#include <MHCEpitopeEnergy.hh>

Inheritance diagram for core::energy_methods::MHCEpitopeEnergy:

[legend]

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

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

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
	MHCEpitopeEnergy (core::scoring::methods::EnergyMethodOptions const &options)
	Options constructor. More...

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

	~MHCEpitopeEnergy () 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
	MHCEpitopeEnergy is context-independent and thus indicates that no context graphs need to be maintained by class Energies. More...

core::Size	version () const override
	MHCEpitopeEnergy 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...

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

void	report () const
	Get a summary of all loaded data. More...

void	set_up_residuearrayannealableenergy_for_packing (core::pose::Pose &pose, core::pack::rotamer_set::RotamerSets const &rotamersets, core::scoring::ScoreFunction const &sfxn) override
	Cache data from the pose in this EnergyMethod in anticipation of scoring. More...

void	setup_for_minimizing (pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap) const override
	Disable this energy during minimization. More...

void	finalize_after_minimizing (pose::Pose &pose) const override
	Re-enable this energy after minimization. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation for this 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...

	~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_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 bool	has_atomistic_energies () const
	Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method? Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it's not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods. More...

virtual bool	has_atomistic_pairwise_energies () const
	Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method? NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. More...

virtual void	atomistic_energy (core::Size atmno, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const
	Evaluate the (one body) energy associated with a particular atom This may be a "self" energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies() More...

virtual void	atomistic_pair_energy (core::Size atmno1, conformation::Residue const &rsd1, core::Size atomno2, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const
	Evaluate the energy for a particular pair of atoms This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies() 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...

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	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...

Private Member Functions
core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP	setup_helper_cop (core::Size const index) const
	Get a const-access pointer to a setup helper object. More...

core::Size	setup_helper_count () const
	Get the number of setup helper objects: More...

void	get_helpers_from_pose (core::pose::Pose const &pose, utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP > &setup_helpers, utility::vector1< core::select::residue_selector::ResidueSubset > &masks, utility::vector1< core::Real > &cst_weights) const
	Given a pose, pull out the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects stored in SequenceConstraints in the pose and append them to the setup_helpers_ vector, returning a new vector. This also generates a vector of masks simultaneously. More...

void	setup_symmetry (core::pose::Pose const &pose) const
	Check for symmetry and set up the symm_multipliers_ vector so that scoring is done just on the asymmetric part and scaled up accordingly. More...

core::Real	difference_btw_cached_and_full_rescore (utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP > const &setup_helpers, utility::vector1< core::select::residue_selector::ResidueSubset > const &masks, utility::vector1< core::Real > const &cst_weights) const
	Debugging function that will check total_ against a full_rescore total score, and returns the difference. More...

core::Real	full_rescore (utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP > const &setup_helpers, utility::vector1< core::select::residue_selector::ResidueSubset > const &masks, utility::vector1< core::Real > const &cst_weights, bool cache, bool native) const
	Compute and return the total score for the whole sequence (resvect), according to the given energy setups (helpers) and their focused positions (masks). More...

core::Real	update_score (utility::vector1< core::conformation::ResidueCOP > const &resvect, core::Size const substitution_position, utility::vector1< core::Real > const &cst_weights) const
	Update and return the total considered score for the sequence (resvect) by computing deltas for those position potentially affected by a considered mutation (at substitution_position). More...

Private Attributes
bool	disabled_
	Is this energy disabled (e.g. for minimization)? More...

utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupOP >	setup_helpers_
	The vector of helper objects that store all of the data for setting up this scoring function. More...

utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP >	setup_helpers_for_packing_
	A cache of the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects to be used for packing. More...

utility::vector1< core::select::residue_selector::ResidueSubset >	setup_helper_masks_for_packing_
	A vector of masks corresponding to the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects in setup_helpers_for_packing_. @detalis These are generated from ResidueSelectors. More...

utility::vector1< core::Real >	setup_helper_weights_for_packing_
	A vector of cst weights corresponding to the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects in setup_helpers_for_packing_. More...

utility::vector1< ScoreCacheOP >	score_caches_
	@brif A cache for each of the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects in setup_helpers_for_packing_. More...

core::Real	total_
	The current commited total energy. More...

core::Real	considered_total_
	The current considered total energy (when considering a substitution, before commiting it) More...

bool	symm_
	Is the protein symmetric? More...

utility::vector1< core::Size >	symm_multipliers_
	If it is symmetric, only maintain scores (considered and accepted) for the asymmetric portions, and multiply them by these factors (a constant for each position). More...

const char	pad = '-'
	The character to use for padding sequences that extend past the end of a chain. 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...

Member Typedef Documentation

◆ parent1

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

◆ parent2

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

Constructor & Destructor Documentation

◆ MHCEpitopeEnergy() [1/2]

core::energy_methods::MHCEpitopeEnergy::MHCEpitopeEnergy ( core::scoring::methods::EnergyMethodOptions const & options )

Options constructor.

References report(), setup_helpers_, and core::energy_methods::TR().

◆ MHCEpitopeEnergy() [2/2]

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

Copy constructor.

References score_caches_, setup_helpers_, and setup_helpers_for_packing_.

◆ ~MHCEpitopeEnergy()

core::energy_methods::MHCEpitopeEnergy::~MHCEpitopeEnergy ( )

overridedefault

Default destructor.

Member Function Documentation

◆ calculate_energy()

core::Real core::energy_methods::MHCEpitopeEnergy::calculate_energy	(	utility::vector1< core::conformation::ResidueCOP > const &	reslist,
		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 directly by the ResidueArrayAnnealingEvaluator during packer runs.

Called directly by the ResidueArrayAnnealingEvaluator during packer runs. Requires that set_up_residuearrayannealablenergy_for_packing() be called first.

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

References disabled_, full_rescore(), setup_helper_masks_for_packing_, setup_helper_weights_for_packing_, setup_helpers_for_packing_, and update_score().

◆ clone()

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

overridevirtual

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

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

◆ commit_considered_substitution()

void core::energy_methods::MHCEpitopeEnergy::commit_considered_substitution ( )

overridevirtual

What to do when a substitution that was considered is accepted.

Reimplemented from core::scoring::annealing::ResidueArrayAnnealableEnergy.

References considered_total_, score_caches_, and total_.

◆ difference_btw_cached_and_full_rescore()

core::Real core::energy_methods::MHCEpitopeEnergy::difference_btw_cached_and_full_rescore	(	utility::vector1< core::conformation::ResidueCOP > const &	resvect,
		utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP > const &	setup_helpers,
		utility::vector1< core::select::residue_selector::ResidueSubset > const &	masks,
		utility::vector1< core::Real > const &	cst_weights
	)		const

private

Debugging function that will check total_ against a full_rescore total score, and returns the difference.

This function essentially checks the integrity of the cache. It will add significant time to the run if used during packing, as every substitution will re-calculate the score for the entire pose. Should be used for debugging only.

References considered_total_, full_rescore(), core::scoring::packstat::old::masks, total_, and core::energy_methods::TR().

Referenced by update_score().

◆ finalize_after_minimizing()

void core::energy_methods::MHCEpitopeEnergy::finalize_after_minimizing ( pose::Pose & pose ) const

overridevirtual

Re-enable this energy after minimization.

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

References disabled_, and core::energy_methods::TR().

◆ finalize_total_energy()

void core::energy_methods::MHCEpitopeEnergy::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 protocols::cluster::calibur::aa, disabled_, full_rescore(), get_helpers_from_pose(), core::conformation::Residue::get_self_ptr(), core::scoring::packstat::old::masks, core::scoring::mhc_epitope, core::chemical::num_canonical_aas, core::pose::Pose::residue(), setup_symmetry(), core::pose::Pose::size(), symm_multipliers_, and core::energy_methods::TR().

◆ full_rescore()

core::Real core::energy_methods::MHCEpitopeEnergy::full_rescore	(	utility::vector1< core::conformation::ResidueCOP > const &	resvect,
		utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP > const &	setup_helpers,
		utility::vector1< core::select::residue_selector::ResidueSubset > const &	masks,
		utility::vector1< core::Real > const &	cst_weights,
		bool	cache,
		bool	native
	)		const

private

Compute and return the total score for the whole sequence (resvect), according to the given energy setups (helpers) and their focused positions (masks).

Cache indicates whether to store the score in the score cache, while native indicates whether this is the native / reference pose for relative scoring Note that method can be called either by finalize_score (setup_helpers_ and masks_ from pose) or by calculate_energy within packing simulated annealing (set_helpers_/masks_for_packing_ initialized at start of packing)

References core::energy_methods::get_seq(), core::scoring::packstat::old::masks, core::chemical::num_canonical_aas, pad, protocols::hybridization::score, score_caches_, protocols::loops::start, protocols::loops::stop, symm_multipliers_, total_, and core::energy_methods::TR().

Referenced by calculate_energy(), difference_btw_cached_and_full_rescore(), finalize_total_energy(), and set_up_residuearrayannealableenergy_for_packing().

◆ get_helpers_from_pose()

void core::energy_methods::MHCEpitopeEnergy::get_helpers_from_pose	(	core::pose::Pose const &	pose,
		utility::vector1< core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP > &	setup_helpers,
		utility::vector1< core::select::residue_selector::ResidueSubset > &	masks,
		utility::vector1< core::Real > &	cst_weights
	)		const

private

Given a pose, pull out the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects stored in SequenceConstraints in the pose and append them to the setup_helpers_ vector, returning a new vector. This also generates a vector of masks simultaneously.

