NatbiasSecondaryStructureEnergy. More...

#include <NatbiasSecondaryStructureEnergy.hh>

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

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

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 Types inherited from core::scoring::methods::WholeStructureEnergy
typedef EnergyMethod	parent

Public Types inherited from core::scoring::methods::EnergyMethod
typedef utility::pointer::ReferenceCount	parent

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
	Return the version of the energy method. More...

Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy
	WholeStructureEnergy (EnergyMethodCreatorOP)
	Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More...

virtual	~WholeStructureEnergy ()

EnergyMethodType	method_type () const
	Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...

Public Member Functions inherited from core::scoring::methods::EnergyMethod
	EnergyMethod (EnergyMethodCreatorOP creator)
	Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...

	EnergyMethod (EnergyMethod const &src)
	Copy constructor copies over the score types of the source. More...

virtual	~EnergyMethod ()

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const

virtual void	prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const

virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	ensure this function gets called. The default behavior is to do nothing. More...

virtual void	setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const
	Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More...

virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...

virtual void	finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
	called at the end of derivatives evaluation More...

virtual bool	minimize_in_whole_structure_context (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More...

virtual bool	defines_high_order_terms (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...

virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const
	Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More...

ScoreTypes const &	score_types () const
	Returns the score types that this energy method computes. More...

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...

Additional Inherited Members
Protected Member Functions inherited from core::scoring::methods::EnergyMethod
void	set_score_types (EnergyMethodCreatorOP creator)
	Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. 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.

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 hhpot_, hspot_, core::scoring::natbias_hh, core::scoring::natbias_hs, core::scoring::natbias_ss, native_secstruct_, sspot_, core::pose::Pose::total_residue(), 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.

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

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

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, and use_nobias_.

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

virtual

Return the version of the energy method.

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

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:

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

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation