A class to sample sequences from a PerResidueProbabilitiesMetric and thread them onto the pose. More...

#include <SampleSequenceFromProbabilities.hh>

Inheritance diagram for protocols::simple_moves::SampleSequenceFromProbabilities:

[legend]

Public Member Functions
	SampleSequenceFromProbabilities ()
	Constructors ///. More...

	~SampleSequenceFromProbabilities () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

void	show (std::ostream &output=std::cout) const override
	Show the contents of the Mover. 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_pos_temp (core::Real pos_temp)
	Set the positional temperature option. More...

void	set_aa_temp (core::Real aa_temp)
	Set the amino acid temperature option. 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	set_max_mutations (core::Size max_mutations)
	Set the maximum number of mutations allowed option. More...

void	set_packing (bool packing)
	Set a bool to define whether we repack. More...

void	set_task_factory (core::pack::task::TaskFactoryOP &task_factory)
	Set the taskfactory option. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Rosetta Scripts Support ///. More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
	This mover is unpublished. It returns Moritz Ertelt as its author. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Member Functions
std::map< core::Size, core::chemical::AA >	sample_mutations (std::map< core::Size, std::map< core::chemical::AA, core::Real >> &values, core::pose::Pose const &pose) const
	Main function to sample mutations from a probability distribution. More...

std::vector< core::Size >	sample_positions (std::map< core::Size, std::map< core::chemical::AA, core::Real >> &values, core::pose::Pose const &pose) const
	Helper function to get the ranked positions based on maximum difference in probabilities. More...

core::chemical::AA	sample_amino_acid (std::map< core::chemical::AA, core::Real > const &aa_probs) const
	Helper function to sample an amino acid from a transformed probability distribution. More...

utility::vector1< std::pair< core::Size, core::Real > >	calculate_position_diffs (std::map< core::Size, std::map< core::chemical::AA, core::Real >> &probabilities, core::pose::Pose const &pose) const
	Helper function to calculate differences between current and other AAs, as well as disabling unwanted AAs. More...

std::vector< core::Size >	get_ranked_positions (utility::vector1< std::pair< core::Size, core::Real >> &position_diffs, core::pose::Pose const &pose) const
	Helper function to return positions ranked based on their delta_probability value to the current AA. More...

Static Private Member Functions
static std::string	construct_modified_sequence (core::pose::Pose &pose, std::map< core::Size, core::chemical::AA > &mutations)
	Helper function to return a string of three amino acid letters from the proposed mutations for the SimpleThreadingMover. More...

static bool	is_aa_allowed_by_task (core::pack::task::ResidueLevelTask const &rlt, core::chemical::AA aa)
	Helper function to check whether the AA is set to designable in the Packer. More...

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

core::Real	pos_temp_ = 1.0

core::Real	aa_temp_ = 1.0

core::Real	prob_cutoff_ = 0.0001

core::Real	delta_prob_cutoff_ = 0.0

core::Size	max_mutations_ = 10000

bool	packing_ = true

bool	use_cache_ = false

std::string	cache_prefix_

std::string	cache_suffix_

bool	fail_on_missing_cache_ = true

core::pack::task::TaskFactoryOP	task_factory_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

A class to sample sequences from a PerResidueProbabilitiesMetric and thread them onto the pose.

Constructor & Destructor Documentation

◆ SampleSequenceFromProbabilities()

protocols::simple_moves::SampleSequenceFromProbabilities::SampleSequenceFromProbabilities ( )

Constructors ///.

Default constructor

◆ ~SampleSequenceFromProbabilities()

protocols::simple_moves::SampleSequenceFromProbabilities::~SampleSequenceFromProbabilities ( )

overridedefault

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

◆ apply()

void protocols::simple_moves::SampleSequenceFromProbabilities::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover

Implements protocols::moves::Mover.

References cache_prefix_, cache_suffix_, construct_modified_sequence(), fail_on_missing_cache_, metric_, packing_, sample_mutations(), protocols::simple_moves::TR(), and use_cache_.

◆ calculate_position_diffs()

utility::vector1< std::pair< core::Size, core::Real > > protocols::simple_moves::SampleSequenceFromProbabilities::calculate_position_diffs	(	std::map< core::Size, std::map< core::chemical::AA, core::Real >> &	probabilities,
		core::pose::Pose const &	pose
	)		const

private

Helper function to calculate differences between current and other AAs, as well as disabling unwanted AAs.

References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, delta_prob_cutoff_, is_aa_allowed_by_task(), prob_cutoff_, core::pose::Pose::residue(), task_factory_, and protocols::simple_moves::TR().

Referenced by sample_positions().

◆ clone()

protocols::moves::MoverOP protocols::simple_moves::SampleSequenceFromProbabilities::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ construct_modified_sequence()

std::string protocols::simple_moves::SampleSequenceFromProbabilities::construct_modified_sequence	(	core::pose::Pose &	pose,
		std::map< core::Size, core::chemical::AA > &	mutations
	)

staticprivate

Helper function to return a string of three amino acid letters from the proposed mutations for the SimpleThreadingMover.

References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, core::chemical::name_from_aa(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::simple_moves::SampleSequenceFromProbabilities::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::simple_moves::SampleSequenceFromProbabilities::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

◆ get_ranked_positions()

std::vector< core::Size > protocols::simple_moves::SampleSequenceFromProbabilities::get_ranked_positions	(	utility::vector1< std::pair< core::Size, core::Real >> &	position_diffs,
		core::pose::Pose const &	pose
	)		const

private

Helper function to return positions ranked based on their delta_probability value to the current AA.

References max_mutations_, pos_temp_, core::scoring::rg, core::id::swap(), and core::pose::Pose::total_residue().

Referenced by sample_positions().

◆ is_aa_allowed_by_task()

bool protocols::simple_moves::SampleSequenceFromProbabilities::is_aa_allowed_by_task	(	core::pack::task::ResidueLevelTask const &	rlt,
		core::chemical::AA	aa
	)

staticprivate

Helper function to check whether the AA is set to designable in the Packer.

References protocols::cluster::calibur::aa, core::pack::task::ResidueLevelTask::allowed_residue_types(), core::pack::task::ResidueLevelTask::being_designed(), and core::pack::task::ResidueLevelTask::being_packed().

Referenced by calculate_position_diffs().

◆ mover_name()

std::string protocols::simple_moves::SampleSequenceFromProbabilities::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::SampleSequenceFromProbabilitiesCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::simple_moves::SampleSequenceFromProbabilities::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Rosetta Scripts Support ///.

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References aa_temp_, delta_prob_cutoff_, fail_on_missing_cache_, core::simple_metrics::get_metric_from_datamap_and_subtags(), max_mutations_, core::pack::task::parse_task_operations(), pos_temp_, prob_cutoff_, set_aa_temp(), set_delta_prob_cutoff(), set_fail_on_missing_cache(), set_max_mutations(), set_metric(), set_packing(), set_pos_temp(), set_prob_cutoff(), set_task_factory(), and set_use_cached_data().

◆ provide_citation_info()

void protocols::simple_moves::SampleSequenceFromProbabilities::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

This mover is unpublished. It returns Moritz Ertelt as its author.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

void protocols::simple_moves::SampleSequenceFromProbabilities::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::simple_moves::SampleSequenceFromProbabilitiesCreator::provide_xml_schema().

◆ sample_amino_acid()

core::chemical::AA protocols::simple_moves::SampleSequenceFromProbabilities::sample_amino_acid ( std::map< core::chemical::AA, core::Real > const & aa_probs ) const

private

Helper function to sample an amino acid from a transformed probability distribution.

References aa_temp_, core::kinematics::distance(), and protocols::simple_moves::TR().

Referenced by sample_mutations().

◆ sample_mutations()

std::map< core::Size, core::chemical::AA > protocols::simple_moves::SampleSequenceFromProbabilities::sample_mutations	(	std::map< core::Size, std::map< core::chemical::AA, core::Real >> &	values,
		core::pose::Pose const &	pose
	)		const

private

Main function to sample mutations from a probability distribution.

Creates a discrete distribution based on the delta_prob (curr_AA - max_prob_AA) of each position and draws from that distribution taking into a account the pos_temp_ which controls the randomness. The idea behind this is that positions with the larges disagreement between current AA and predicted AAs will be mutated first. Also checks the probability_cutoff_, delta_probability_cutoff and present TaskOperations and sets probabilities not meeting the requirements to zero. Returns as many positions with their proposed AA as are set through the max_mutation_ option set by the user. The randomness of choice of AA is controlled by the aa_temp_ option.

Parameters

[in]	pose	Uses the pose to get the current residues and check for TaksOps.
[in]	values	The values of a PerResidueProbabilitiesMetric.

Returns: A map containing positions and their proposed AA drawn from the input probabilities.

References sample_amino_acid(), sample_positions(), and protocols::simple_moves::TR().

Referenced by apply().

◆ sample_positions()

std::vector< core::Size > protocols::simple_moves::SampleSequenceFromProbabilities::sample_positions	(	std::map< core::Size, std::map< core::chemical::AA, core::Real >> &	values,
		core::pose::Pose const &	pose
	)		const

private

Helper function to get the ranked positions based on maximum difference in probabilities.

private methods ///

References calculate_position_diffs(), and get_ranked_positions().

Referenced by sample_mutations().

◆ set_aa_temp()

void protocols::simple_moves::SampleSequenceFromProbabilities::set_aa_temp ( core::Real aa_temp )

Set the amino acid temperature option.

References aa_temp_.

Referenced by parse_my_tag().

◆ set_delta_prob_cutoff()

void protocols::simple_moves::SampleSequenceFromProbabilities::set_delta_prob_cutoff ( core::Real delta_prob_cutoff )

Set the delta probability cutoff option.

References delta_prob_cutoff_.

Referenced by parse_my_tag().

◆ set_fail_on_missing_cache()

void protocols::simple_moves::SampleSequenceFromProbabilities::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_my_tag().

◆ set_max_mutations()

void protocols::simple_moves::SampleSequenceFromProbabilities::set_max_mutations ( core::Size max_mutations )

Set the maximum number of mutations allowed option.