Parameters

[in]	pose	The pose from which the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOPs will be extracted.
[out]	setup_helpers	The output vector of core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOPs that is the concatenation of those stored in setup_helpers_ and those from the pose.
[out]	masks	The output vector of ResidueSubsets, which will be equal in size to the helpers vector.

The output vectors are first cleared by this operation.

References core::pose::Pose::constraint_set(), core::scoring::packstat::old::masks, setup_helpers_, core::pose::Pose::size(), and core::energy_methods::TR().

Referenced by finalize_total_energy(), and set_up_residuearrayannealableenergy_for_packing().

◆ indicate_required_context_graphs()

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

overridevirtual

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

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

◆ provide_citation_info()

void core::energy_methods::MHCEpitopeEnergy::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation for this energy method.

Provides the citation for this energy method.

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

◆ report()

void core::energy_methods::MHCEpitopeEnergy::report ( ) const

Get a summary of all loaded data.

References setup_helper_cop(), setup_helper_count(), and core::energy_methods::TR().

Referenced by MHCEpitopeEnergy().

◆ set_up_residuearrayannealableenergy_for_packing()

void core::energy_methods::MHCEpitopeEnergy::set_up_residuearrayannealableenergy_for_packing	(	core::pose::Pose &	pose,
		core::pack::rotamer_set::RotamerSets const &	rotamersets,
		core::scoring::ScoreFunction const &	sfxn
	)

overridevirtual

Cache data from the pose in this EnergyMethod in anticipation of scoring.

Reimplemented from core::scoring::annealing::ResidueArrayAnnealableEnergy.

References disabled_, full_rescore(), get_helpers_from_pose(), core::conformation::Residue::get_self_ptr(), core::pose::Pose::residue(), score_caches_, setup_helper_masks_for_packing_, setup_helper_weights_for_packing_, setup_helpers_for_packing_, setup_symmetry(), core::pose::Pose::size(), and core::energy_methods::TR().

◆ setup_for_minimizing()

void core::energy_methods::MHCEpitopeEnergy::setup_for_minimizing	(	pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		kinematics::MinimizerMapBase const &	minmap
	)		const

overridevirtual

Disable this energy during minimization.

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

References disabled_, and core::energy_methods::TR().

◆ setup_helper_cop()

core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP core::energy_methods::MHCEpitopeEnergy::setup_helper_cop ( core::Size const index ) const

inlineprivate

Get a const-access pointer to a setup helper object.

References setup_helpers_.

Referenced by report().

◆ setup_helper_count()

core::Size core::energy_methods::MHCEpitopeEnergy::setup_helper_count ( ) const

inlineprivate

Get the number of setup helper objects:

References setup_helpers_.

Referenced by report().

◆ setup_symmetry()

void core::energy_methods::MHCEpitopeEnergy::setup_symmetry ( core::pose::Pose const & pose ) const

private

Check for symmetry and set up the symm_multipliers_ vector so that scoring is done just on the asymmetric part and scaled up accordingly.

References core::pose::Pose::conformation_ptr(), core::pose::symmetry::is_symmetric(), core::pose::Pose::size(), symm_, symm_multipliers_, and core::energy_methods::TR().

Referenced by finalize_total_energy(), and set_up_residuearrayannealableenergy_for_packing().

◆ update_score()

core::Real core::energy_methods::MHCEpitopeEnergy::update_score	(	utility::vector1< core::conformation::ResidueCOP > const &	resvect,
		core::Size const	substitution_position,
		utility::vector1< core::Real > const &	cst_weights
	)		const

private

Update and return the total considered score for the sequence (resvect) by computing deltas for those position potentially affected by a considered mutation (at substitution_position).

Updates the cached per-position considered scores

References considered_total_, difference_btw_cached_and_full_rescore(), core::energy_methods::get_seq(), core::chemical::num_canonical_aas, pad, score_caches_, setup_helper_masks_for_packing_, setup_helper_weights_for_packing_, setup_helpers_for_packing_, protocols::loops::start, symm_multipliers_, total_, and core::energy_methods::TR().

Referenced by calculate_energy().

◆ version()

core::Size core::energy_methods::MHCEpitopeEnergy::version ( ) const

overridevirtual

MHCEpitopeEnergy is version 1.0 right now.

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

Member Data Documentation

◆ considered_total_

core::Real core::energy_methods::MHCEpitopeEnergy::considered_total_

mutableprivate

The current considered total energy (when considering a substitution, before commiting it)

Referenced by commit_considered_substitution(), difference_btw_cached_and_full_rescore(), and update_score().

◆ disabled_

bool core::energy_methods::MHCEpitopeEnergy::disabled_

mutableprivate

Is this energy disabled (e.g. for minimization)?

