protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential Class Reference

#include <NatbiasHelicesSheetPotential.hh>

Inheritance 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...
	~NatbiasHelicesSheetPotential () override
	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 Member Functions
HSSTripletOP	get_hssop (core::Size const helix_id) const
	Gets HSS Triplet containing helix helix_id. 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...

Member Typedef Documentation

HelixPairingSet

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

HelixPairingSetOP

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

HSSConstIterator

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

HSSTripletOP

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

HSSTripletSetOP

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

Real

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

Size

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

SS_Info2_COP

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

Vector

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

Constructor & Destructor Documentation

NatbiasHelicesSheetPotential() [1/4]

protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::NatbiasHelicesSheetPotential

(

)

default constructor

@Brief default constructor

References set_params().

NatbiasHelicesSheetPotential() [2/4]

protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::NatbiasHelicesSheetPotential

(

HSSTripletSetOP const

hss3set

)

value constructor

References set_params().

NatbiasHelicesSheetPotential() [3/4]

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

value constructor

References set_params().

NatbiasHelicesSheetPotential() [4/4]

protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::NatbiasHelicesSheetPotential

(

NatbiasHelicesSheetPotential const &

src

)

copy constructor

value constructor

~NatbiasHelicesSheetPotential()

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

overridedefault

default destructor

Member Function Documentation

get_hssop()

NatbiasHelicesSheetPotential::HSSTripletOP protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::get_hssop ( core::Size const  helix_id ) const

private

Gets HSS Triplet containing helix helix_id.

Currently exits with error if more than one HSS triplet contain the helix

References hss3set_.

Referenced by score().

hpairset()

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hpairset

(

HelixPairingSetOP const

hpairset

)

set HelixPairingSet

References hpairset_.

hss_triplet_set()

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hss_triplet_set

(

HSSTripletSetOP const

hss3set

)

set HSSTripletSet

@brif set HSSTrirpletSet

References hss3set_.

score()

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

calc score

References get_hssop(), protocols::antibody::h1, protocols::antibody::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().

set_angle_params_helices_on_sheet()

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

References hh_align_angle_, hh_align_angle_sigma2_, and hh_align_angle_wts_.

set_angle_params_helix_sheet()

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

References hs_angle_, hs_angle_sigma2_, and hs_angle_wts_.

set_atrdist_params_helix_strands()

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

References hs_dist_, hs_dist_sigma2_, and hs_dist_wts_.

set_hh_angle()

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

inline

References hh_align_angle_.

set_hh_angle_sigma2()

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

inline

References hh_align_angle_sigma2_.

set_hh_angle_wts()

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

inline

References hh_align_angle_wts_.

set_hs_angle()

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

inline

References hs_angle_.

set_hs_angle_sigma2()

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

inline

References hs_angle_sigma2_.

set_hs_angle_wts()

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

inline

References hs_angle_wts_.

set_hs_atr_dist()

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

inline

References hs_dist_.

set_hs_atr_dist_sigma2()

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

inline

References hs_dist_sigma2_.

set_hs_atr_dist_wts()

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

inline

set dist parameters for helix-sheet interaction

References hs_dist_wts_.

set_hsheet_repl_dist()

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

inline

References hsheet_dist_repulsive_.

set_params()

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

(

)

set parameters

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().

set_repldist_params_helix_sheet()

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_repldist_params_helix_sheet

(

Real const

hsheet_dist_repulsive

)

set dist parameters for helix-sheet interaction

References hsheet_dist_repulsive_.

show_params()

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::show_params

(

)

const

shows parameters for score calculation

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

hh_align_angle_

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

private

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

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

hh_align_angle_sigma2_

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

private

sigma for angle score of helix pair

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

hh_align_angle_wts_

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

private

weight for angle score of helix pair

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

hh_scores_

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

mutableprivate

score of helix pair on sheet

Referenced by score().

hpairset_

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

private

HelixPairingSet.

Referenced by hpairset(), and score().

hs_angle_

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

private

maximum angle for the most favorable interaction between helix and sheet

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

hs_angle_sigma2_

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

private

sigma for angle score between helix and sheet

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

hs_angle_wts_

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

private

weights for angle score between helix and sheet

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

hs_dist_

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

private

maximum distance for the most favorable interaction between helix and sheet

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

hs_dist_sigma2_

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

private

sigma for distance score between helix and sheet

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

hs_dist_wts_

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

private

weights for distant score between helix and sheet

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

hs_scores_

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

mutableprivate

score between helix and sheet

Referenced by score().

hsheet_dist_repulsive_

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

private

repulsive distance between helix and sheet

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

hss3set_

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

private

HSSTripletSet.

Referenced by get_hssop(), 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