#include <NatbiasHelixPairPotential.hh>

Inheritance diagram for protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential:

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef core::Vector	Vector

typedef core::pose::Pose	Pose

typedef protocols::fldsgn::topology::SS_Info2	SS_Info2

typedef protocols::fldsgn::topology::SS_Info2_OP	SS_Info2_OP

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

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

typedef protocols::fldsgn::topology::HelixPairings	HelixPairings

typedef protocols::fldsgn::topology::HelixPairingSetOP	HelixPairingSetOP

Public Member Functions
	NatbiasHelixPairPotential ()
	default constructor More...

	NatbiasHelixPairPotential (HelixPairingSetOP const hpairset)
	value constructor More...

	NatbiasHelixPairPotential (NatbiasHelixPairPotential const &src)
	copy constructor More...

	~NatbiasHelixPairPotential () override
	default destructor More...

void	set_params ()
	set parmeters More...

void	set_hpairset (HelixPairingSetOP const hpairset)
	set HelixPairingSet More...

void	set_params_distance_pot (Real w, Real d, Real s)
	set parameters for distance score between mid points of helices More...

void	set_params_angle_pot (Real w, Real d, Real s)
	set parameters for angle score of helix pair More...

void	set_dist_wts (Real const r)

void	set_dist (Real const r)
	set distance parmeter More...

void	set_dist_sigma2 (Real const r)

void	set_angle_wts (Real const r)

void	set_angle (Real const r)

void	set_angle_sigma2 (Real const r)

void	set_bendangle (Real r)
	set bend angle More...

void	show (Pose const &pose) const

void	show_params () const
	show parameters More...

void	score (SS_Info2_COP const ss_info, Real &hh_score) const
	score secondary structure More...

Private Attributes
Real	bend_angle_

Real	dist_wts_

Real	mid_dist_
	optimal maximum length between mid points of helices More...

Real	dist_sigma2_

Real	angle_wts_

Real	cross_angle_
	optimal maximum angle of helix pair More...

Real	angle_sigma2_

HelixPairingSetOP	hpairset_

utility::vector1< Real >	hh_scores_

Member Typedef Documentation

◆ HelixPairing

typedef protocols::fldsgn::topology::HelixPairing protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::HelixPairing

◆ HelixPairings

typedef protocols::fldsgn::topology::HelixPairings protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::HelixPairings

◆ HelixPairingSetOP

typedef protocols::fldsgn::topology::HelixPairingSetOP protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::HelixPairingSetOP

◆ Pose

typedef core::pose::Pose protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::Pose

◆ Real

typedef core::Real protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::Real

◆ Size

typedef core::Size protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::Size

◆ SS_Info2

typedef protocols::fldsgn::topology::SS_Info2 protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::SS_Info2

◆ SS_Info2_COP

typedef protocols::fldsgn::topology::SS_Info2_COP protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::SS_Info2_COP

◆ SS_Info2_OP

typedef protocols::fldsgn::topology::SS_Info2_OP protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::SS_Info2_OP

◆ Vector

typedef core::Vector protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::Vector

Constructor & Destructor Documentation

◆ NatbiasHelixPairPotential() [1/3]

protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::NatbiasHelixPairPotential ( )

default constructor

@Brief default constructor

References set_params().

◆ NatbiasHelixPairPotential() [2/3]

protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::NatbiasHelixPairPotential ( HelixPairingSetOP const hpairset )

value constructor

References set_params().

◆ NatbiasHelixPairPotential() [3/3]

protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::NatbiasHelixPairPotential ( NatbiasHelixPairPotential const & src )

copy constructor

◆ ~NatbiasHelixPairPotential()

protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::~NatbiasHelixPairPotential ( )

overridedefault

default destructor

Member Function Documentation

◆ score()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::score	(	SS_Info2_COP const	ss_info,
		Real &	hh_score
	)		const

score secondary structure

References angle_sigma2_, angle_wts_, bend_angle_, protocols::fldsgn::topology::HelixPairing::cross_angle(), cross_angle_, protocols::fldsgn::topology::HelixPairing::dist(), dist_sigma2_, dist_wts_, protocols::fldsgn::topology::HelixPairing::h1(), protocols::fldsgn::topology::HelixPairing::h2(), hh_scores_, hpairset_, mid_dist_, core::scoring::electron_density::square(), and protocols::fldsgn::potentials::TR().

Referenced by show().

◆ set_angle()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_angle ( Real const r )

inline

References cross_angle_.

◆ set_angle_sigma2()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_angle_sigma2 ( Real const r )

inline

References angle_sigma2_.

