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

#include <BetaAlphaBetaMotif.hh>

Inheritance diagram for protocols::fldsgn::topology::BetaAlphaBetaMotif:
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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 (core::Size const strand1, core::Size const strand2, core::Size const helix, core::Size const cross_over)
 value constructor More...
 
 BetaAlphaBetaMotif (BetaAlphaBetaMotif const &s)
 copy constructor More...
 
 ~BetaAlphaBetaMotif () override
 destructor More...
 
String name () const
 return name More...
 
core::Size helix () const
 
core::Size strand1 () const
 
core::Size strand2 () const
 
core::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< core::Size > helix_cycle () const
 
String helix_cycle_as_string () const
 return helix cycle as string More...
 
core::Size calc_inout (SS_Info2_COP const ssinfo, core::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

core::Size strand1_
 data More...
 
core::Size strand2_
 id of strand More...
 
core::Size helix_
 id of helix More...
 
core::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< core::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

◆ Real

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

◆ Size

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

◆ SS_Info2_COP

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

◆ String

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

◆ Vector

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

Constructor & Destructor Documentation

◆ BetaAlphaBetaMotif() [1/3]

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

default constructor

References helix_cycle_.

◆ BetaAlphaBetaMotif() [2/3]

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

value constructor

References helix_cycle_.

◆ BetaAlphaBetaMotif() [3/3]

protocols::fldsgn::topology::BetaAlphaBetaMotif::BetaAlphaBetaMotif ( BetaAlphaBetaMotif const &  s)

copy constructor

◆ ~BetaAlphaBetaMotif()

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

destructor

Member Function Documentation

◆ calc_geometry()

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

References protocols::fldsgn::topology::BB_Pos::C(), protocols::fldsgn::topology::HSSTriplet::calc_geometry(), calc_helix_cycle(), protocols::fldsgn::topology::SS_Base::Cend_pos(), cross_over_, geometry_is_initialized_, protocols::antibody::h1, protocols::antibody::h2, helix_, hs1_dist_, hs2_dist_, hs_angle_, hs_dist_, hsheet_elev_angle_, protocols::fldsgn::topology::SS_Base::is_geometry_initialized(), protocols::fldsgn::topology::HSSTriplet::left_handed(), left_handed_, protocols::fldsgn::topology::SS_Base::mid_pos(), protocols::fldsgn::topology::BB_Pos::N(), protocols::fldsgn::topology::SS_Base::Nend_pos(), protocols::fldsgn::topology::SS_Base::orient(), core::scoring::sheet, sheet_plane_, sheet_pos_, strand1_, strand2_, and protocols::fldsgn::topology::StrandPairingSet::strand_pairing().

◆ calc_helix_cycle()

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::SS_Base::begin(), protocols::fldsgn::topology::BB_Pos::CA(), protocols::fldsgn::topology::BB_Pos::CB(), protocols::fldsgn::topology::compare(), core::sequence::end, geometry_is_initialized_, helix_, helix_cycle_, protocols::fldsgn::topology::SS_Base::length(), protocols::fldsgn::topology::SS_Base::Nend_orient(), protocols::fldsgn::topology::SS_Base::Nend_pos(), sheet_plane_, sheet_pos_, strand1_, strand2_, and protocols::fldsgn::TR().

Referenced by calc_geometry().

◆ calc_inout()

core::Size protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_inout ( SS_Info2_COP const  ssinfo,
core::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 core::scoring::burial, protocols::fldsgn::topology::BB_Pos::CA(), protocols::fldsgn::topology::BB_Pos::CB(), core::sequence::end, protocols::loops::start, strand1_, and strand2_.

◆ cross_over()

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

References cross_over_.

◆ helix()

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

References helix_.

Referenced by name().

◆ helix_cycle()

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

References helix_cycle_.

◆ helix_cycle_as_string()

std::string protocols::fldsgn::topology::BetaAlphaBetaMotif::helix_cycle_as_string ( ) const

return helix cycle as string

References helix_cycle_, and name().

◆ hs1_dist()

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

References hs1_dist_.

◆ hs2_dist()

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

References hs2_dist_.

◆ hs_angle()

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

References hs_angle_.

◆ hsheet_dist()

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

References hs_dist_.

◆ hsheet_elev_angle()

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

References hsheet_elev_angle_.

◆ is_lefthanded()

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

References left_handed_.

◆ left_handed()

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

References left_handed_.

◆ name()

std::string protocols::fldsgn::topology::BetaAlphaBetaMotif::name ( ) const

return name

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

Referenced by helix_cycle_as_string().

◆ strand1()

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

References strand1_.

Referenced by name().

◆ strand2()

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

References strand2_.

Referenced by name().

Friends And Related Function Documentation

◆ operator<<

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

IO Operator.

Member Data Documentation

◆ cross_over_

core::Size protocols::fldsgn::topology::BetaAlphaBetaMotif::cross_over_
private

number of strands crossed over by bab-motif

Referenced by calc_geometry(), and cross_over().

◆ geometry_is_initialized_

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

Referenced by calc_geometry(), and calc_helix_cycle().

◆ helix_

core::Size protocols::fldsgn::topology::BetaAlphaBetaMotif::helix_
private

id of helix

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

◆ helix_cycle_

utility::vector1< core::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().

◆ hs1_dist_

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

distance between helix and mid point of strand1_

Referenced by calc_geometry(), and hs1_dist().

◆ hs2_dist_

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

distance between helix and mid point of strand2_

Referenced by calc_geometry(), and hs2_dist().

◆ hs_angle_

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

angle between helix projected on sheet and strands

Referenced by calc_geometry(), and hs_angle().

◆ hs_dist_

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

distance between helix and sheet

Referenced by calc_geometry(), and hsheet_dist().

◆ hsheet_elev_angle_

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

elevation angle of helix respect to sheet

Referenced by calc_geometry(), and hsheet_elev_angle().

◆ left_handed_

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

is this left handed ?

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

◆ sheet_plane_

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

vector to define sheet plane

Referenced by calc_geometry(), and calc_helix_cycle().

◆ sheet_pos_

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

one positional vector in beta sheet plane

Referenced by calc_geometry(), and calc_helix_cycle().

◆ strand1_

core::Size protocols::fldsgn::topology::BetaAlphaBetaMotif::strand1_
private

data

id of strand

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

◆ strand2_

core::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:
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