base class for the energy method hierarchy More...

#include <EnergyMethod.hh>

Inheritance diagram for core::scoring::methods::EnergyMethod:

Collaboration diagram for core::scoring::methods::EnergyMethod:

Public Types
typedef utility::pointer::ReferenceCount	parent
Public Member Functions
	EnergyMethod (EnergyMethodCreatorOP creator)
	Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for.
	EnergyMethod (EnergyMethod const &src)
	Copy constructor copies over the score types of the source.
virtual	~EnergyMethod ()
virtual EnergyMethodOP	clone () const =0
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.
virtual void	setup_for_scoring (pose::Pose &, ScoreFunction const &) const
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.
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.
virtual void	finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
	called at the end of derivatives evaluation
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.
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".
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.
virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) const
	called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.
ScoreTypes const &	score_types () const
	Returns the score types that this energy method computes.
virtual EnergyMethodType	method_type () const =0
	Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure.
virtual void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const =0
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
virtual core::Size	version () const =0
	Return the version of the energy method.
Protected Member Functions
void	set_score_types (EnergyMethodCreatorOP creator)
	Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor.

Detailed Description

base class for the energy method hierarchy

Member Typedef Documentation

typedef utility::pointer::ReferenceCount core::scoring::methods::EnergyMethod::parent

Constructor & Destructor Documentation

core::scoring::methods::EnergyMethod::EnergyMethod ( EnergyMethodCreatorOP creator )

Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for.

core::scoring::methods::EnergyMethod::EnergyMethod ( EnergyMethod const & src )

Copy constructor copies over the score types of the source.

core::scoring::methods::EnergyMethod::~EnergyMethod ( ) [virtual]

Member Function Documentation

virtual EnergyMethodOP core::scoring::methods::EnergyMethod::clone ( ) const [pure virtual]

Referenced by core::scoring::ScoreFunction::add_extra_method().

bool core::scoring::methods::EnergyMethod::defines_high_order_terms ( pose::Pose const & ) const [virtual]

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".

Reimplemented in core::scoring::constraints::ConstraintsEnergy.

void core::scoring::methods::EnergyMethod::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 `[virtual]`

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.

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) "Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations" Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

default implementation does not alter either the F1 or F2 vectors.

void core::scoring::methods::EnergyMethod::finalize_after_derivatives	(	pose::Pose &	,
		ScoreFunction const &
	)		const `[virtual]`

called at the end of derivatives evaluation

default implementation noop

Reimplemented in core::scoring::electron_density::PattersonCorrEnergy, and core::scoring::orbitals::OrbitalsScore.

void core::scoring::methods::EnergyMethod::finalize_total_energy	(	pose::Pose &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	total_energy
	)		const `[virtual]`

called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

called at the end of energy evaluation

virtual void core::scoring::methods::EnergyMethod::indicate_required_context_graphs ( utility::vector1< bool > & context_graphs_required ) const [pure virtual]

Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

virtual EnergyMethodType core::scoring::methods::EnergyMethod::method_type ( ) const [pure virtual]

Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure.

Implemented in core::scoring::methods::ContextDependentLRTwoBodyEnergy, core::scoring::methods::ContextDependentOneBodyEnergy, core::scoring::methods::ContextDependentTwoBodyEnergy, core::scoring::methods::ContextIndependentLRTwoBodyEnergy, core::scoring::methods::ContextIndependentOneBodyEnergy, core::scoring::methods::ContextIndependentTwoBodyEnergy, and core::scoring::methods::WholeStructureEnergy.

bool core::scoring::methods::EnergyMethod::minimize_in_whole_structure_context ( pose::Pose const & ) const [virtual]

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.