Referenced by calculate_energy(), finalize_after_minimizing(), finalize_total_energy(), set_up_residuearrayannealableenergy_for_packing(), and setup_for_minimizing().

◆ pad

const char core::energy_methods::MHCEpitopeEnergy::pad = '-'

private

The character to use for padding sequences that extend past the end of a chain.

For example, nmer SVMs require the have non-core termini that need to be padded with dummy residues to avoid skipping the first and last few peptides in scoring. Pad with something that guarantees not to be scored. I think NetMHC actually scores an 'X', so using '-' here, but can change as needed.

Referenced by full_rescore(), and update_score().

◆ score_caches_

utility::vector1< ScoreCacheOP > core::energy_methods::MHCEpitopeEnergy::score_caches_

private

@brif A cache for each of the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects in setup_helpers_for_packing_.

Referenced by commit_considered_substitution(), full_rescore(), MHCEpitopeEnergy(), set_up_residuearrayannealableenergy_for_packing(), and update_score().

◆ setup_helper_masks_for_packing_

utility::vector1< core::select::residue_selector::ResidueSubset > core::energy_methods::MHCEpitopeEnergy::setup_helper_masks_for_packing_

private

A vector of masks corresponding to the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects in setup_helpers_for_packing_. @detalis These are generated from ResidueSelectors.

Referenced by calculate_energy(), set_up_residuearrayannealableenergy_for_packing(), and update_score().

◆ setup_helper_weights_for_packing_

utility::vector1< core::Real > core::energy_methods::MHCEpitopeEnergy::setup_helper_weights_for_packing_

private

A vector of cst weights corresponding to the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects in setup_helpers_for_packing_.

Referenced by calculate_energy(), set_up_residuearrayannealableenergy_for_packing(), and update_score().

◆ setup_helpers_

utility::vector1<core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupOP> core::energy_methods::MHCEpitopeEnergy::setup_helpers_

private

The vector of helper objects that store all of the data for setting up this scoring function.

Initialized on scoreterm initialization.

Referenced by get_helpers_from_pose(), MHCEpitopeEnergy(), setup_helper_cop(), and setup_helper_count().

◆ setup_helpers_for_packing_

utility::vector1<core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP> core::energy_methods::MHCEpitopeEnergy::setup_helpers_for_packing_

private

A cache of the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects to be used for packing.

This is the list in setup_helpers_ plus all of the core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup objects stored in MHCEpitopeConstraint objects in the pose. Initialized by the ResidueArrayAnnealingEvaluator in its initialize() function.

Referenced by calculate_energy(), MHCEpitopeEnergy(), set_up_residuearrayannealableenergy_for_packing(), and update_score().

◆ symm_

bool core::energy_methods::MHCEpitopeEnergy::symm_

mutableprivate

Is the protein symmetric?

Referenced by setup_symmetry().

◆ symm_multipliers_

utility::vector1<core::Size> core::energy_methods::MHCEpitopeEnergy::symm_multipliers_

mutableprivate

If it is symmetric, only maintain scores (considered and accepted) for the asymmetric portions, and multiply them by these factors (a constant for each position).

The value 0 indicates that the position is in a symmetric clone.

Referenced by finalize_total_energy(), full_rescore(), setup_symmetry(), and update_score().

◆ total_

core::Real core::energy_methods::MHCEpitopeEnergy::total_

mutableprivate

The current commited total energy.

Referenced by commit_considered_substitution(), difference_btw_cached_and_full_rescore(), full_rescore(), and update_score().

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

src/core/energy_methods/MHCEpitopeEnergy.hh
src/core/energy_methods/MHCEpitopeEnergy.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ parent1

◆ parent2

Constructor & Destructor Documentation

◆ MHCEpitopeEnergy() [1/2]

◆ MHCEpitopeEnergy() [2/2]

◆ ~MHCEpitopeEnergy()

Member Function Documentation

◆ calculate_energy()

◆ clone()

◆ commit_considered_substitution()

◆ difference_btw_cached_and_full_rescore()

◆ finalize_after_minimizing()

◆ finalize_total_energy()

◆ full_rescore()

◆ get_helpers_from_pose()

◆ indicate_required_context_graphs()

◆ provide_citation_info()

◆ report()

◆ set_up_residuearrayannealableenergy_for_packing()

◆ setup_for_minimizing()

◆ setup_helper_cop()

◆ setup_helper_count()

◆ setup_symmetry()

◆ update_score()

◆ version()

Member Data Documentation

◆ considered_total_

◆ disabled_

◆ pad

◆ score_caches_

◆ setup_helper_masks_for_packing_

◆ setup_helper_weights_for_packing_

◆ setup_helpers_

◆ setup_helpers_for_packing_

◆ symm_

◆ symm_multipliers_

◆ total_