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

#include <StrandPairing.hh>

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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< Sizepleats1 () const
 the pleating at the begining of strand_pairing More...
 
utility::vector1< Sizepleats2 () 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< Sizepleats1_
 pleats of end residues More...
 
utility::vector1< Sizepleats2_
 
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, Sizeresidue_pair_
 residue pair More...
 

Friends

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

Member Typedef Documentation

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 
)
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
Size protocols::fldsgn::topology::StrandPairing::end1_
private
Size protocols::fldsgn::topology::StrandPairing::end2_
private
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: