#include <NatbiasHelicesSheetPotential.hh>

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

Collaboration diagram for protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential:

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef core::Vector	Vector

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

typedef protocols::fldsgn::topology::HSSTripletOP	HSSTripletOP

typedef protocols::fldsgn::topology::HSSTripletSetOP	HSSTripletSetOP

typedef protocols::fldsgn::topology::HelixPairingSet	HelixPairingSet

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

typedef protocols::fldsgn::topology::HSSConstIterator	HSSConstIterator

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

	NatbiasHelicesSheetPotential (HSSTripletSetOP const hss3set)
	value constructor More...

	NatbiasHelicesSheetPotential (HSSTripletSetOP const hss3set, HelixPairingSetOP const hpairset)
	value constructor More...

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

virtual	~NatbiasHelicesSheetPotential ()
	default destructor More...

void	set_params ()
	set parameters More...

void	hss_triplet_set (HSSTripletSetOP const hss3set)
	set HSSTripletSet More...

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

void	set_atrdist_params_helix_strands (Real const hs_dist_wts, Real const hs_dist, Real const hs_dist_sigma2)
	set dist parameters for helix-strands interaction More...

void	set_hs_atr_dist_wts (Real const r)
	set dist parameters for helix-sheet interaction More...

void	set_hs_atr_dist (Real const r)

void	set_hs_atr_dist_sigma2 (Real const r)

void	set_hs_angle_wts (Real const r)

void	set_hs_angle (Real const r)

void	set_hs_angle_sigma2 (Real const r)

void	set_hsheet_repl_dist (Real const r)

void	set_hh_angle_wts (Real const r)

void	set_hh_angle (Real const r)

void	set_hh_angle_sigma2 (Real const r)

void	set_repldist_params_helix_sheet (Real const hsheet_dist_repulsive)
	set dist parameters for helix-sheet interaction More...

void	set_angle_params_helix_sheet (Real const hs_angle_wts, Real const hs_angle, Real const hs_angle_sigma2)
	set angle parameters for helix-sheet interaction More...

void	set_angle_params_helices_on_sheet (Real const hh_align_angle_wts, Real const hh_align_angle, Real const hh_align_angle_sigma2)
	set angle parameters for helices projected onto sheet More...

void	show_params () const
	shows parameters for score calculation More...

void	score (SS_Info2_COP const ss_info, Real &hh_score, Real &hs_score) const
	calc score More...

Private Attributes
HSSTripletSetOP	hss3set_
	HSSTripletSet. More...

HelixPairingSetOP	hpairset_
	HelixPairingSet. More...

utility::vector1< Real >	hs_scores_
	score between helix and sheet More...

Real	hs_dist_wts_
	weights for distant score between helix and sheet More...

Real	hs_dist_
	maximum distance for the most favorable interaction between helix and sheet More...

Real	hs_dist_sigma2_
	sigma for distance score between helix and sheet More...

Real	hsheet_dist_repulsive_
	repulsive distance between helix and sheet More...

Real	hs_angle_wts_
	weights for angle score between helix and sheet More...

Real	hs_angle_
	maximum angle for the most favorable interaction between helix and sheet More...

Real	hs_angle_sigma2_
	sigma for angle score between helix and sheet More...

utility::vector1< Real >	hh_scores_
	score of helix pair on sheet More...

Real	hh_align_angle_wts_
	weight for angle score of helix pair More...

Real	hh_align_angle_
	maximum angle for the most favorable interaction of helix-pair on sheet More...

Real	hh_align_angle_sigma2_
	sigma for angle score of helix pair More...

Detailed Description

Definition at line 40 of file NatbiasHelicesSheetPotential.hh.

Member Typedef Documentation

typedef protocols::fldsgn::topology::HelixPairingSet protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::HelixPairingSet

Definition at line 50 of file NatbiasHelicesSheetPotential.hh.

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

Definition at line 51 of file NatbiasHelicesSheetPotential.hh.

typedef protocols::fldsgn::topology::HSSConstIterator protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::HSSConstIterator

Definition at line 52 of file NatbiasHelicesSheetPotential.hh.

typedef protocols::fldsgn::topology::HSSTripletOP protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::HSSTripletOP

Definition at line 48 of file NatbiasHelicesSheetPotential.hh.

typedef protocols::fldsgn::topology::HSSTripletSetOP protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::HSSTripletSetOP

Definition at line 49 of file NatbiasHelicesSheetPotential.hh.

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

Definition at line 45 of file NatbiasHelicesSheetPotential.hh.

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

Definition at line 44 of file NatbiasHelicesSheetPotential.hh.

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

Definition at line 47 of file NatbiasHelicesSheetPotential.hh.

