A class to restrict designable amino acids depending on the probabilities from a PerResidueProbabilitiesMetric. More...

#include <RestrictAAsFromProbabilities.hh>

Inheritance diagram for protocols::task_operations::RestrictAAsFromProbabilities:

Public Member Functions
	RestrictAAsFromProbabilities ()

	~RestrictAAsFromProbabilities () override

core::pack::task::operation::TaskOperationOP	clone () const override
	Create another task operation of the type matching the most-derived version of the class. More...

void	parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Configure from a RosettaScripts XML tag. More...

void	apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const override
	Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...

void	set_metric (core::simple_metrics::PerResidueProbabilitiesMetricCOP metric)
	Set the PerResidueProbabilitiesMetric that will be used to calculate the pseudo-perplexity. More...

void	set_use_cached_data (bool use_cache, std::string const &prefix="", std::string const &suffix="")
	Set a boolean to attempt to find cached data matching the name/custom_type of the passed in simple_metric. Optionally pass any set prefix/suffix. More...

void	set_fail_on_missing_cache (bool fail)
	If use_cache is set to false, do we fail if no data is found in the pose? Default True. More...

void	set_prob_cutoff (core::Real prob_cutoff)
	Set the probability cutoff option. More...

void	set_delta_prob_cutoff (core::Real delta_prob_cutoff)
	Set the delta probability cutoff option. More...

void	disable_AAs (std::map< core::Size, std::map< core::chemical::AA, core::Real >> &probabilities, core::pose::Pose const &pose, core::pack::task::PackerTask &task) const
	disable all amino acids that do not meet user provided probability cutoffs More...

Public Member Functions inherited from core::pack::task::operation::TaskOperation
	~TaskOperation () override

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...

Static Public Member Functions
static std::string	keyname ()
	Return the name used to construct this TaskOperation from an XML file. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	Describe the format of XML file used to initialize this TaskOperation. More...

Private Attributes
core::simple_metrics::PerResidueProbabilitiesMetricCOP	metric_ = nullptr

core::Real	prob_cutoff_ = 0.0001

core::Real	delta_prob_cutoff_ = 0.0

bool	use_cache_ = false

std::string	cache_prefix_

std::string	cache_suffix_

bool	fail_on_missing_cache_ = true

Additional Inherited Members
Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

typedef pose::Pose	Pose

Detailed Description

A class to restrict designable amino acids depending on the probabilities from a PerResidueProbabilitiesMetric.

Constructor & Destructor Documentation

◆ RestrictAAsFromProbabilities()

protocols::task_operations::RestrictAAsFromProbabilities::RestrictAAsFromProbabilities ( )

Referenced by clone().

◆ ~RestrictAAsFromProbabilities()

protocols::task_operations::RestrictAAsFromProbabilities::~RestrictAAsFromProbabilities ( )

override

Member Function Documentation

◆ apply()

void protocols::task_operations::RestrictAAsFromProbabilities::apply	(	core::pose::Pose const &	,
		core::pack::task::PackerTask &
	)		const

overridevirtual

Change a packer task in some way. The input pose is the one to which the input task will be later applied.

Implements core::pack::task::operation::TaskOperation.

References cache_prefix_, cache_suffix_, delta_prob_cutoff_, disable_AAs(), fail_on_missing_cache_, metric_, prob_cutoff_, protocols::task_operations::TR(), and use_cache_.

◆ clone()

TaskOperationOP protocols::task_operations::RestrictAAsFromProbabilities::clone ( ) const

overridevirtual

Create another task operation of the type matching the most-derived version of the class.

Implements core::pack::task::operation::TaskOperation.

References RestrictAAsFromProbabilities().

◆ disable_AAs()

void protocols::task_operations::RestrictAAsFromProbabilities::disable_AAs	(	std::map< core::Size, std::map< core::chemical::AA, core::Real >> &	probabilities,
		core::pose::Pose const &	pose,
		core::pack::task::PackerTask &	task
	)		const

disable all amino acids that do not meet user provided probability cutoffs

References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, delta_prob_cutoff_, core::pack::task::PackerTask::nonconst_residue_task(), prob_cutoff_, core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::pack::task::ResidueLevelTask::restrict_restypes(), and protocols::task_operations::TR().

Referenced by apply().

◆ keyname()

std::string protocols::task_operations::RestrictAAsFromProbabilities::keyname ( )

static

Return the name used to construct this TaskOperation from an XML file.

Referenced by protocols::task_operations::RestrictAAsFromProbabilitiesCreator::keyname(), and provide_xml_schema().

◆ parse_tag()

void protocols::task_operations::RestrictAAsFromProbabilities::parse_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Configure from a RosettaScripts XML tag.

Reimplemented from core::pack::task::operation::TaskOperation.

References delta_prob_cutoff_, fail_on_missing_cache_, core::simple_metrics::get_metric_from_datamap_and_subtags(), prob_cutoff_, set_delta_prob_cutoff(), set_fail_on_missing_cache(), set_metric(), set_prob_cutoff(), and set_use_cached_data().

◆ provide_xml_schema()

void protocols::task_operations::RestrictAAsFromProbabilities::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Describe the format of XML file used to initialize this TaskOperation.

References keyname(), and core::pack::task::operation::task_op_schema_w_attributes().

Referenced by protocols::task_operations::RestrictAAsFromProbabilitiesCreator::provide_xml_schema().

◆ set_delta_prob_cutoff()

void protocols::task_operations::RestrictAAsFromProbabilities::set_delta_prob_cutoff ( core::Real delta_prob_cutoff )

Set the delta probability cutoff option.

References delta_prob_cutoff_.

Referenced by parse_tag().

◆ set_fail_on_missing_cache()

void protocols::task_operations::RestrictAAsFromProbabilities::set_fail_on_missing_cache ( bool fail )

If use_cache is set to false, do we fail if no data is found in the pose? Default True.

References fail_on_missing_cache_.

Referenced by parse_tag().

◆ set_metric()

void protocols::task_operations::RestrictAAsFromProbabilities::set_metric ( core::simple_metrics::PerResidueProbabilitiesMetricCOP metric )

Set the PerResidueProbabilitiesMetric that will be used to calculate the pseudo-perplexity.

References metric_.

Referenced by parse_tag().

◆ set_prob_cutoff()

void protocols::task_operations::RestrictAAsFromProbabilities::set_prob_cutoff ( core::Real prob_cutoff )

Set the probability cutoff option.

References prob_cutoff_.

Referenced by parse_tag().

◆ set_use_cached_data()

void protocols::task_operations::RestrictAAsFromProbabilities::set_use_cached_data	(	bool	use_cache,
		std::string const &	prefix = `""`,
		std::string const &	suffix = `""`
	)

Set a boolean to attempt to find cached data matching the name/custom_type of the passed in simple_metric. Optionally pass any set prefix/suffix.

This will allow the filter to re-use previously calculated data.

References cache_prefix_, cache_suffix_, protocols::task_operations::TR(), and use_cache_.

Referenced by parse_tag().

Member Data Documentation

◆ cache_prefix_

std::string protocols::task_operations::RestrictAAsFromProbabilities::cache_prefix_

private

Referenced by apply(), and set_use_cached_data().

◆ cache_suffix_

std::string protocols::task_operations::RestrictAAsFromProbabilities::cache_suffix_

private

Referenced by apply(), and set_use_cached_data().

◆ delta_prob_cutoff_

core::Real protocols::task_operations::RestrictAAsFromProbabilities::delta_prob_cutoff_ = 0.0

private

Referenced by apply(), disable_AAs(), parse_tag(), and set_delta_prob_cutoff().

◆ fail_on_missing_cache_

bool protocols::task_operations::RestrictAAsFromProbabilities::fail_on_missing_cache_ = true

private

Referenced by apply(), parse_tag(), and set_fail_on_missing_cache().

◆ metric_

core::simple_metrics::PerResidueProbabilitiesMetricCOP protocols::task_operations::RestrictAAsFromProbabilities::metric_ = nullptr

private

Referenced by apply(), and set_metric().

◆ prob_cutoff_

core::Real protocols::task_operations::RestrictAAsFromProbabilities::prob_cutoff_ = 0.0001

private

Referenced by apply(), disable_AAs(), parse_tag(), and set_prob_cutoff().

◆ use_cache_

bool protocols::task_operations::RestrictAAsFromProbabilities::use_cache_ = false

private

Referenced by apply(), and set_use_cached_data().

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

src/protocols/task_operations/RestrictAAsFromProbabilities.hh
src/protocols/task_operations/RestrictAAsFromProbabilities.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RestrictAAsFromProbabilities()

◆ ~RestrictAAsFromProbabilities()

Member Function Documentation

◆ apply()

◆ clone()

◆ disable_AAs()

◆ keyname()

◆ parse_tag()

◆ provide_xml_schema()

◆ set_delta_prob_cutoff()

◆ set_fail_on_missing_cache()

◆ set_metric()

◆ set_prob_cutoff()

◆ set_use_cached_data()

Member Data Documentation

◆ cache_prefix_

◆ cache_suffix_

◆ delta_prob_cutoff_

◆ fail_on_missing_cache_

◆ metric_

◆ prob_cutoff_

◆ use_cache_