st strand

return length of 1st strand

Definition at line 275 of file StrandPairing.cc.

References begin1_, and end1_.

Referenced by add_pair(), and elongate().

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

the length of 2nd strand

return length of 2nd strand

Definition at line 283 of file StrandPairing.cc.

References begin2_, and end2_.

Referenced by add_pair(), and elongate().

Friends And Related Function Documentation

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

friend

return strand pairing

Definition at line 179 of file StrandPairing.cc.

Member Data Documentation

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

private

end resides of first and second strands

Definition at line 173 of file StrandPairing.hh.

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

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

private

Definition at line 173 of file StrandPairing.hh.

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

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

private

Definition at line 173 of file StrandPairing.hh.

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

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

private

Definition at line 173 of file StrandPairing.hh.

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

bool protocols::fldsgn::topology::StrandPairing::has_bulge_

private

Definition at line 186 of file StrandPairing.hh.

Referenced by add_pair(), elongate(), and has_bulge().

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

private

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

Definition at line 189 of file StrandPairing.hh.

Referenced by initialize(), name(), and StrandPairing().

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

private

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

Definition at line 183 of file StrandPairing.hh.

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

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

private

pleats of end residues

Definition at line 176 of file StrandPairing.hh.

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

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

private

Definition at line 176 of file StrandPairing.hh.

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

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

private

residue pair

Definition at line 192 of file StrandPairing.hh.

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

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

private

register shift between two strands

Definition at line 179 of file StrandPairing.hh.

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

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

private

Strand number of first strand in the strand pair.

Definition at line 167 of file StrandPairing.hh.

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

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

private

Strand number of second strand in the strand pair.

Definition at line 170 of file StrandPairing.hh.

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

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation