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

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

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

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

clone

References NatbiasSecondaryStructureEnergy().

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

virtual

scoring

all scoring happens here

References hhpot_, hspot_, core::scoring::natbias_hh, core::scoring::natbias_hs, core::scoring::natbias_ss, native_secstruct_, sspot_, use_hhpot_, use_hspot_, and use_sspot_.

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 )

set NatbiasHelicesSheetPotential

References hspot_, and use_hspot_.

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot ( HelixPairingSetOP const hpairset )

set NatbiasHelixPairPotential

References hhpot_, and use_hhpot_.

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot ( NatbiasHelixPairPotentialOP const hhpot )

set NatbiasHelixPairPotential

References hhpot_, and use_hhpot_.

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot ( StrandPairingSetOP const spairset )

set NatbiasStrandPairPotential

set native NatbiasStrandPairPotential

References sspot_, and use_sspot_.

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

pointer of NatbiasHelixPairPotential

Referenced by finalize_total_energy(), and set_natbias_hpairpot().

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

pointer of NatbiasStrandPairPotential

Referenced by finalize_total_energy(), and set_natbias_spairpot().

bool protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_hhpot_

private

Is NatbiasHelixPairPotential to be used ?

Referenced by finalize_total_energy(), and set_natbias_hpairpot().

bool protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_hspot_

private

Is NatbiasHelicesSheetPotential to be used ?

Referenced by finalize_total_energy(), and set_natbias_helices_sheet_pot().

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

Is NatbiasStrandPairPotential to be used ?

Referenced by finalize_total_energy(), and set_natbias_spairpot().

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

symlinks/rosetta/src/protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergy.hh
symlinks/rosetta/src/protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergy.cc

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation