Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Attributes | List of all members
protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy Class Reference

NatbiasSecondaryStructureEnergy. More...

#include <NatbiasSecondaryStructureEnergy.hh>

Public Types

typedef
core::scoring::methods::WholeStructureEnergy 
parent
 
typedef std::string String
 
typedef core::Real Real
 
typedef core::Distance Distance
 
typedef core::pose::Pose Pose
 
typedef core::scoring::EnergyMap EnergyMap
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::scoring::methods::EnergyMethodOP 
EnergyMethodOP
 
typedef
protocols::fldsgn::topology::StrandPairingSetOP 
StrandPairingSetOP
 
typedef
protocols::fldsgn::topology::HelixPairingSetOP 
HelixPairingSetOP
 
typedef
protocols::fldsgn::topology::HSSTripletSetOP 
HSSTripletSetOP
 
typedef
protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotentialOP 
NatbiasHelixPairPotentialOP
 
typedef
protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotentialOP 
NatbiasHelicesSheetPotentialOP
 
typedef
protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotentialOP 
NatbiasStrandPairPotentialOP
 

Public Member Functions

 NatbiasSecondaryStructureEnergy ()
 default constructor More...
 
 NatbiasSecondaryStructureEnergy (NatbiasSecondaryStructureEnergy const &src)
 copy constructor More...
 
virtual EnergyMethodOP clone () const
 clone More...
 
void native_secstruct (String const &secstruct)
 set native secondary structure More...
 
void set_natbias_spairpot (StrandPairingSetOP const spairset)
 set NatbiasStrandPairPotential More...
 
void set_natbias_hpairpot (HelixPairingSetOP const hpairset)
 set NatbiasHelixPairPotential More...
 
void set_natbias_helices_sheet_pot (HSSTripletSetOP const hss3set)
 set NatbiasHelicesSheetPotential More...
 
void set_natbias_spairpot (NatbiasStrandPairPotentialOP const sspot)
 set native NatbiasStrandPairPotential More...
 
void set_natbias_hpairpot (NatbiasHelixPairPotentialOP const hhpot)
 set NatbiasHelixPairPotential More...
 
void set_natbias_helices_sheet_pot (NatbiasHelicesSheetPotentialOP const hspot)
 set NatbiasHelicesSheetPotential More...
 
void use_nobias (bool const b)
 use use original secondary structure potential More...
 
virtual void setup_for_scoring (Pose &pose, ScoreFunction const &scorefxn) const
 scoring More...
 
virtual void finalize_total_energy (Pose &pose, ScoreFunction const &, EnergyMap &totals) const
 scoring More...
 
virtual Distance atomic_interaction_cutoff () const
 The NatbiasSecondaryStructureEnergy class requires that the EnergyGraph span 12 Angstroms between centroids. The centroids residues build-in a 3 Angstrom radius each. More...
 
virtual void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
 SecondaryStructureEnergy. More...
 
virtual Size version () const
 

Private Attributes

String native_secstruct_
 native secondary structure More...
 
bool use_sspot_
 Is NatbiasStrandPairPotential to be used ? More...
 
bool use_hhpot_
 Is NatbiasHelixPairPotential to be used ? More...
 
bool use_hspot_
 Is NatbiasHelicesSheetPotential to be used ? More...
 
bool use_nobias_
 use original secondary structure potential if this is true More...
 
NatbiasStrandPairPotentialOP sspot_
 pointer of NatbiasStrandPairPotential More...
 
NatbiasHelixPairPotentialOP hhpot_
 pointer of NatbiasHelixPairPotential More...
 
NatbiasHelicesSheetPotentialOP hspot_
 pointer of NatbiasHeliceesSheetPotential More...
 

Detailed Description

NatbiasSecondaryStructureEnergy.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasSecondaryStructureEnergy ( )

default constructor

Referenced by clone().

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

copy constructor

Member Function Documentation

core::Distance protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::atomic_interaction_cutoff ( ) const
virtual

The NatbiasSecondaryStructureEnergy class requires that the EnergyGraph span 12 Angstroms between centroids. The centroids residues build-in a 3 Angstrom radius each.

SecondaryStructureEnergy distance cutoff.

NatbiasSecondaryStructureEnergy::EnergyMethodOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::clone ( ) const
virtual
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::finalize_total_energy ( Pose pose,
ScoreFunction const &  ,
EnergyMap totals 
) const
virtual
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const
virtual

SecondaryStructureEnergy.

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::native_secstruct ( String const &  secstruct)

set native secondary structure

References native_secstruct_.

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_helices_sheet_pot ( HSSTripletSetOP const  hss3set)

set NatbiasHelicesSheetPotential

set HelicesSheetPotential

References hspot_, and use_hspot_.

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_helices_sheet_pot ( NatbiasHelicesSheetPotentialOP const  hspot)
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot ( HelixPairingSetOP const  hpairset)
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot ( NatbiasHelixPairPotentialOP const  hhpot)
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot ( StrandPairingSetOP const  spairset)
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot ( NatbiasStrandPairPotentialOP const  sspot)

set native NatbiasStrandPairPotential

References sspot_, and use_sspot_.

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::setup_for_scoring ( Pose pose,
ScoreFunction const &  scorefxn 
) const
virtual

scoring

set up for scoring

References core::pose::Pose::update_residue_neighbors().

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_nobias ( bool const  b)
inline

use use original secondary structure potential

References protocols::match::upstream::b, and use_nobias_.

core::Size protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::version ( ) const
virtual

Member Data Documentation

NatbiasHelixPairPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::hhpot_
private
NatbiasHelicesSheetPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::hspot_
private

pointer of NatbiasHeliceesSheetPotential

Referenced by finalize_total_energy(), and set_natbias_helices_sheet_pot().

String protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::native_secstruct_
private

native secondary structure

Referenced by finalize_total_energy(), and native_secstruct().

NatbiasStrandPairPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::sspot_
private
bool protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_hhpot_
private
bool protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_hspot_
private
bool protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_nobias_
private

use original secondary structure potential if this is true

Referenced by use_nobias().

bool protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_sspot_
private

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