#include <ResidueArrayAnnealableEnergy.hh>

Inheritance diagram for core::scoring::annealing::ResidueArrayAnnealableEnergy:

Public Member Functions
	ResidueArrayAnnealableEnergy ()
	Constructor. More...

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

virtual	~ResidueArrayAnnealableEnergy ()
	Destructor. More...

virtual core::Real	calculate_energy (utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::Size > const &current_rotamer_ids, core::Size const substitution_position=0) const =0
	Calculate the energy given a vector of const-owning pointers to Residue objects. 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...

Constructor & Destructor Documentation

core::scoring::annealing::ResidueArrayAnnealableEnergy::ResidueArrayAnnealableEnergy ( )

default

Constructor.

core::scoring::annealing::ResidueArrayAnnealableEnergy::ResidueArrayAnnealableEnergy ( ResidueArrayAnnealableEnergy const & src )

default

Copy constructor.

core::scoring::annealing::ResidueArrayAnnealableEnergy::~ResidueArrayAnnealableEnergy ( )

virtualdefault

Destructor.

Member Function Documentation

virtual core::Real core::scoring::annealing::ResidueArrayAnnealableEnergy::calculate_energy	(	utility::vector1< core::conformation::ResidueCOP > const &	resvect,
		utility::vector1< core::Size > const &	current_rotamer_ids,
		core::Size const	substitution_position = `0`
	)		const

pure virtual

Calculate the energy given a vector of const-owning pointers to Residue objects.

Must be implemented by derived classes.

Implemented in core::energy_methods::DumpTrajectoryEnergy, core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, core::energy_methods::MHCEpitopeEnergy, core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy, core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy, core::energy_methods::AACompositionEnergy, core::energy_methods::NetChargeEnergy, core::energy_methods::AARepeatEnergy, core::pack::guidance_scoreterms::sap::SapConstraintEnergy, and core::energy_methods::RNA_PartitionEnergy.

void core::scoring::annealing::ResidueArrayAnnealableEnergy::clean_up_residuearrayannealableenergy_after_packing ( core::pose::Pose & pose )

virtual

Allows the ResidueArrayAnnealableEnergy to clean up cached data, either within the EnergyMethod or in the pose, after a packer run.

Base class version does nothing; may be overridden by derived classes.

Reimplemented in core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, core::energy_methods::DumpTrajectoryEnergy, core::energy_methods::AACompositionEnergy, and core::pack::guidance_scoreterms::sap::SapConstraintEnergy.

void core::scoring::annealing::ResidueArrayAnnealableEnergy::commit_considered_substitution ( )

virtual

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

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Reimplemented in core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, core::energy_methods::MHCEpitopeEnergy, core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy, and core::pack::guidance_scoreterms::sap::SapConstraintEnergy.

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

virtual

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.

Note that this is generally intended so that data can be cached FROM the Pose or ScoreFunction, not TO the Pose or ScoreFunction. There are exceptions, though: sometimes it is necessary to cache a large, reusable object within the Pose itself (e.g. in the datacache of the Energies object in the Pose), and for that reason the pose is nonconst, here.

Note: The method is nonconst to permit caching within the ResidueArrayAnnealableEnergy-derived EnergyMethod.

Reimplemented in core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, core::energy_methods::MHCEpitopeEnergy, core::energy_methods::DumpTrajectoryEnergy, core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy, core::energy_methods::AACompositionEnergy, core::energy_methods::NetChargeEnergy, core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy, core::pack::guidance_scoreterms::sap::SapConstraintEnergy, and core::energy_methods::RNA_PartitionEnergy.

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

src/core/scoring/annealing/ResidueArrayAnnealableEnergy.hh
src/core/scoring/annealing/ResidueArrayAnnealableEnergy.cc

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation