A class to save a PerResidueProbabilitiesMetric to a weight file. More...

#include <SaveProbabilitiesMetricMover.hh>

Inheritance diagram for protocols::simple_moves::SaveProbabilitiesMetricMover:

[legend]

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

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

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

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

void	set_filename (std::string const &filename)
	Set the name of the output file. More...

void	set_filetype (std::string const &filetype)
	Set the type of the output file. 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	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	This mover is unpublished.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 moritzertelt 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 void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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 void	save_aa_probabilities_to_file (std::string const &weights_file, std::map< core::Size, std::map< core::chemical::AA, core::Real >> const &prob_set)
	Save a set of amino acid probabilities to a weight file with formatting: PoseNum ResidueType Weight. More...

static std::string	get_selection_sequence (std::string const &pose_sequence, std::map< core::Size, std::map< core::chemical::AA, core::Real >> const &position_map)
	Get the sequence of the selection present in the probability map. More...

static std::map< core::Size, std::map< core::chemical::AA, core::Real > >	convert_probabilities_to_logits (std::map< core::Size, std::map< core::chemical::AA, core::Real >> const &probabilities_map)
	convert the map of probabilities to one of logits for writing out to a PSSM More...

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 Attributes
core::simple_metrics::PerResidueProbabilitiesMetricCOP	metric_ = nullptr

std::string	filename_

std::string	filetype_ = "weights"

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 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 save a PerResidueProbabilitiesMetric to a weight file.

Constructor & Destructor Documentation

◆ SaveProbabilitiesMetricMover()

protocols::simple_moves::SaveProbabilitiesMetricMover::SaveProbabilitiesMetricMover ( )

Constructors ///.

Default constructor

◆ ~SaveProbabilitiesMetricMover()

protocols::simple_moves::SaveProbabilitiesMetricMover::~SaveProbabilitiesMetricMover ( )

override

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

Member Function Documentation

◆ apply()

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

overridevirtual

Mover Methods ///.

Apply the mover

Implements protocols::moves::Mover.

References cache_prefix_, cache_suffix_, convert_probabilities_to_logits(), fail_on_missing_cache_, filename_, filetype_, get_selection_sequence(), metric_, core::simple_metrics::PerResidueProbabilitiesMetric::output_sequence_profile(), save_aa_probabilities_to_file(), core::pose::Pose::sequence(), protocols::simple_moves::TR(), and use_cache_.

◆ clone()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ convert_probabilities_to_logits()

std::map< core::Size, std::map< core::chemical::AA, core::Real > > protocols::simple_moves::SaveProbabilitiesMetricMover::convert_probabilities_to_logits ( std::map< core::Size, std::map< core::chemical::AA, core::Real >> const & probabilities_map )

static

convert the map of probabilities to one of logits for writing out to a PSSM

References protocols::cluster::calibur::aa, core::scoring::epr_deer::logit(), protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::simple_moves::SaveProbabilitiesMetricMover::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::SaveProbabilitiesMetricMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_selection_sequence()

std::string protocols::simple_moves::SaveProbabilitiesMetricMover::get_selection_sequence	(	std::string const &	pose_sequence,
		std::map< core::Size, std::map< core::chemical::AA, core::Real >> const &	position_map
	)

static

Get the sequence of the selection present in the probability map.

References core::scoring::pair.

Referenced by apply().

◆ mover_name()

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

static

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

◆ parse_my_tag()

void protocols::simple_moves::SaveProbabilitiesMetricMover::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 fail_on_missing_cache_, core::simple_metrics::get_metric_from_datamap_and_subtags(), set_fail_on_missing_cache(), set_filename(), set_filetype(), set_metric(), and set_use_cached_data().

◆ provide_citation_info()

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

overridevirtual

This mover is unpublished. It returns moritzertelt as its author.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

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

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

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

◆ save_aa_probabilities_to_file()

void protocols::simple_moves::SaveProbabilitiesMetricMover::save_aa_probabilities_to_file	(	std::string const &	weights_file,
		std::map< core::Size, std::map< core::chemical::AA, core::Real >> const &	prob_set
	)

static

Save a set of amino acid probabilities to a weight file with formatting: PoseNum ResidueType Weight.

References protocols::cluster::calibur::aa, core::chemical::name_from_aa(), protocols::noesy_assign::round(), and core::id::to_string().

Referenced by apply().

◆ set_fail_on_missing_cache()

void protocols::simple_moves::SaveProbabilitiesMetricMover::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_filename()

void protocols::simple_moves::SaveProbabilitiesMetricMover::set_filename ( std::string const & filename )

Set the name of the output file.

References protocols::abinitio::filename(), and filename_.

Referenced by parse_my_tag().

◆ set_filetype()

void protocols::simple_moves::SaveProbabilitiesMetricMover::set_filetype ( std::string const & filetype )

Set the type of the output file.

References protocols::cluster::calibur::filetype(), and filetype_.

Referenced by parse_my_tag().

◆ set_metric()

void protocols::simple_moves::SaveProbabilitiesMetricMover::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_use_cached_data()

void protocols::simple_moves::SaveProbabilitiesMetricMover::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().

Member Data Documentation

◆ cache_prefix_

std::string protocols::simple_moves::SaveProbabilitiesMetricMover::cache_prefix_

private

Referenced by apply(), and set_use_cached_data().

◆ cache_suffix_

std::string protocols::simple_moves::SaveProbabilitiesMetricMover::cache_suffix_

private

Referenced by apply(), and set_use_cached_data().

◆ fail_on_missing_cache_

bool protocols::simple_moves::SaveProbabilitiesMetricMover::fail_on_missing_cache_ = true

private

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

◆ filename_

std::string protocols::simple_moves::SaveProbabilitiesMetricMover::filename_

private

Referenced by apply(), and set_filename().

◆ filetype_

std::string protocols::simple_moves::SaveProbabilitiesMetricMover::filetype_ = "weights"

private

Referenced by apply(), and set_filetype().

◆ metric_

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

private

Referenced by apply(), and set_metric().

◆ use_cache_

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

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SaveProbabilitiesMetricMover()

◆ ~SaveProbabilitiesMetricMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ convert_probabilities_to_logits()

◆ fresh_instance()

◆ get_name()

◆ get_selection_sequence()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ save_aa_probabilities_to_file()

◆ set_fail_on_missing_cache()

◆ set_filename()

◆ set_filetype()

◆ set_metric()

◆ set_use_cached_data()

Member Data Documentation

◆ cache_prefix_

◆ cache_suffix_

◆ fail_on_missing_cache_

◆ filename_

◆ filetype_

◆ metric_

◆ use_cache_