protocols::fldsgn::topology::HelixPairing Class Reference

#include <HelixPairing.hh>

Inheritance diagram for protocols::fldsgn::topology::HelixPairing:

Collaboration diagram for protocols::fldsgn::topology::HelixPairing:

Public Types
typedef std::string	String
typedef core::Size	Size
typedef core::Real	Real
typedef core::Vector	Vector
typedef protocols::fldsgn::topology::SS_Info2_COP	SS_Info2_COP

Public Member Functions
	HelixPairing ()
	default constructor More...
	HelixPairing (Size const h1, Size const h2, char const o)
	value constructor More...
	HelixPairing (String const &hp)
	copy constructor More...
	HelixPairing (HelixPairing const &hp)
	copy constructor More...
virtual	~HelixPairing ()
	default destructor More...
HelixPairingOP	clone ()
	clone this object More...
Size	h1 () const
	the strand number of the 1st strand in strand pairing More...
Size	h2 () const
	the strand number of the 2nd strand in strand pairing More...
char	orient () const
	orientation, parallel or anti-parallel, of helix pairing More...
String	name () const
	HelixPairing is descripbed as s1()-s2().orient() For example, 2-3.A means 2nd and 3rd helices make anti-parallel helix_pairing. More...
Real	dist () const
Real	cross_angle () const
Real	align_angle () const
	helix angle projected on sheet helices belongs to More...
bool	is_parallel () const
	is parallel More...
void	calc_geometry (SS_Info2_COP const ss_info)
void	initialize ()

Private Attributes
Size	h1_
	Helix number of first strand in the strand pair. More...
Size	h2_
	Helix number of second strand in the strand pair. More...
char	orient_
	two helices make a pair by parallel, "P", anti parallel, "A", and if not defined, "N" More...
String	name_
	helix_pairing as in the style: h1_-h2_.orient_ More...
Real	dist_
Real	cross_angle_
Real	align_angle_
Size	loop_length_

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

Member Typedef Documentation

typedef core::Real protocols::fldsgn::topology::HelixPairing::Real

typedef core::Size protocols::fldsgn::topology::HelixPairing::Size

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

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

typedef core::Vector protocols::fldsgn::topology::HelixPairing::Vector

Constructor & Destructor Documentation

protocols::fldsgn::topology::HelixPairing::HelixPairing

(

)

default constructor

default constructor

Referenced by clone().

protocols::fldsgn::topology::HelixPairing::HelixPairing	(	Size const	h1,
		Size const	h2,
		char const	o
	)

value constructor

References initialize().

protocols::fldsgn::topology::HelixPairing::HelixPairing

(

String const &

hp)

copy constructor

value constructor

References h1_, h2_, name_, and orient_.

protocols::fldsgn::topology::HelixPairing::HelixPairing

(

HelixPairing const &

hp)

copy constructor

protocols::fldsgn::topology::HelixPairing::~HelixPairing ( )

virtual

default destructor

Member Function Documentation

Real protocols::fldsgn::topology::HelixPairing::align_angle ( ) const

inline

helix angle projected on sheet helices belongs to

References align_angle_.

Referenced by protocols::fldsgn::filters::HelixPairingFilter::apply(), and protocols::fldsgn::topology::operator<<().

void protocols::fldsgn::topology::HelixPairing::calc_geometry

(

SS_Info2_COP const

ss_info)

References align_angle_, protocols::fldsgn::topology::SS_Base::begin(), protocols::fldsgn::topology::SS_Base::Cend_pos(), cross_angle_, dist_, h1(), h2(), protocols::antibody2::h3, loop_length_, protocols::fldsgn::topology::SS_Base::mid_pos(), protocols::fldsgn::topology::SS_Base::Nend_pos(), protocols::fldsgn::topology::SS_Base::orient(), and orient().

HelixPairingOP protocols::fldsgn::topology::HelixPairing::clone

(

)

clone this object

References HelixPairing().

Real protocols::fldsgn::topology::HelixPairing::cross_angle ( ) const

inline

References cross_angle_.

Referenced by protocols::fldsgn::filters::HelixPairingFilter::apply(), protocols::fldsgn::topology::operator<<(), and protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::score().

Real protocols::fldsgn::topology::HelixPairing::dist ( ) const

inline

References dist_.

Referenced by protocols::fldsgn::filters::HelixPairingFilter::apply(), protocols::fldsgn::topology::operator<<(), and protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::score().

Size protocols::fldsgn::topology::HelixPairing::h1 ( ) const

inline

the strand number of the 1st strand in strand pairing

References h1_.

Referenced by protocols::fldsgn::filters::HelixPairingFilter::apply(), calc_geometry(), and protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::score().

Size protocols::fldsgn::topology::HelixPairing::h2 ( ) const

inline

the strand number of the 2nd strand in strand pairing

References h2_.

Referenced by protocols::fldsgn::filters::HelixPairingFilter::apply(), calc_geometry(), protocols::fldsgn::topology::HelixPairingSet::create_map_helix_pairings(), and protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::score().

void protocols::fldsgn::topology::HelixPairing::initialize

(

)

References h1_, h2_, name_, and orient_.

Referenced by HelixPairing().

bool protocols::fldsgn::topology::HelixPairing::is_parallel

(

)

const

is parallel

References orient_.

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

inline

HelixPairing is descripbed as s1()-s2().orient() For example, 2-3.A means 2nd and 3rd helices make anti-parallel helix_pairing.

References name_.

Referenced by protocols::fldsgn::topology::HelixPairingSet::HelixPairingSet(), and protocols::fldsgn::topology::operator<<().

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

inline

orientation, parallel or anti-parallel, of helix pairing

References orient_.

Referenced by calc_geometry().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out, const HelixPairing &  hp  )

friend

return strand pairing

Member Data Documentation

Real protocols::fldsgn::topology::HelixPairing::align_angle_

private

Referenced by align_angle(), and calc_geometry().

Real protocols::fldsgn::topology::HelixPairing::cross_angle_

private

Referenced by calc_geometry(), and cross_angle().

Real protocols::fldsgn::topology::HelixPairing::dist_

private

Referenced by calc_geometry(), and dist().

Size protocols::fldsgn::topology::HelixPairing::h1_

private

Helix number of first strand in the strand pair.

Referenced by h1(), HelixPairing(), and initialize().

Size protocols::fldsgn::topology::HelixPairing::h2_

private

Helix number of second strand in the strand pair.

Referenced by h2(), HelixPairing(), and initialize().

Size protocols::fldsgn::topology::HelixPairing::loop_length_

private

Referenced by calc_geometry().

String protocols::fldsgn::topology::HelixPairing::name_

private

helix_pairing as in the style: h1_-h2_.orient_

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

char protocols::fldsgn::topology::HelixPairing::orient_

private

two helices make a pair by parallel, "P", anti parallel, "A", and if not defined, "N"

Referenced by HelixPairing(), initialize(), is_parallel(), and orient().

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

• src/protocols/fldsgn/topology/HelixPairing.hh
• src/protocols/fldsgn/topology/HelixPairing.cc