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

#include <NatbiasHelicesSheetPotential.hh>

Inheritance diagram for protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential:
Inheritance graph
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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< Realhs_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< Realhh_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

Constructor & Destructor Documentation

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

default constructor

default constructor

References set_params().

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

value constructor

References set_params().

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

value constructor

References set_params().

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

copy constructor

value constructor

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

default destructor

Member Function Documentation

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().

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

set HelixPairingSet

References hpairset_.

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

set HSSTripletSet

set HSSTrirpletSet

References hss3set_.

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

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_.

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_.

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

References hh_align_angle_.

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

References hh_align_angle_wts_.

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

References hs_angle_.

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

References hs_angle_sigma2_.

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

References hs_angle_wts_.

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

References hs_dist_.

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

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

References hs_dist_wts_.

void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hsheet_repl_dist ( Real const  r)
inline
void protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_params ( )
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_.

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

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

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

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

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

Referenced by score().

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

HelixPairingSet.

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

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

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

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

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

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

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

Referenced by score().

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().

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: