#include <RotamerBoltzCalculator.hh>

Inheritance diagram for protocols::pose_metric_calculators::RotamerBoltzCalculator:

[legend]

Public Member Functions
	RotamerBoltzCalculator (core::scoring::ScoreFunctionOP scorefxn, core::Real temp, core::Real repacking_radius=6.0)

void	computeAllBoltz (core::pose::Pose const &pose)

RotamerProbability	computeBoltzWeight (core::pose::Pose &pose, core::Size resi)

core::pose::metrics::PoseMetricCalculatorOP	clone () const override

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)

void	set_energy_landscape_evaluator (protocols::toolbox::EnergyLandscapeEvaluatorCOP evaluator)

void	set_lazy (bool const lazy)

void	set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)

Public Member Functions inherited from core::pose::metrics::StructureDependentCalculator
	StructureDependentCalculator ()

void	notify_structure_change () override

void	get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose) override

std::string	get (std::string const &key, Pose const &this_pose) override

Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
	PoseMetricCalculator ()

virtual void	notify_energy_change ()

Protected Member Functions
void	lookup (std::string const &key, basic::MetricValueBase *valptr) const override

std::string	print (std::string const &key) const override

void	recompute (core::pose::Pose const &this_pose) override

core::Real	computeBoltzWeight (core::pose::Pose &pose, core::Size resi, protocols::minimization_packing::MinMoverOP min_mover, core::pack::task::PackerTaskOP task)

core::scoring::ScoreFunctionOP	scorefxn () const

core::Real	computeBoltzSum (core::Real init_score, utility::vector1< core::Real > scores)

protocols::minimization_packing::MinMoverOP	init_minmover (core::pose::Pose &pose, core::Size resi, bool unbound, core::pack::task::PackerTaskOP task)

core::pack::task::PackerTaskOP	init_task (core::pose::Pose const &pose, core::Size const resi)

void	temperature (core::Real temp)

void	repacking_radius (core::Real rad)

core::Real	repacking_radius () const

core::Real	temperature () const

Private Member Functions
core::Real	rb_jump ()

core::Real	compute_boltz_weight_packrotamers (core::pose::Pose &pose, core::Size const resi, protocols::minimization_packing::MinMoverOP min_mover, core::pack::task::PackerTaskOP task) const

core::Real	computeBoltzWeight_lazy (core::pose::Pose &pose, core::Size resi, protocols::minimization_packing::MinMoverOP min_mover, core::pack::task::PackerTaskOP task)

core::pack::rotamer_set::RotamerSetOP	create_rotamer_set (core::pose::Pose const &pose, core::Size const resi) const

utility::vector0< int >	init_rot_to_pack (core::pack::rotamer_set::RotamerSetsCOP rotamer_sets, core::Size moltenres, core::Size rot_to_fix)

Private Attributes
core::select::residue_selector::ResidueSelectorCOP	selector_
	selects residues to compute rotamer boltz on More...

protocols::toolbox::EnergyLandscapeEvaluatorCOP	evaluator_
	computes probability from scores of rotamers More...

bool	lazy_

core::Real	rb_jump_

core::Real	repacking_radius_

core::scoring::ScoreFunctionOP	scorefxn_

core::Real	temperature_

utility::vector1< core::Real >	all_boltz_

RotamerProbabilities	probabilities_

core::pack::rotamer_set::RotamerSetOP	rotset_

Constructor & Destructor Documentation

◆ RotamerBoltzCalculator()

protocols::pose_metric_calculators::RotamerBoltzCalculator::RotamerBoltzCalculator	(	core::scoring::ScoreFunctionOP	scorefxn,
		core::Real	temp,
		core::Real	repacking_radius = `6.0`
	)

Member Function Documentation

◆ clone()

core::pose::metrics::PoseMetricCalculatorOP protocols::pose_metric_calculators::RotamerBoltzCalculator::clone ( ) const

overridevirtual

Implements core::pose::metrics::PoseMetricCalculator.

◆ compute_boltz_weight_packrotamers()

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::compute_boltz_weight_packrotamers	(	core::pose::Pose &	pose,
		core::Size const	resi,
		protocols::minimization_packing::MinMoverOP	min_mover,
		core::pack::task::PackerTaskOP	task
	)		const

private

References protocols::toolbox::ScoreRmsPoints::bg(), protocols::score_filters::ScoreTypeFilter::compute(), protocols::pose_metric_calculators::compute_rmsd(), create_rotamer_set(), evaluator_, core::conformation::Residue::name1(), core::pack::pack_rotamers(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), protocols::hybridization::score, protocols::toolbox::ScoreRmsPoint::score(), scorefxn_, core::pose::Pose::size(), core::scoring::total_score, and protocols::pose_metric_calculators::TR().

Referenced by computeBoltzWeight().

◆ computeAllBoltz()

void protocols::pose_metric_calculators::RotamerBoltzCalculator::computeAllBoltz ( core::pose::Pose const & pose )

References all_boltz_, computeBoltzWeight(), probabilities_, selector_, core::pose::Pose::size(), and protocols::pose_metric_calculators::TR().

Referenced by recompute().

◆ computeBoltzSum()

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzSum	(	core::Real	init_score,
		utility::vector1< core::Real >	scores
	)

protected

References protocols::hybridization::score, and temperature().

Referenced by computeBoltzWeight_lazy().

◆ computeBoltzWeight() [1/2]

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight	(	core::pose::Pose &	pose,
		core::Size	resi
	)

References init_minmover(), and init_task().

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute(), and computeAllBoltz().

◆ computeBoltzWeight() [2/2]

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight	(	core::pose::Pose &	pose,
		core::Size	resi,
		protocols::minimization_packing::MinMoverOP	min_mover,
		core::pack::task::PackerTaskOP	task
	)

protected

References compute_boltz_weight_packrotamers(), computeBoltzWeight_lazy(), and lazy_.

◆ computeBoltzWeight_lazy()

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight_lazy	(	core::pose::Pose &	pose,
		core::Size	resi,
		protocols::minimization_packing::MinMoverOP	min_mover,
		core::pack::task::PackerTaskOP	task
	)

private

References protocols::minimization_packing::PackRotamersMover::apply(), protocols::minimization_packing::PackRotamersMoverLazy::apply_to_rotpack(), protocols::minimization_packing::PackRotamersMoverLazy::call_setup(), protocols::score_filters::ScoreTypeFilter::compute(), computeBoltzSum(), init_rot_to_pack(), protocols::minimization_packing::PackRotamersMover::rotamer_sets(), rotset_, protocols::hybridization::score, scorefxn(), scorefxn_, protocols::minimization_packing::PackRotamersMover::task(), and core::scoring::total_score.

Referenced by computeBoltzWeight().

◆ create_rotamer_set()

core::pack::rotamer_set::RotamerSetOP protocols::pose_metric_calculators::RotamerBoltzCalculator::create_rotamer_set	(	core::pose::Pose const &	pose,
		core::Size const	resi
	)		const

private

References core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::pose::symmetry::is_symmetric(), core::pack::make_symmetric_PackerTask_by_truncation(), scorefxn_, and core::pose::Pose::size().

Referenced by compute_boltz_weight_packrotamers().

◆ init_minmover()

protocols::minimization_packing::MinMoverOP protocols::pose_metric_calculators::RotamerBoltzCalculator::init_minmover	(	core::pose::Pose &	pose,
		core::Size	resi,
		bool	unbound,
		core::pack::task::PackerTaskOP	task
	)

protected

References core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), rb_jump(), scorefxn(), and core::pose::Pose::size().

Referenced by computeBoltzWeight().

◆ init_rot_to_pack()

utility::vector0< int > protocols::pose_metric_calculators::RotamerBoltzCalculator::init_rot_to_pack	(	core::pack::rotamer_set::RotamerSetsCOP	rotamer_sets,
		core::Size	moltenres,
		core::Size	rot_to_fix
	)

private

References rot().

Referenced by computeBoltzWeight_lazy().

◆ init_task()

core::pack::task::PackerTaskOP protocols::pose_metric_calculators::RotamerBoltzCalculator::init_task	(	core::pose::Pose const &	pose,
		core::Size const	resi
	)

protected

References core::pose::symmetry::is_symmetric(), core::pack::make_symmetric_PackerTask_by_truncation(), repacking_radius(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), rotset_, scorefxn_, and core::pose::Pose::size().

Referenced by computeBoltzWeight().

◆ lookup()

void protocols::pose_metric_calculators::RotamerBoltzCalculator::lookup	(	std::string const &	key,
		basic::MetricValueBase *	valptr
	)		const

overrideprotectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References all_boltz_, and probabilities_.

◆ print()

std::string protocols::pose_metric_calculators::RotamerBoltzCalculator::print ( std::string const & key ) const

overrideprotectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References all_boltz_, probabilities_, and core::id::to_string().

◆ rb_jump()

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::rb_jump ( )

inlineprivate

References rb_jump_.

Referenced by init_minmover().

◆ recompute()

void protocols::pose_metric_calculators::RotamerBoltzCalculator::recompute ( core::pose::Pose const & this_pose )

overrideprotectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References computeAllBoltz().

◆ repacking_radius() [1/2]

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::repacking_radius ( ) const

inlineprotected

References repacking_radius_.

Referenced by init_task().

◆ repacking_radius() [2/2]

void protocols::pose_metric_calculators::RotamerBoltzCalculator::repacking_radius ( core::Real rad )

inlineprotected

References repacking_radius_.

◆ scorefxn()

core::scoring::ScoreFunctionOP protocols::pose_metric_calculators::RotamerBoltzCalculator::scorefxn ( ) const

inlineprotected

References scorefxn_.

Referenced by computeBoltzWeight_lazy(), init_minmover(), and set_scorefxn().

◆ set_energy_landscape_evaluator()

void protocols::pose_metric_calculators::RotamerBoltzCalculator::set_energy_landscape_evaluator ( protocols::toolbox::EnergyLandscapeEvaluatorCOP evaluator )

References evaluator_, and core::pose::metrics::StructureDependentCalculator::notify_structure_change().

◆ set_lazy()

void protocols::pose_metric_calculators::RotamerBoltzCalculator::set_lazy ( bool const lazy )

References lazy_, and core::pose::metrics::StructureDependentCalculator::notify_structure_change().

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute().

◆ set_residue_selector()

void protocols::pose_metric_calculators::RotamerBoltzCalculator::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

References core::pose::metrics::StructureDependentCalculator::notify_structure_change(), and selector_.

◆ set_scorefxn()

void protocols::pose_metric_calculators::RotamerBoltzCalculator::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

References scorefxn(), and scorefxn_.

◆ temperature() [1/2]

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::temperature ( ) const

inlineprotected

References temperature_.

Referenced by computeBoltzSum().

◆ temperature() [2/2]

void protocols::pose_metric_calculators::RotamerBoltzCalculator::temperature ( core::Real temp )

inlineprotected

Note: This function returns an uninitialized filter; this should probably not be used.

References temperature_.

Member Data Documentation

◆ all_boltz_

utility::vector1< core::Real > protocols::pose_metric_calculators::RotamerBoltzCalculator::all_boltz_

private

Referenced by computeAllBoltz(), lookup(), and print().

◆ evaluator_

protocols::toolbox::EnergyLandscapeEvaluatorCOP protocols::pose_metric_calculators::RotamerBoltzCalculator::evaluator_

private

computes probability from scores of rotamers

Referenced by compute_boltz_weight_packrotamers(), and set_energy_landscape_evaluator().

◆ lazy_

bool protocols::pose_metric_calculators::RotamerBoltzCalculator::lazy_

private

Referenced by computeBoltzWeight(), and set_lazy().

◆ probabilities_

RotamerProbabilities protocols::pose_metric_calculators::RotamerBoltzCalculator::probabilities_

private

Referenced by computeAllBoltz(), lookup(), and print().

◆ rb_jump_

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::rb_jump_

private

Referenced by rb_jump().

◆ repacking_radius_

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::repacking_radius_

private

Referenced by repacking_radius().

◆ rotset_

core::pack::rotamer_set::RotamerSetOP protocols::pose_metric_calculators::RotamerBoltzCalculator::rotset_

private

Referenced by computeBoltzWeight_lazy(), and init_task().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::pose_metric_calculators::RotamerBoltzCalculator::scorefxn_

private

Referenced by compute_boltz_weight_packrotamers(), computeBoltzWeight_lazy(), create_rotamer_set(), init_task(), scorefxn(), and set_scorefxn().

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::pose_metric_calculators::RotamerBoltzCalculator::selector_

private

selects residues to compute rotamer boltz on

Referenced by computeAllBoltz(), and set_residue_selector().

◆ temperature_

core::Real protocols::pose_metric_calculators::RotamerBoltzCalculator::temperature_

private

Referenced by temperature().

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

src/protocols/pose_metric_calculators/RotamerBoltzCalculator.hh
src/protocols/pose_metric_calculators/RotamerBoltzCalculator.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ RotamerBoltzCalculator()

Member Function Documentation

◆ clone()

◆ compute_boltz_weight_packrotamers()

◆ computeAllBoltz()

◆ computeBoltzSum()

◆ computeBoltzWeight() [1/2]

◆ computeBoltzWeight() [2/2]

◆ computeBoltzWeight_lazy()

◆ create_rotamer_set()

◆ init_minmover()

◆ init_rot_to_pack()

◆ init_task()

◆ lookup()

◆ print()

◆ rb_jump()

◆ recompute()

◆ repacking_radius() [1/2]

◆ repacking_radius() [2/2]

◆ scorefxn()

◆ set_energy_landscape_evaluator()

◆ set_lazy()

◆ set_residue_selector()

◆ set_scorefxn()

◆ temperature() [1/2]

◆ temperature() [2/2]

Member Data Documentation

◆ all_boltz_

◆ evaluator_

◆ lazy_

◆ probabilities_

◆ rb_jump_

◆ repacking_radius_

◆ rotset_

◆ scorefxn_

◆ selector_

◆ temperature_