References max_mutations_.

Referenced by parse_my_tag().

◆ set_metric()

void protocols::simple_moves::SampleSequenceFromProbabilities::set_metric ( core::simple_metrics::PerResidueProbabilitiesMetricCOP metric )

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

References metric_.

Referenced by parse_my_tag().

◆ set_packing()

void protocols::simple_moves::SampleSequenceFromProbabilities::set_packing ( bool packing )

Set a bool to define whether we repack.

References packing_.

Referenced by parse_my_tag().

◆ set_pos_temp()

void protocols::simple_moves::SampleSequenceFromProbabilities::set_pos_temp ( core::Real pos_temp )

Set the positional temperature option.

References pos_temp_.

Referenced by parse_my_tag().

◆ set_prob_cutoff()

void protocols::simple_moves::SampleSequenceFromProbabilities::set_prob_cutoff ( core::Real prob_cutoff )

Set the probability cutoff option.

References prob_cutoff_.

Referenced by parse_my_tag().

◆ set_task_factory()

void protocols::simple_moves::SampleSequenceFromProbabilities::set_task_factory ( core::pack::task::TaskFactoryOP & task_factory )

Set the taskfactory option.

References task_factory_.

Referenced by parse_my_tag().

◆ set_use_cached_data()

void protocols::simple_moves::SampleSequenceFromProbabilities::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::simple_moves::TR(), and use_cache_.

Referenced by parse_my_tag().

◆ show()

void protocols::simple_moves::SampleSequenceFromProbabilities::show ( std::ostream & output = std::cout ) const

overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::simple_moves::operator<<().

Member Data Documentation

◆ aa_temp_

core::Real protocols::simple_moves::SampleSequenceFromProbabilities::aa_temp_ = 1.0

private

Referenced by parse_my_tag(), sample_amino_acid(), and set_aa_temp().

◆ cache_prefix_

std::string protocols::simple_moves::SampleSequenceFromProbabilities::cache_prefix_

private

Referenced by apply(), and set_use_cached_data().

◆ cache_suffix_

std::string protocols::simple_moves::SampleSequenceFromProbabilities::cache_suffix_

private

Referenced by apply(), and set_use_cached_data().

◆ delta_prob_cutoff_

core::Real protocols::simple_moves::SampleSequenceFromProbabilities::delta_prob_cutoff_ = 0.0

private

Referenced by calculate_position_diffs(), parse_my_tag(), and set_delta_prob_cutoff().

◆ fail_on_missing_cache_

bool protocols::simple_moves::SampleSequenceFromProbabilities::fail_on_missing_cache_ = true

private

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

◆ max_mutations_

core::Size protocols::simple_moves::SampleSequenceFromProbabilities::max_mutations_ = 10000

private

Referenced by get_ranked_positions(), parse_my_tag(), and set_max_mutations().

◆ metric_

core::simple_metrics::PerResidueProbabilitiesMetricCOP protocols::simple_moves::SampleSequenceFromProbabilities::metric_ = nullptr

private

Referenced by apply(), and set_metric().

◆ packing_

bool protocols::simple_moves::SampleSequenceFromProbabilities::packing_ = true

private

Referenced by apply(), and set_packing().

◆ pos_temp_

core::Real protocols::simple_moves::SampleSequenceFromProbabilities::pos_temp_ = 1.0

private

Referenced by get_ranked_positions(), parse_my_tag(), and set_pos_temp().

◆ prob_cutoff_

core::Real protocols::simple_moves::SampleSequenceFromProbabilities::prob_cutoff_ = 0.0001

private

Referenced by calculate_position_diffs(), parse_my_tag(), and set_prob_cutoff().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::simple_moves::SampleSequenceFromProbabilities::task_factory_

private

Referenced by calculate_position_diffs(), and set_task_factory().

◆ use_cache_

bool protocols::simple_moves::SampleSequenceFromProbabilities::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/simple_moves/SampleSequenceFromProbabilities.hh
src/protocols/simple_moves/SampleSequenceFromProbabilities.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SampleSequenceFromProbabilities()

◆ ~SampleSequenceFromProbabilities()

Member Function Documentation

◆ apply()

◆ calculate_position_diffs()

◆ clone()

◆ construct_modified_sequence()

◆ fresh_instance()

◆ get_name()

◆ get_ranked_positions()

◆ is_aa_allowed_by_task()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ sample_amino_acid()

◆ sample_mutations()

◆ sample_positions()

◆ set_aa_temp()

◆ set_delta_prob_cutoff()

◆ set_fail_on_missing_cache()

◆ set_max_mutations()

◆ set_metric()

◆ set_packing()

◆ set_pos_temp()

◆ set_prob_cutoff()

◆ set_task_factory()

◆ set_use_cached_data()

◆ show()

Member Data Documentation

◆ aa_temp_

◆ cache_prefix_

◆ cache_suffix_

◆ delta_prob_cutoff_

◆ fail_on_missing_cache_

◆ max_mutations_

◆ metric_

◆ packing_

◆ pos_temp_

◆ prob_cutoff_

◆ task_factory_

◆ use_cache_