Rosetta 3.4
Public Types | Public Member Functions
protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy Class Reference

NatbiasSecondaryStructureEnergy. More...

#include <NatbiasSecondaryStructureEnergy.hh>

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List of all members.

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
 NatbiasSecondaryStructureEnergy (NatbiasSecondaryStructureEnergy const &src)
 copy constructor
virtual EnergyMethodOP clone () const
 clone
void native_secstruct (String const &secstruct)
 set native secondary structure
void set_natbias_spairpot (StrandPairingSetOP const spairset)
 set NatbiasStrandPairPotential
void set_natbias_hpairpot (HelixPairingSetOP const hpairset)
 set NatbiasHelixPairPotential
void set_natbias_helices_sheet_pot (HSSTripletSetOP const hss3set)
 set NatbiasHelicesSheetPotential
void set_natbias_spairpot (NatbiasStrandPairPotentialOP const sspot)
 set native NatbiasStrandPairPotential
void set_natbias_hpairpot (NatbiasHelixPairPotentialOP const hhpot)
 set NatbiasHelixPairPotential
void set_natbias_helices_sheet_pot (NatbiasHelicesSheetPotentialOP const hspot)
 set NatbiasHelicesSheetPotential
void use_nobias (bool const b)
 use use original secondary structure potential
virtual void setup_for_scoring (Pose &pose, ScoreFunction const &scorefxn) const
 scoring
virtual void finalize_total_energy (Pose &pose, ScoreFunction const &, EnergyMap &totals) const
 scoring
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.
virtual void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
 SecondaryStructureEnergy.
virtual Size version () const
 Return the version of the energy method.

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.

Reimplemented from core::scoring::methods::WholeStructureEnergy.

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.

Implements core::scoring::methods::EnergyMethod.

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

set native secondary structure

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

set NatbiasHelicesSheetPotential

set HelicesSheetPotential

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 ( NatbiasStrandPairPotentialOP const  sspot)
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot ( StrandPairingSetOP const  spairset)
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::setup_for_scoring ( Pose pose,
ScoreFunction const &  scorefxn 
) const [virtual]

scoring

set up for scoring

Reimplemented from core::scoring::methods::EnergyMethod.

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.

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

Return the version of the energy method.

Implements core::scoring::methods::EnergyMethod.


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