AARepeatEnergy, an energy function to penalize stretches of the same residue, derived from base class for EnergyMethods, which are meaningful only on entire structures. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation. More...

#include <AARepeatEnergy.hh>

Inheritance diagram for core::energy_methods::AARepeatEnergy:

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Public Types
typedef core::scoring::methods::WholeStructureEnergy	parent1

typedef core::scoring::annealing::ResidueArrayAnnealableEnergy	parent2

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::EnergyMap	EnergyMap

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

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

Public Member Functions
	AARepeatEnergy ()
	Default constructor. More...

	AARepeatEnergy (AARepeatEnergy const &src)
	Copy constructor. More...

	~AARepeatEnergy () override
	Default destructor. More...

core::scoring::methods::EnergyMethodOP	clone () const override
	Clone: create a copy of this object, and return an owning pointer to the copy. More...

void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const override
	AARepeatEnergy is context-independent and thus indicates that no context graphs need to be maintained by class Energies. More...

core::Size	version () const override
	AARepeatEnergy is version 1.0 right now. More...

void	finalize_total_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &totals) const override
	Actually calculate the total energy. More...

core::Real	calculate_energy (utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::Size > const &rotamer_ids, core::Size const substitution_position=0) const override
	Calculate the total energy given a vector of const owning pointers to residues. More...

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

	~WholeStructureEnergy () override

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

virtual Distance	atomic_interaction_cutoff () const
	how far apart must two heavy atoms be to have a zero interaction energy? 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...

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
	if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...

virtual void	setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const
	if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More...

virtual void	prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const
	If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...

virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More...

virtual void	setup_for_scoring (pose::Pose &, ScoreFunction const &) const
	if an energy method needs to cache something in the pose (e.g. in pose.energies()), before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing. More...

virtual bool	requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More...

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const
	Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) 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	finalize_after_minimizing (pose::Pose &pose) const
	Called after minimization, allowing a derived class to do some teardown steps. 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...

virtual void	show_additional_info (std::ostream &, pose::Pose &, bool) const
	show additional information of the energy method More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Public Member Functions inherited from core::scoring::annealing::ResidueArrayAnnealableEnergy
	ResidueArrayAnnealableEnergy ()
	Constructor. More...

	ResidueArrayAnnealableEnergy (ResidueArrayAnnealableEnergy const &src)
	Copy constructor. More...

virtual	~ResidueArrayAnnealableEnergy ()
	Destructor. More...

virtual void	set_up_residuearrayannealableenergy_for_packing (core::pose::Pose &pose, core::pack::rotamer_set::RotamerSets const &rotamersets, core::scoring::ScoreFunction const &sfxn)
	ResidueArrayAnnealableEnergy objects may optionally cache data within the EnergyMethod prior to a packer run. This function is defined as doing nothing by default, but can be redefined on a per-EnergyMethod basis to cache whatever data are necessary. More...

virtual void	clean_up_residuearrayannealableenergy_after_packing (core::pose::Pose &pose)
	Allows the ResidueArrayAnnealableEnergy to clean up cached data, either within the EnergyMethod or in the pose, after a packer run. More...

virtual void	commit_considered_substitution ()
	What to do when a substitution that was considered is accepted. More...

Private Member Functions
core::Real	penalties (core::Size const nres) const
	Return a penalty for N residues in a row, from a lookup table. More...

void	load_penalty_table_from_file (std::string const &filename)
	Read a penalty data file and load the penalties into the energy method. Called once by the constructor. More...

bool	parse_line (std::string const &line, utility::vector1< core::Real > &penalties) const
	Parse a series of floats from a string and store them in the penalties vector. Return true if successful and false otherwise. More...

Private Attributes
utility::vector1< core::Real >	penalties_

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

AARepeatEnergy, an energy function to penalize stretches of the same residue, derived from base class for EnergyMethods, which are meaningful only on entire structures. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation.

Member Typedef Documentation

typedef core::scoring::EnergyMap core::energy_methods::AARepeatEnergy::EnergyMap

typedef core::scoring::methods::WholeStructureEnergy core::energy_methods::AARepeatEnergy::parent1

typedef core::scoring::annealing::ResidueArrayAnnealableEnergy core::energy_methods::AARepeatEnergy::parent2

typedef core::scoring::ScoreFunction core::energy_methods::AARepeatEnergy::ScoreFunction

Constructor & Destructor Documentation

core::energy_methods::AARepeatEnergy::AARepeatEnergy ( )

Default constructor.

References load_penalty_table_from_file().

core::energy_methods::AARepeatEnergy::AARepeatEnergy ( AARepeatEnergy const & src )

Copy constructor.

core::energy_methods::AARepeatEnergy::~AARepeatEnergy ( )

overridedefault

Default destructor.

Member Function Documentation

core::Real core::energy_methods::AARepeatEnergy::calculate_energy	(	utility::vector1< core::conformation::ResidueCOP > const &	resvect,
		utility::vector1< core::Size > const &	rotamer_ids,
		core::Size const	substitution_position = `0`
	)		const

overridevirtual

Calculate the total energy given a vector of const owning pointers to residues.

Called by finalize_total_energy().

Implements core::scoring::annealing::ResidueArrayAnnealableEnergy.

References penalties().

Referenced by finalize_total_energy().

core::scoring::methods::EnergyMethodOP core::energy_methods::AARepeatEnergy::clone ( ) const

overridevirtual

Clone: create a copy of this object, and return an owning pointer to the copy.

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

void core::energy_methods::AARepeatEnergy::finalize_total_energy	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	,
		core::scoring::EnergyMap &	totals
	)		const

overridevirtual

Actually calculate the total energy.

Called by the scoring machinery.

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

References core::scoring::aa_repeat, calculate_energy(), core::conformation::Residue::get_self_ptr(), core::pose::Pose::residue(), and core::pose::Pose::size().

void core::energy_methods::AARepeatEnergy::indicate_required_context_graphs ( utility::vector1< bool > & context_graphs_required ) const

overridevirtual

AARepeatEnergy is context-independent and thus indicates that no context graphs need to be maintained by class Energies.

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

void core::energy_methods::AARepeatEnergy::load_penalty_table_from_file ( std::string const & filename )

private

Read a penalty data file and load the penalties into the energy method. Called once by the constructor.

Comment lines are ignored in the penalty data file. The file should have one line that's a whitespace-separated row of numbers. The numbers represent the penalty for having a stretch of 1, 2, 3, 4, etc. of the same residue as a repeating stretch. The function looks in the working directory and in database/scoring/score_functions/aa_repeat_energy/ for the penalty file.

References protocols::abinitio::filename(), parse_line(), penalties_, and core::energy_methods::TR().

Referenced by AARepeatEnergy().