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

Definition at line 46 of file NatbiasHelicesSheetPotential.hh.

Constructor & Destructor Documentation

protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::NatbiasHelicesSheetPotential ( )

default constructor

Definition at line 39 of file NatbiasHelicesSheetPotential.cc.

References set_params().

protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::NatbiasHelicesSheetPotential ( HSSTripletSetOP const hss3set)

value constructor

Definition at line 47 of file NatbiasHelicesSheetPotential.cc.

References set_params().

protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::NatbiasHelicesSheetPotential	(	HSSTripletSetOP const	hss3set,
		HelixPairingSetOP const	hpairset
	)

value constructor

Definition at line 55 of file NatbiasHelicesSheetPotential.cc.

References set_params().

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

copy constructor

value constructor

Definition at line 63 of file NatbiasHelicesSheetPotential.cc.

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

virtual

default destructor

Definition at line 80 of file NatbiasHelicesSheetPotential.cc.

Member Function Documentation

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hpairset ( HelixPairingSetOP const hpairset)

set HelixPairingSet

Definition at line 112 of file NatbiasHelicesSheetPotential.cc.

References hpairset_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hss_triplet_set ( HSSTripletSetOP const hss3set)

set HSSTripletSet

set HSSTrirpletSet

Definition at line 105 of file NatbiasHelicesSheetPotential.cc.

References hss3set_.

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

calc score

Definition at line 179 of file NatbiasHelicesSheetPotential.cc.

References protocols::antibody2::h1, protocols::antibody2::h2, hh_align_angle_, hh_align_angle_sigma2_, hh_align_angle_wts_, hh_scores_, hpairset_, hs_angle_, hs_angle_sigma2_, hs_angle_wts_, hs_dist_, hs_dist_sigma2_, hs_dist_wts_, hs_scores_, hsheet_dist_repulsive_, hss3set_, core::scoring::electron_density::square(), and protocols::fldsgn::potentials::TR().

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_angle_params_helices_on_sheet	(	Real const	hh_align_angle_wts,
		Real const	hh_align_angle,
		Real const	hh_align_angle_sigma2
	)

set angle parameters for helices projected onto sheet

set angle parameters for helices on sheet

Definition at line 150 of file NatbiasHelicesSheetPotential.cc.

References hh_align_angle_, hh_align_angle_sigma2_, and hh_align_angle_wts_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_angle_params_helix_sheet	(	Real const	hs_angle_wts,
		Real const	hs_angle,
		Real const	hs_angle_sigma2
	)

set angle parameters for helix-sheet interaction

Definition at line 138 of file NatbiasHelicesSheetPotential.cc.

References hs_angle_, hs_angle_sigma2_, and hs_angle_wts_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_atrdist_params_helix_strands	(	Real const	hs_dist_wts,
		Real const	hs_dist,
		Real const	hs_dist_sigma2
	)

set dist parameters for helix-strands interaction

set dist parameters for helix-sheet interaction

Definition at line 119 of file NatbiasHelicesSheetPotential.cc.

References hs_dist_, hs_dist_sigma2_, and hs_dist_wts_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hh_angle ( Real const r)

inline

Definition at line 109 of file NatbiasHelicesSheetPotential.hh.

References hh_align_angle_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hh_angle_sigma2 ( Real const r)

inline

Definition at line 110 of file NatbiasHelicesSheetPotential.hh.

References hh_align_angle_sigma2_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hh_angle_wts ( Real const r)

inline

Definition at line 108 of file NatbiasHelicesSheetPotential.hh.

References hh_align_angle_wts_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_angle ( Real const r)

inline

Definition at line 105 of file NatbiasHelicesSheetPotential.hh.

References hs_angle_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_angle_sigma2 ( Real const r)

inline

Definition at line 106 of file NatbiasHelicesSheetPotential.hh.

References hs_angle_sigma2_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_angle_wts ( Real const r)

inline

Definition at line 104 of file NatbiasHelicesSheetPotential.hh.

References hs_angle_wts_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_atr_dist ( Real const r)

inline

Definition at line 102 of file NatbiasHelicesSheetPotential.hh.

References hs_dist_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_atr_dist_sigma2 ( Real const r)

inline

Definition at line 103 of file NatbiasHelicesSheetPotential.hh.

References hs_dist_sigma2_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_atr_dist_wts ( Real const r)

inline

set dist parameters for helix-sheet interaction

Definition at line 101 of file NatbiasHelicesSheetPotential.hh.

References hs_dist_wts_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hsheet_repl_dist ( Real const r)

inline

Definition at line 107 of file NatbiasHelicesSheetPotential.hh.

References hsheet_dist_repulsive_.

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

set parameters

Definition at line 85 of file NatbiasHelicesSheetPotential.cc.

References hh_align_angle_, hh_align_angle_sigma2_, hh_align_angle_wts_, hs_angle_, hs_angle_sigma2_, hs_angle_wts_, hs_dist_, hs_dist_sigma2_, hs_dist_wts_, and hsheet_dist_repulsive_.

Referenced by NatbiasHelicesSheetPotential().

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_repldist_params_helix_sheet ( Real const hsheet_dist_repulsive)

set dist parameters for helix-sheet interaction

Definition at line 131 of file NatbiasHelicesSheetPotential.cc.

References hsheet_dist_repulsive_.

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

shows parameters for score calculation

Definition at line 162 of file NatbiasHelicesSheetPotential.cc.

References hh_align_angle_, hh_align_angle_sigma2_, hh_align_angle_wts_, hs_angle_, hs_angle_sigma2_, hs_angle_wts_, hs_dist_, hs_dist_sigma2_, hs_dist_wts_, hsheet_dist_repulsive_, and protocols::fldsgn::potentials::TR().

Member Data Documentation

Real protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hh_align_angle_

private

maximum angle for the most favorable interaction of helix-pair on sheet

Definition at line 184 of file NatbiasHelicesSheetPotential.hh.

Referenced by score(), set_angle_params_helices_on_sheet(), set_hh_angle(), set_params(), and show_params().

Real protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hh_align_angle_sigma2_

private

sigma for angle score of helix pair

Definition at line 187 of file NatbiasHelicesSheetPotential.hh.

Referenced by score(), set_angle_params_helices_on_sheet(), set_hh_angle_sigma2(), set_params(), and show_params().

Real protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hh_align_angle_wts_

private

weight for angle score of helix pair

Definition at line 181 of file NatbiasHelicesSheetPotential.hh.

Referenced by score(), set_angle_params_helices_on_sheet(), set_hh_angle_wts(), set_params(), and show_params().

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

mutableprivate

score of helix pair on sheet

Definition at line 178 of file NatbiasHelicesSheetPotential.hh.

Referenced by score().

HelixPairingSetOP protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hpairset_

private

HelixPairingSet.

Definition at line 151 of file NatbiasHelicesSheetPotential.hh.

Referenced by hpairset(), and score().

Real protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hs_angle_

private

maximum angle for the most favorable interaction between helix and sheet

Definition at line 172 of file NatbiasHelicesSheetPotential.hh.

Referenced by score(), set_angle_params_helix_sheet(), set_hs_angle(), set_params(), and show_params().

Real protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hs_angle_sigma2_

private

sigma for angle score between helix and sheet

Definition at line 175 of file NatbiasHelicesSheetPotential.hh.

Referenced by score(), set_angle_params_helix_sheet(), set_hs_angle_sigma2(), set_params(), and show_params().

Real protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hs_angle_wts_

private

weights for angle score between helix and sheet

Definition at line 169 of file NatbiasHelicesSheetPotential.hh.

Referenced by score(), set_angle_params_helix_sheet(), set_hs_angle_wts(), set_params(), and show_params().

Real protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hs_dist_

private

maximum distance for the most favorable interaction between helix and sheet

Definition at line 160 of file NatbiasHelicesSheetPotential.hh.

Referenced by score(), set_atrdist_params_helix_strands(), set_hs_atr_dist(), set_params(), and show_params().

Real protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hs_dist_sigma2_

private

sigma for distance score between helix and sheet

Definition at line 163 of file NatbiasHelicesSheetPotential.hh.

Referenced by score(), set_atrdist_params_helix_strands(), set_hs_atr_dist_sigma2(), set_params(), and show_params().

Real protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hs_dist_wts_

private

weights for distant score between helix and sheet

Definition at line 157 of file NatbiasHelicesSheetPotential.hh.

Referenced by score(), set_atrdist_params_helix_strands(), set_hs_atr_dist_wts(), set_params(), and show_params().

utility::vector1< Real > protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hs_scores_

mutableprivate

score between helix and sheet

Definition at line 154 of file NatbiasHelicesSheetPotential.hh.

Referenced by score().

Real protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hsheet_dist_repulsive_

private

repulsive distance between helix and sheet

Definition at line 166 of file NatbiasHelicesSheetPotential.hh.

Referenced by score(), set_hsheet_repl_dist(), set_params(), set_repldist_params_helix_sheet(), and show_params().

HSSTripletSetOP protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hss3set_

private

HSSTripletSet.

Definition at line 148 of file NatbiasHelicesSheetPotential.hh.

Referenced by hss_triplet_set(), and score().

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

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

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation