#include <NatbiasHelixPairPotential.hh>

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

Collaboration 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...

virtual	~NatbiasHelixPairPotential ()
	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_

Detailed Description

Definition at line 35 of file NatbiasHelixPairPotential.hh.

Member Typedef Documentation

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

Definition at line 46 of file NatbiasHelixPairPotential.hh.

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

Definition at line 47 of file NatbiasHelixPairPotential.hh.

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

Definition at line 48 of file NatbiasHelixPairPotential.hh.

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

Definition at line 42 of file NatbiasHelixPairPotential.hh.

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

Definition at line 40 of file NatbiasHelixPairPotential.hh.

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

Definition at line 39 of file NatbiasHelixPairPotential.hh.

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

Definition at line 43 of file NatbiasHelixPairPotential.hh.

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

Definition at line 45 of file NatbiasHelixPairPotential.hh.

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

Definition at line 44 of file NatbiasHelixPairPotential.hh.

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

Definition at line 41 of file NatbiasHelixPairPotential.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 37 of file NatbiasHelixPairPotential.cc.

References set_params().

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

value constructor

Definition at line 45 of file NatbiasHelixPairPotential.cc.

References set_params().

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

copy constructor

Definition at line 67 of file NatbiasHelixPairPotential.cc.

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

virtual

default destructor

Definition at line 81 of file NatbiasHelixPairPotential.cc.

Member Function Documentation

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

score secondary structure

Definition at line 147 of file NatbiasHelixPairPotential.cc.

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().

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

inline

Definition at line 97 of file NatbiasHelixPairPotential.hh.

References cross_angle_.

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

inline

Definition at line 100 of file NatbiasHelixPairPotential.hh.

References angle_sigma2_.

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

inline

Definition at line 94 of file NatbiasHelixPairPotential.hh.

References angle_wts_.

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

inline

set bend angle

Definition at line 103 of file NatbiasHelixPairPotential.hh.

References bend_angle_.

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

inline

set distance parmeter

Definition at line 88 of file NatbiasHelixPairPotential.hh.

References mid_dist_.

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

inline

Definition at line 91 of file NatbiasHelixPairPotential.hh.

References dist_sigma2_.

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

inline

Definition at line 85 of file NatbiasHelixPairPotential.hh.

References dist_wts_.

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

set HelixPairingSet

Definition at line 86 of file NatbiasHelixPairPotential.cc.

References hpairset_.

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

set parmeters

Definition at line 53 of file NatbiasHelixPairPotential.cc.

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

Referenced by NatbiasHelixPairPotential().

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

set parameters for angle score of helix pair

Definition at line 102 of file NatbiasHelixPairPotential.cc.

References angle_sigma2_, angle_wts_, and cross_angle_.

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

Definition at line 93 of file NatbiasHelixPairPotential.cc.

References dist_sigma2_, dist_wts_, and mid_dist_.

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

Definition at line 119 of file NatbiasHelixPairPotential.cc.

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

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

show parameters

Definition at line 111 of file NatbiasHelixPairPotential.cc.

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

Member Data Documentation

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

private

Definition at line 145 of file NatbiasHelixPairPotential.hh.

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

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

private

Definition at line 139 of file NatbiasHelixPairPotential.hh.

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

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

private

Definition at line 127 of file NatbiasHelixPairPotential.hh.

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

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

private

optimal maximum angle of helix pair

Definition at line 142 of file NatbiasHelixPairPotential.hh.

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

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

private

Definition at line 136 of file NatbiasHelixPairPotential.hh.

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

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

private

Definition at line 130 of file NatbiasHelixPairPotential.hh.

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

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

mutableprivate

Definition at line 151 of file NatbiasHelixPairPotential.hh.

Referenced by score(), and show().

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

private

Definition at line 148 of file NatbiasHelixPairPotential.hh.

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

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

private

optimal maximum length between mid points of helices

Definition at line 133 of file NatbiasHelixPairPotential.hh.

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
src/protocols/fldsgn/potentials/sspot/NatbiasSheetPotential.cc

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation