protocols::fldsgn::topology::BetaAlphaBetaMotif Class Reference

#include <BetaAlphaBetaMotif.hh>

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

Public Member Functions
	BetaAlphaBetaMotif ()
	default constructor More...
	BetaAlphaBetaMotif (Size const &strand1, Size const &strand2, Size const &helix, Size const &cross_over)
	value constructor More...
	BetaAlphaBetaMotif (BetaAlphaBetaMotif const &s)
	copy constructor More...
virtual	~BetaAlphaBetaMotif ()
	destructor More...
String	name () const
	return name More...
Size	helix () const
Size	strand1 () const
Size	strand2 () const
Size	cross_over () const
bool	is_lefthanded () const
Real	hsheet_dist () const
Real	hs1_dist () const
Real	hs2_dist () const
Real	hs_angle () const
Real	hsheet_elev_angle () const
utility::vector1< Size >	helix_cycle () const
String	helix_cycle_as_string () const
	return helix cycle as string More...
Size	calc_inout (SS_Info2_COP const ssinfo, Size const resi) const
	whether the CB->CA vector of the C-term residue of 1st strand is pointing inward or outward 1: inward, 2: outward More...
void	calc_geometry (SS_Info2_COP const ssinfo, SheetSetCOP const sheet_set)

Private Member Functions
void	left_handed (bool const v)
void	calc_helix_cycle (SS_Info2_COP const ssinfo)
	calc helix cycle against sheet. Helix cycle is classified as 0, 1, 2, 3, 4, which denote the position on helix, where the residue pointing to sheet plane. 0 means helix cycle is not calculated, or it's impossible to determine the helix cycle. More...

Private Attributes
Size	strand1_
	data More...
Size	strand2_
	id of strand More...
Size	helix_
	id of helix More...
Size	cross_over_
	number of strands crossed over by bab-motif More...
bool	left_handed_
	is this left handed ? More...
Vector	sheet_plane_
	vector to define sheet plane More...
Vector	sheet_pos_
	one positional vector in beta sheet plane More...
Real	hs_dist_
	distance between helix and sheet More...
Real	hs_angle_
	angle between helix projected on sheet and strands More...
Real	hs1_dist_
	distance between helix and mid point of strand1_ More...
Real	hs2_dist_
	distance between helix and mid point of strand2_ More...
Real	hsheet_elev_angle_
	elevation angle of helix respect to sheet More...
utility::vector1< Size >	helix_cycle_
	cylce of helix against sheet More...
bool	geometry_is_initialized_

Friends
std::ostream &	operator<< (std::ostream &out, const BetaAlphaBetaMotif &s)
	IO Operator. More...

Member Typedef Documentation

typedef core::Real protocols::fldsgn::topology::BetaAlphaBetaMotif::Real

typedef core::Size protocols::fldsgn::topology::BetaAlphaBetaMotif::Size

typedef protocols::fldsgn::topology::SS_Info2_COP protocols::fldsgn::topology::BetaAlphaBetaMotif::SS_Info2_COP

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

typedef core::Vector protocols::fldsgn::topology::BetaAlphaBetaMotif::Vector

Constructor & Destructor Documentation

protocols::fldsgn::topology::BetaAlphaBetaMotif::BetaAlphaBetaMotif

(

)

default constructor

References helix_cycle_.

protocols::fldsgn::topology::BetaAlphaBetaMotif::BetaAlphaBetaMotif	(	Size const &	strand1,
		Size const &	strand2,
		Size const &	helix,
		Size const &	cross_over
	)

value constructor

References helix_cycle_.

protocols::fldsgn::topology::BetaAlphaBetaMotif::BetaAlphaBetaMotif

(

BetaAlphaBetaMotif const &

s

)

copy constructor

protocols::fldsgn::topology::BetaAlphaBetaMotif::~BetaAlphaBetaMotif ( )

virtual

destructor

Member Function Documentation

void protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_geometry	(	SS_Info2_COP const	ssinfo,
		SheetSetCOP const	sheet_set
	)

References angle, angle_of(), protocols::fldsgn::topology::HSSTriplet::calc_geometry(), calc_helix_cycle(), numeric::xyzVector< class >::cross(), cross(), cross_over_, numeric::conversions::degrees(), numeric::xyzVector< class >::dot(), geometry_is_initialized_, protocols::antibody::h1, protocols::antibody::h2, helix_, hs1_dist_, hs2_dist_, hs_angle_, hs_dist_, hsheet_elev_angle_, protocols::fldsgn::topology::HSSTriplet::left_handed(), left_handed_, length, runtime_assert, s1, s2, sheet, sheet_plane_, sheet_pos_, sign(), strand1_, strand2_, and protocols::fldsgn::topology::StrandPairingSet::strand_pairing().

void protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_helix_cycle ( SS_Info2_COP const  ssinfo )

private

calc helix cycle against sheet. Helix cycle is classified as 0, 1, 2, 3, 4, which denote the position on helix, where the residue pointing to sheet plane. 0 means helix cycle is not calculated, or it's impossible to determine the helix cycle.

References protocols::fldsgn::topology::compare(), cos_of(), numeric::xyzVector< class >::dot(), geometry_is_initialized_, helix_, helix_cycle_, runtime_assert, s1, s2, sheet_plane_, sheet_pos_, strand1_, strand2_, and protocols::fldsgn::TR.

Referenced by calc_geometry().

core::Size protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_inout	(	SS_Info2_COP const	ssinfo,
		Size const	resi
	)		const

whether the CB->CA vector of the C-term residue of 1st strand is pointing inward or outward 1: inward, 2: outward

References burial, end, numeric::xyzVector< class >::length(), neighbor_dist, protocols::loops::start, strand1_, strand2_, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Size protocols::fldsgn::topology::BetaAlphaBetaMotif::cross_over ( ) const

inline

References cross_over_.

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

Size protocols::fldsgn::topology::BetaAlphaBetaMotif::helix ( ) const

inline

References helix_.

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

utility::vector1< Size > protocols::fldsgn::topology::BetaAlphaBetaMotif::helix_cycle ( ) const

inline

References helix_cycle_.

std::string protocols::fldsgn::topology::BetaAlphaBetaMotif::helix_cycle_as_string

(

)

const

return helix cycle as string

References helix_cycle_, and name().

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

Real protocols::fldsgn::topology::BetaAlphaBetaMotif::hs1_dist ( ) const

inline

References hs1_dist_.

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

Real protocols::fldsgn::topology::BetaAlphaBetaMotif::hs2_dist ( ) const

inline

References hs2_dist_.

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

Real protocols::fldsgn::topology::BetaAlphaBetaMotif::hs_angle ( ) const

inline

References hs_angle_.

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

Real protocols::fldsgn::topology::BetaAlphaBetaMotif::hsheet_dist ( ) const

inline

References hs_dist_.

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

Real protocols::fldsgn::topology::BetaAlphaBetaMotif::hsheet_elev_angle ( ) const

inline

References hsheet_elev_angle_.

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

bool protocols::fldsgn::topology::BetaAlphaBetaMotif::is_lefthanded ( ) const

inline

References left_handed_.

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

void protocols::fldsgn::topology::BetaAlphaBetaMotif::left_handed ( bool const  v )

inlineprivate

References left_handed_.

std::string protocols::fldsgn::topology::BetaAlphaBetaMotif::name

(

)

const

return name

References helix(), strand1(), and strand2().

Referenced by helix_cycle_as_string().

Size protocols::fldsgn::topology::BetaAlphaBetaMotif::strand1 ( ) const

inline

References strand1_.

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

Size protocols::fldsgn::topology::BetaAlphaBetaMotif::strand2 ( ) const

inline

References strand2_.

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

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out, const BetaAlphaBetaMotif &  s  )

friend

IO Operator.

Member Data Documentation

Size protocols::fldsgn::topology::BetaAlphaBetaMotif::cross_over_

private

number of strands crossed over by bab-motif

Referenced by calc_geometry(), and cross_over().

bool protocols::fldsgn::topology::BetaAlphaBetaMotif::geometry_is_initialized_

private

Referenced by calc_geometry(), and calc_helix_cycle().

Size protocols::fldsgn::topology::BetaAlphaBetaMotif::helix_

private

id of helix

Referenced by calc_geometry(), calc_helix_cycle(), and helix().

utility::vector1< Size > protocols::fldsgn::topology::BetaAlphaBetaMotif::helix_cycle_

private

cylce of helix against sheet

Referenced by BetaAlphaBetaMotif(), calc_helix_cycle(), helix_cycle(), and helix_cycle_as_string().

Real protocols::fldsgn::topology::BetaAlphaBetaMotif::hs1_dist_

private

distance between helix and mid point of strand1_

Referenced by calc_geometry(), and hs1_dist().

Real protocols::fldsgn::topology::BetaAlphaBetaMotif::hs2_dist_

private

distance between helix and mid point of strand2_

Referenced by calc_geometry(), and hs2_dist().

Real protocols::fldsgn::topology::BetaAlphaBetaMotif::hs_angle_

private

angle between helix projected on sheet and strands

Referenced by calc_geometry(), and hs_angle().

Real protocols::fldsgn::topology::BetaAlphaBetaMotif::hs_dist_

private

distance between helix and sheet

Referenced by calc_geometry(), and hsheet_dist().

Real protocols::fldsgn::topology::BetaAlphaBetaMotif::hsheet_elev_angle_

private

elevation angle of helix respect to sheet

Referenced by calc_geometry(), and hsheet_elev_angle().

bool protocols::fldsgn::topology::BetaAlphaBetaMotif::left_handed_

private

is this left handed ?

Referenced by calc_geometry(), is_lefthanded(), and left_handed().

Vector protocols::fldsgn::topology::BetaAlphaBetaMotif::sheet_plane_

private

vector to define sheet plane

Referenced by calc_geometry(), and calc_helix_cycle().

Vector protocols::fldsgn::topology::BetaAlphaBetaMotif::sheet_pos_

private

one positional vector in beta sheet plane

Referenced by calc_geometry(), and calc_helix_cycle().

Size protocols::fldsgn::topology::BetaAlphaBetaMotif::strand1_

private

data

id of strand

Referenced by calc_geometry(), calc_helix_cycle(), calc_inout(), and strand1().

Size protocols::fldsgn::topology::BetaAlphaBetaMotif::strand2_

private

id of strand

Referenced by calc_geometry(), calc_helix_cycle(), calc_inout(), and strand2().

---

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

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