void core::scoring::methods::EnergyMethod::prepare_rotamers_for_packing	(	pose::Pose const &	,
		conformation::RotamerSetBase &
	)		const `[virtual]`

default implementation noop

Reimplemented in core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::hackelec::HackElecEnergy, core::scoring::hackelec::HackElecEnergyAroAll, core::scoring::hackelec::HackElecEnergyAroAro, core::scoring::hackelec::RNAHackElecEnergy, core::scoring::hbonds::HBondEnergy, core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::methods::CustomAtomPairEnergy, core::scoring::methods::GenBornEnergy, core::scoring::methods::LK_BallEnergy, core::scoring::methods::MMLJEnergyInter, core::scoring::methods::PairEnergy, core::scoring::orbitals::OrbitalsScore, core::scoring::etable::BaseEtableEnergy< CoarseEtableEnergy >, core::scoring::etable::BaseEtableEnergy< CoarseEtableEnergy >, core::scoring::etable::BaseEtableEnergy< CoarseEtableEnergy >, core::scoring::etable::BaseEtableEnergy< EtableEnergy >, core::scoring::etable::BaseEtableEnergy< EtableEnergy >, and core::scoring::etable::BaseEtableEnergy< EtableEnergy >.

ScoreTypes const& core::scoring::methods::EnergyMethod::score_types ( ) const [inline]

Returns the score types that this energy method computes.

Referenced by core::scoring::ScoreFunction::add_extra_method().

void core::scoring::methods::EnergyMethod::set_score_types ( EnergyMethodCreatorOP creator ) [protected]

Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor.

Enforce that the derived class which has been instantiated does not attempt to use an inactive score type. If an inactive score type should be used, the ScoreType enumeration in ScoreType.hh must be modified so that the desired type appears before the n_score_types position in the enumeration. Rosetta must then be recompiled.

Referenced by core::scoring::hackelec::HackElecEnergyAroAll::HackElecEnergyAroAll(), core::scoring::hackelec::HackElecEnergyAroAro::HackElecEnergyAroAro(), and core::scoring::hackelec::RNAHackElecEnergy::RNAHackElecEnergy().

void core::scoring::methods::EnergyMethod::setup_for_derivatives	(	pose::Pose &	pose,
		ScoreFunction const &	sfxn
	)		const `[virtual]`

Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.

default implementation noop

void core::scoring::methods::EnergyMethod::setup_for_minimizing	(	pose::Pose &	,
		ScoreFunction const &	,
		kinematics::MinimizerMapBase const &
	)		const `[virtual]`

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.

default implementation noop

Reimplemented in core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy, core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody, core::scoring::hackelec::HackElecEnergy, core::scoring::etable::BaseEtableEnergy< Derived >, core::scoring::methods::MMLJEnergyInter, core::scoring::methods::MMLJEnergyIntra, core::scoring::methods::ResidualDipolarCouplingEnergy, core::scoring::nv::NVscore, core::scoring::etable::BaseEtableEnergy< CoarseEtableEnergy >, core::scoring::etable::BaseEtableEnergy< CoarseEtableEnergy >, core::scoring::etable::BaseEtableEnergy< CoarseEtableEnergy >, core::scoring::etable::BaseEtableEnergy< EtableEnergy >, core::scoring::etable::BaseEtableEnergy< EtableEnergy >, and core::scoring::etable::BaseEtableEnergy< EtableEnergy >.

void core::scoring::methods::EnergyMethod::setup_for_packing	(	pose::Pose &	,
		utility::vector1< bool > const &	,
		utility::vector1< bool > const &
	)		const `[virtual]`

default implementation noop

void core::scoring::methods::EnergyMethod::setup_for_scoring	(	pose::Pose &	,
		ScoreFunction const &
	)		const `[virtual]`

void core::scoring::methods::EnergyMethod::update_residue_for_packing	(	pose::Pose &	,
		Size	resid
	)		const `[virtual]`

ensure this function gets called. The default behavior is to do nothing.

default implementation noop

Reimplemented in core::scoring::methods::CustomAtomPairEnergy, core::scoring::methods::GenBornEnergy, core::scoring::methods::LK_BallEnergy, core::scoring::methods::MMLJEnergyInter, and core::scoring::methods::PairEnergy.

virtual core::Size core::scoring::methods::EnergyMethod::version ( ) const [pure virtual]

Return the version of the energy method.

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

src/core/scoring/methods/EnergyMethod.hh
src/core/scoring/methods/EnergyMethod.cc

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation