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

#include <StrandPairing.hh>

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

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

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_, and residue_pair_.

protocols::fldsgn::topology::StrandPairing::StrandPairing ( core::Size const  s1,
core::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 orient_, rgstr_shift_, s1_, and s2_.

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

default destructor

Member Function Documentation

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_, protocols::hybridization::r1, protocols::hybridization::r2, residue_pair_, and rgstr_shift_.

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(), and protocols::fldsgn::topology::operator<<().

core::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

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().

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(), and protocols::fldsgn::topology::operator<<().

core::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 bulges1_, and bulges2_.

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().

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

initialize StrandPairing

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

Referenced by StrandPairing().

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_.

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_.

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_.

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

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

the pleating at the begining of strand_pairing

References pleats1_.

utility::vector1< core::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,
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().

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().

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().

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(), and protocols::fldsgn::topology::SheetSet::initialize().

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(), and protocols::fldsgn::topology::SheetSet::initialize().

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().

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

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

return strand pairing

Member Data Documentation

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().

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

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

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().

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().

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

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

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

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

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

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

Referenced by initialize(), and name().

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< core::Size > protocols::fldsgn::topology::StrandPairing::pleats1_
private

pleats of end residues

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

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

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

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().

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().

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().

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:
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