#include <LoopAnalyzerMover.hh>

Inheritance diagram for protocols::analysis::LoopAnalyzerMover:

[legend]

Public Member Functions
	LoopAnalyzerMover (protocols::loops::Loops const &loops, bool const tracer=false)

	LoopAnalyzerMover ()

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

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

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

bool	reinitialize_for_new_input () const override
	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...

void	apply (core::pose::Pose &input_pose) override
	apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects) although it may toss data into the DataCache or a Job object. More...

void	set_loops (protocols::loops::LoopsCOP loops)
	set loops object, because public setters/getters are a rule More...

protocols::loops::LoopsCOP	get_loops (void) const
	get loops object, because public setters/getters are a rule More...

void	set_use_tracer (bool tracer)
	set tracer bool, because public setters/getters are a rule More...

bool	get_use_tracer (void) const
	get tracer bool, because public setters/getters are a rule More...

core::Real	get_total_score () const
	Return the total score found from the last apply call. More...

core::Real	get_max_rama () const

core::Real	get_max_omega () const

core::Real	get_max_pbond () const

core::Real	get_max_chainbreak () const

utility::vector1< core::Real >	get_chainbreak_scores ()
	Return the vector of chainbreak scores. More...

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

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...

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	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
void	reset ()
	reset stored data More...

void	calculate_all_chainbreaks (core::pose::Pose &pose)
	places cutpoints in the loops, scores chainbreak, removes cutpoints More...

void	set_sf ()
	ctor helper: create scorefunction More...

void	find_positions (core::pose::Pose const &pose)
	convert loops into positions (must wait until pose, thus not in ctor) More...

Private Attributes
utility::pointer::DeepCopyOP< protocols::loops::Loops const >	loops_
	used to store a copy of the input loops More...

bool	tracer_ = true
	output to tracer or PDB/silent file More...

utility::vector1< core::Size >	positions_
	used to calculate positions to examine - loops +- 1 position are interesting, but vary w/termini, etc More...

utility::pointer::DeepCopyOP< core::scoring::ScoreFunction >	sf_
	scorefunction used to apply multiple individual terms at once, not as a cohesive unit More...

utility::pointer::DeepCopyOP< core::scoring::ScoreFunction >	chbreak_sf_
	scorefunction for chainbreak score More...

utility::vector1< core::Real >	scores_
	brief remember chainbreak scores More...

core::Real	total_score_ = 0

core::Real	max_rama_ = REAL_FAKE_MIN

core::Real	max_chainbreak_ = REAL_FAKE_MIN

core::Real	max_omega_ = REAL_FAKE_MIN

core::Real	max_pbond_ = REAL_FAKE_MIN

Static Private Attributes
static constexpr core::Real	REAL_FAKE_MIN = -1000000

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...

Constructor & Destructor Documentation

◆ LoopAnalyzerMover() [1/2]

protocols::analysis::LoopAnalyzerMover::LoopAnalyzerMover	(	protocols::loops::Loops const &	loops,
		bool const	tracer = `false`
	)

References set_sf(), and protocols::moves::Mover::type().

◆ LoopAnalyzerMover() [2/2]

protocols::analysis::LoopAnalyzerMover::LoopAnalyzerMover ( )

References set_sf(), and protocols::moves::Mover::type().

Member Function Documentation

◆ apply()

void protocols::analysis::LoopAnalyzerMover::apply ( core::pose::Pose & input_pose )

overridevirtual

apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects) although it may toss data into the DataCache or a Job object.

LoopAnalyzerMover

Implements protocols::moves::Mover.

References protocols::jd2::add_string_real_pair_to_current_job(), protocols::jd2::add_string_to_current_job(), core::conformation::Residue::atom(), calculate_all_chainbreaks(), core::pose::Pose::energies(), core::pose::symmetry::extract_asymmetric_unit(), core::scoring::fa_dun, find_positions(), loops_, protocols::mean_field::max(), max_chainbreak_, max_omega_, max_pbond_, max_rama_, core::pose::Pose::omega(), core::scoring::omega, core::scoring::peptide_bond, core::pose::Pose::phi(), positions_, core::pose::Pose::psi(), core::scoring::rama, reset(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), scores_, total_score_, protocols::TR(), tracer_, protocols::analysis::which_ostream(), and core::conformation::Atom::xyz().

Referenced by protocols::anchored_design::AnchoredDesignMover::apply(), and protocols::loops::filters::LoopAnalyzerFilter::report_sm().

◆ calculate_all_chainbreaks()

void protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks ( core::pose::Pose & pose )

private

places cutpoints in the loops, scores chainbreak, removes cutpoints

References core::kinematics::FoldTree::add_edge(), core::pose::add_variant_type_to_pose_residue(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::delete_self_edges(), core::pose::Pose::fold_tree(), core::kinematics::Edge::PEPTIDE, positions_, core::pose::remove_variant_type_from_pose_residue(), core::kinematics::FoldTree::reorder(), scores_, and core::pose::Pose::size().

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::analysis::LoopAnalyzerMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ find_positions()

void protocols::analysis::LoopAnalyzerMover::find_positions ( core::pose::Pose const & pose )

private

convert loops into positions (must wait until pose, thus not in ctor)

References core::sequence::end, core::conformation::Residue::is_terminus(), loops_, positions_, core::pose::Pose::residue(), scores_, core::pose::Pose::size(), protocols::loops::start, and protocols::TR().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::analysis::LoopAnalyzerMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_chainbreak_scores()

utility::vector1< core::Real > protocols::analysis::LoopAnalyzerMover::get_chainbreak_scores ( )

Return the vector of chainbreak scores.

References scores_.

◆ get_loops()

protocols::loops::LoopsCOP protocols::analysis::LoopAnalyzerMover::get_loops ( void ) const

get loops object, because public setters/getters are a rule

References loops_.

◆ get_max_chainbreak()

core::Real protocols::analysis::LoopAnalyzerMover::get_max_chainbreak ( ) const

References max_chainbreak_.

◆ get_max_omega()

core::Real protocols::analysis::LoopAnalyzerMover::get_max_omega ( ) const

References max_omega_.

◆ get_max_pbond()

core::Real protocols::analysis::LoopAnalyzerMover::get_max_pbond ( ) const

References max_pbond_.

◆ get_max_rama()

core::Real protocols::analysis::LoopAnalyzerMover::get_max_rama ( ) const

References max_rama_.

◆ get_name()

std::string protocols::analysis::LoopAnalyzerMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_total_score()

core::Real protocols::analysis::LoopAnalyzerMover::get_total_score ( ) const

Return the total score found from the last apply call.

References total_score_.

Referenced by protocols::loops::filters::LoopAnalyzerFilter::report_sm().

◆ get_use_tracer()

bool protocols::analysis::LoopAnalyzerMover::get_use_tracer ( void ) const

inline

get tracer bool, because public setters/getters are a rule

References tracer_.

◆ mover_name()

std::string protocols::analysis::LoopAnalyzerMover::mover_name ( )

static

Referenced by get_name(), protocols::analysis::LoopAnalyzerMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::analysis::LoopAnalyzerMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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

Reimplemented from protocols::moves::Mover.

References protocols::loop_modeling::utilities::parse_loops_from_tag(), set_loops(), and set_use_tracer().

◆ provide_xml_schema()

void protocols::analysis::LoopAnalyzerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::loop_modeling::utilities::append_subelement_and_attributes_for_parse_loops_from_tag(), protocols::analysis::LoopAnalyzerMover_subelement_ct_name(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::analysis::LoopAnalyzerMoverCreator::provide_xml_schema().

◆ reinitialize_for_new_input()

bool protocols::analysis::LoopAnalyzerMover::reinitialize_for_new_input ( ) const

inlineoverridevirtual

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).

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

◆ reset()

void protocols::analysis::LoopAnalyzerMover::reset ( )

private

reset stored data

References max_chainbreak_, max_omega_, max_pbond_, max_rama_, REAL_FAKE_MIN, and scores_.

Referenced by apply().

◆ set_loops()

void protocols::analysis::LoopAnalyzerMover::set_loops ( protocols::loops::LoopsCOP loops )

set loops object, because public setters/getters are a rule

getters, setters/////////////

getters, setters/////////////////////

References loops_.

Referenced by parse_my_tag().

◆ set_sf()

void protocols::analysis::LoopAnalyzerMover::set_sf ( )

private

ctor helper: create scorefunction

References core::scoring::chainbreak, chbreak_sf_, core::scoring::fa_dun, core::scoring::omega, core::scoring::peptide_bond, core::scoring::rama, and sf_.

Referenced by LoopAnalyzerMover().

◆ set_use_tracer()

void protocols::analysis::LoopAnalyzerMover::set_use_tracer ( bool tracer )

inline

set tracer bool, because public setters/getters are a rule

References protocols::frag_picker::tracer(), and tracer_.

Referenced by parse_my_tag().

Member Data Documentation

◆ chbreak_sf_

utility::pointer::DeepCopyOP< core::scoring::ScoreFunction > protocols::analysis::LoopAnalyzerMover::chbreak_sf_

private

scorefunction for chainbreak score

Referenced by set_sf().

◆ loops_

utility::pointer::DeepCopyOP< protocols::loops::Loops const > protocols::analysis::LoopAnalyzerMover::loops_

private

used to store a copy of the input loops

Referenced by apply(), find_positions(), get_loops(), and set_loops().

◆ max_chainbreak_

core::Real protocols::analysis::LoopAnalyzerMover::max_chainbreak_ = REAL_FAKE_MIN

private

Referenced by apply(), get_max_chainbreak(), and reset().

◆ max_omega_

core::Real protocols::analysis::LoopAnalyzerMover::max_omega_ = REAL_FAKE_MIN

private

Referenced by apply(), get_max_omega(), and reset().

◆ max_pbond_

core::Real protocols::analysis::LoopAnalyzerMover::max_pbond_ = REAL_FAKE_MIN

private

Referenced by apply(), get_max_pbond(), and reset().

◆ max_rama_

core::Real protocols::analysis::LoopAnalyzerMover::max_rama_ = REAL_FAKE_MIN

private

Referenced by apply(), get_max_rama(), and reset().

◆ positions_

utility::vector1< core::Size > protocols::analysis::LoopAnalyzerMover::positions_

private

used to calculate positions to examine - loops +- 1 position are interesting, but vary w/termini, etc

Referenced by apply(), calculate_all_chainbreaks(), and find_positions().

◆ REAL_FAKE_MIN

constexpr core::Real protocols::analysis::LoopAnalyzerMover::REAL_FAKE_MIN = -1000000

staticconstexprprivate

Referenced by reset().

◆ scores_

utility::vector1< core::Real > protocols::analysis::LoopAnalyzerMover::scores_

private

brief remember chainbreak scores

Referenced by apply(), calculate_all_chainbreaks(), find_positions(), get_chainbreak_scores(), and reset().

◆ sf_

utility::pointer::DeepCopyOP< core::scoring::ScoreFunction > protocols::analysis::LoopAnalyzerMover::sf_

private

scorefunction used to apply multiple individual terms at once, not as a cohesive unit

Referenced by set_sf().

◆ total_score_

core::Real protocols::analysis::LoopAnalyzerMover::total_score_ = 0

private

Referenced by apply(), and get_total_score().

◆ tracer_

bool protocols::analysis::LoopAnalyzerMover::tracer_ = true

private

output to tracer or PDB/silent file

Referenced by apply(), get_use_tracer(), and set_use_tracer().

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

src/protocols/analysis/LoopAnalyzerMover.hh
src/protocols/analysis/LoopAnalyzerMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ LoopAnalyzerMover() [1/2]

◆ LoopAnalyzerMover() [2/2]

Member Function Documentation

◆ apply()

◆ calculate_all_chainbreaks()

◆ clone()

◆ find_positions()

◆ fresh_instance()

◆ get_chainbreak_scores()

◆ get_loops()

◆ get_max_chainbreak()

◆ get_max_omega()

◆ get_max_pbond()

◆ get_max_rama()

◆ get_name()

◆ get_total_score()

◆ get_use_tracer()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ reinitialize_for_new_input()

◆ reset()

◆ set_loops()

◆ set_sf()

◆ set_use_tracer()

Member Data Documentation

◆ chbreak_sf_

◆ loops_

◆ max_chainbreak_

◆ max_omega_

◆ max_pbond_

◆ max_rama_

◆ positions_

◆ REAL_FAKE_MIN

◆ scores_

◆ sf_

◆ total_score_

◆ tracer_