protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy Class Reference

NatbiasSecondaryStructureEnergy. More...

#include <NatbiasSecondaryStructureEnergy.hh>

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

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

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

typedef core::Distance protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::Distance

typedef core::scoring::EnergyMap protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::EnergyMap

typedef core::scoring::methods::EnergyMethodOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::EnergyMethodOP

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

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

typedef protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasHelicesSheetPotentialOP

typedef protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasHelixPairPotentialOP

typedef protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasStrandPairPotentialOP

typedef core::scoring::methods::WholeStructureEnergy protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::parent

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

typedef core::pose::Pose protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::Pose

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

typedef core::scoring::ScoreFunction protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::ScoreFunction

typedef protocols::fldsgn::topology::StrandPairingSetOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::StrandPairingSetOP

typedef std::string protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::String

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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

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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]

clone

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

References NatbiasSecondaryStructureEnergy().

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::finalize_total_energy	(	Pose &	pose,
		ScoreFunction const &	,
		EnergyMap &	totals
	)		const [virtual]

scoring

all scoring happens here

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

References core::scoring::natbias_hh, core::scoring::natbias_hs, core::scoring::natbias_ss, and core::pose::Pose::total_residue().

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

)

set NatbiasHelicesSheetPotential

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

)

set NatbiasHelixPairPotential

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot

(

NatbiasHelixPairPotentialOP const

hhpot

)

set NatbiasHelixPairPotential

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot

(

NatbiasStrandPairPotentialOP const

sspot

)

set native NatbiasStrandPairPotential

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot

(

StrandPairingSetOP const

spairset

)

set NatbiasStrandPairPotential

set native NatbiasStrandPairPotential

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.

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

• src/protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergy.hh
• src/protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergy.cc