◆ set_angle_wts()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_angle_wts ( Real const r )

inline

References angle_wts_.

◆ set_bendangle()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_bendangle ( Real r )

inline

set bend angle

References bend_angle_.

◆ set_dist()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_dist ( Real const r )

inline

set distance parmeter

References mid_dist_.

◆ set_dist_sigma2()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_dist_sigma2 ( Real const r )

inline

References dist_sigma2_.

◆ set_dist_wts()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_dist_wts ( Real const r )

inline

References dist_wts_.

◆ set_hpairset()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_hpairset ( HelixPairingSetOP const hpairset )

set HelixPairingSet

References hpairset_.

◆ set_params()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_params ( )

set parmeters

References angle_sigma2_, angle_wts_, bend_angle_, cross_angle_, dist_sigma2_, dist_wts_, and mid_dist_.

Referenced by NatbiasHelixPairPotential().

◆ set_params_angle_pot()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_params_angle_pot	(	Real	w,
		Real	d,
		Real	s
	)

set parameters for angle score of helix pair

References angle_sigma2_, angle_wts_, and cross_angle_.

◆ set_params_distance_pot()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_params_distance_pot	(	Real	w,
		Real	d,
		Real	s
	)

set parameters for distance score between mid points of helices

References dist_sigma2_, dist_wts_, and mid_dist_.

◆ show()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::show ( Pose const & pose ) const

References hh_scores_, hpairset_, score(), and protocols::fldsgn::potentials::TR().

◆ show_params()

void protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::show_params ( ) const

show parameters

References angle_sigma2_, angle_wts_, cross_angle_, dist_sigma2_, dist_wts_, mid_dist_, and protocols::fldsgn::potentials::TR().

Member Data Documentation

◆ angle_sigma2_

Real protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::angle_sigma2_

private

Referenced by score(), set_angle_sigma2(), set_params(), set_params_angle_pot(), and show_params().

◆ angle_wts_

Real protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::angle_wts_

private

Referenced by score(), set_angle_wts(), set_params(), set_params_angle_pot(), and show_params().

◆ bend_angle_

Real protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::bend_angle_

private

Referenced by score(), set_bendangle(), and set_params().

◆ cross_angle_

Real protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::cross_angle_

private

optimal maximum angle of helix pair

Referenced by score(), set_angle(), set_params(), set_params_angle_pot(), and show_params().

◆ dist_sigma2_

Real protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::dist_sigma2_

private

Referenced by score(), set_dist_sigma2(), set_params(), set_params_distance_pot(), and show_params().

◆ dist_wts_

Real protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::dist_wts_

private

Referenced by score(), set_dist_wts(), set_params(), set_params_distance_pot(), and show_params().

◆ hh_scores_

utility::vector1< Real > protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::hh_scores_

mutableprivate

Referenced by score(), and show().

◆ hpairset_

HelixPairingSetOP protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::hpairset_

private

Referenced by score(), set_hpairset(), and show().

◆ mid_dist_

Real protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::mid_dist_

private

optimal maximum length between mid points of helices

Referenced by score(), set_dist(), set_params(), set_params_distance_pot(), and show_params().

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

src/protocols/fldsgn/potentials/sspot/NatbiasHelixPairPotential.hh
src/protocols/fldsgn/potentials/sspot/NatbiasHelixPairPotential.cc

Public Types

Public Member Functions

Private Attributes

Member Typedef Documentation

◆ HelixPairing

◆ HelixPairings

◆ HelixPairingSetOP

◆ Pose

◆ Real

◆ Size

◆ SS_Info2

◆ SS_Info2_COP

◆ SS_Info2_OP

◆ Vector

Constructor & Destructor Documentation

◆ NatbiasHelixPairPotential() [1/3]

◆ NatbiasHelixPairPotential() [2/3]

◆ NatbiasHelixPairPotential() [3/3]

◆ ~NatbiasHelixPairPotential()

Member Function Documentation

◆ score()

◆ set_angle()

◆ set_angle_sigma2()

◆ set_angle_wts()

◆ set_bendangle()

◆ set_dist()

◆ set_dist_sigma2()

◆ set_dist_wts()

◆ set_hpairset()

◆ set_params()

◆ set_params_angle_pot()

◆ set_params_distance_pot()

◆ show()

◆ show_params()

Member Data Documentation

◆ angle_sigma2_

◆ angle_wts_

◆ bend_angle_

◆ cross_angle_

◆ dist_sigma2_

◆ dist_wts_

◆ hh_scores_

◆ hpairset_

◆ mid_dist_