protocols::fldsgn::topology::StrandPairing Class Reference

#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...

Member Typedef Documentation

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

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

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

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

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

Constructor & Destructor Documentation

protocols::fldsgn::topology::StrandPairing::StrandPairing

(

)

default constructor

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

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

References initialize().

protocols::fldsgn::topology::StrandPairing::StrandPairing

(

String const &

spair)

copy constructor

value constructor

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

protocols::fldsgn::topology::StrandPairing::StrandPairing

(

StrandPairing const &

sp)

copy constructor

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

virtual

default destructor

Member Function Documentation

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

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

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

References begin2_.

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

StrandPairingOP protocols::fldsgn::topology::StrandPairing::clone

(

)

clone this object

References StrandPairing().

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

elongate strand pairings

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

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

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

References has_bulge_.

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

private

initialize StrandPairing

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

References begin1_, begin2_, end1_, and end2_.

bool protocols::fldsgn::topology::StrandPairing::is_parallel

(

)

const

is parallel

return length of 2nd strand

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.

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

References orient_.

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

inline

the pleating at the begining of strand_pairing

References pleats1_.

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

inline

the pleating at the end of strand_pairing

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

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

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

References rgstr_shift_.

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

inline

the strand number of the 1st strand in strand pairing

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

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

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

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

Member Data Documentation

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

private

end resides of first and second strands

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

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

private

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

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

private

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

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

private

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

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

private

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_

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"

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

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

private

pleats of end residues

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

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

private

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

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

private

residue pair

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

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().

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().

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