maintains a list of constraints_ (each PeakAssignment yields one) and peak_constraints_ ( each cross peak with multiple assignments creates one AmbiguousNMRConstraint ). the DistanceMover (prepare scoring and apply directly interacts with the Dk term in CrossPeak (set_decoy_compatibility) More...

#include <DistanceScoreMover.hh>

Inheritance diagram for protocols::noesy_assign::DistanceScoreMover:

[legend]

Public Types
typedef utility::vector1< core::pose::PoseOP >	PoseVector

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

Public Member Functions
	DistanceScoreMover (CrossPeakList &, core::pose::Pose const &pose, core::Real dcut)

void	prepare_scoring (bool use_for_calibration=false)
	set decoy_compatibility in PeakAssignments to zero More...

void	apply (core::pose::Pose &pose) override
	sum up decoy_compatibility score in PeakAssignments More...

void	finalize_scoring () const
	normalize decoy_compatibility of PeakAssignments by count_decoys_ More...

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

void	set_dcut (core::Real setting)

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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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...

Private Types
typedef utility::vector1< core::scoring::constraints::ConstraintOP >	SingleConstraints

typedef utility::vector1< core::Real >	DistanceBoundVector

typedef utility::vector1< DistanceBoundVector >	AllStructureDistanceBoundVector

typedef utility::vector1< core::Size >	PeakViolationCounts
	count for each peak how many decoys have violated More...

Private Attributes
CrossPeakList &	cross_peaks_

core::Size	count_decoys_

core::Size	nr_assignments_

SingleConstraints	constraints_

AllStructureDistanceBoundVector	all_dist_buf_

PeakViolationCounts	peak_violation_counts_

core::Size	total_violation_count_
	cumulative sum of peak_violation_counts_; More...

core::Real	total_assigned_distances_

core::Size	active_peaks_

core::Real	final_dist_power_

bool	used_for_calibration_

core::Real	dcut_

Additional Inherited Members
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...

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

maintains a list of constraints_ (each PeakAssignment yields one) and peak_constraints_ ( each cross peak with multiple assignments creates one AmbiguousNMRConstraint ). the DistanceMover (prepare scoring and apply directly interacts with the Dk term in CrossPeak (set_decoy_compatibility)

Member Typedef Documentation

◆ AllStructureDistanceBoundVector

typedef utility::vector1< DistanceBoundVector > protocols::noesy_assign::DistanceScoreMover::AllStructureDistanceBoundVector

private

◆ DistanceBoundVector

typedef utility::vector1< core::Real > protocols::noesy_assign::DistanceScoreMover::DistanceBoundVector

private

◆ PeakViolationCounts

typedef utility::vector1< core::Size > protocols::noesy_assign::DistanceScoreMover::PeakViolationCounts

private

count for each peak how many decoys have violated

◆ PoseVector

typedef utility::vector1< core::pose::PoseOP > protocols::noesy_assign::DistanceScoreMover::PoseVector

◆ SingleConstraints

typedef utility::vector1< core::scoring::constraints::ConstraintOP > protocols::noesy_assign::DistanceScoreMover::SingleConstraints

private

Constructor & Destructor Documentation

◆ DistanceScoreMover()

protocols::noesy_assign::DistanceScoreMover::DistanceScoreMover	(	CrossPeakList &	cpl,
		core::pose::Pose const &	pose,
		core::Real	dcut
	)

References protocols::noesy_assign::CrossPeakList::begin(), constraints_, cross_peaks_, protocols::noesy_assign::CrossPeakList::end(), nr_assignments_, and protocols::noesy_assign::tr().

Member Function Documentation

◆ apply()

void protocols::noesy_assign::DistanceScoreMover::apply ( core::pose::Pose & pose )

overridevirtual

sum up decoy_compatibility score in PeakAssignments

Implements protocols::moves::Mover.

References active_peaks_, protocols::noesy_assign::CrossPeakList::begin(), constraints_, count_decoys_, cross_peaks_, dcut_, protocols::noesy_assign::CrossPeakList::end(), final_dist_power_, protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::min_volume_, peak_violation_counts_, total_assigned_distances_, total_violation_count_, protocols::noesy_assign::tr(), and used_for_calibration_.

◆ finalize_scoring()

void protocols::noesy_assign::DistanceScoreMover::finalize_scoring ( ) const

normalize decoy_compatibility of PeakAssignments by count_decoys_

References protocols::noesy_assign::CrossPeakList::begin(), count_decoys_, cross_peaks_, and protocols::noesy_assign::CrossPeakList::end().

◆ get_name()

std::string protocols::noesy_assign::DistanceScoreMover::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ prepare_scoring()

void protocols::noesy_assign::DistanceScoreMover::prepare_scoring ( bool use_for_calibration = false )

set decoy_compatibility in PeakAssignments to zero

References protocols::noesy_assign::CrossPeakList::begin(), count_decoys_, cross_peaks_, protocols::noesy_assign::CrossPeakList::end(), peak_violation_counts_, total_assigned_distances_, total_violation_count_, and used_for_calibration_.

◆ set_dcut()

void protocols::noesy_assign::DistanceScoreMover::set_dcut ( core::Real setting )

inline

References dcut_.

Member Data Documentation

◆ active_peaks_

core::Size protocols::noesy_assign::DistanceScoreMover::active_peaks_

private

Referenced by apply().

◆ all_dist_buf_

AllStructureDistanceBoundVector protocols::noesy_assign::DistanceScoreMover::all_dist_buf_

private

◆ constraints_

SingleConstraints protocols::noesy_assign::DistanceScoreMover::constraints_

private

Referenced by apply(), and DistanceScoreMover().

◆ count_decoys_

core::Size protocols::noesy_assign::DistanceScoreMover::count_decoys_

private

Referenced by apply(), finalize_scoring(), and prepare_scoring().

◆ cross_peaks_

CrossPeakList& protocols::noesy_assign::DistanceScoreMover::cross_peaks_

private

Referenced by apply(), DistanceScoreMover(), finalize_scoring(), and prepare_scoring().

◆ dcut_

core::Real protocols::noesy_assign::DistanceScoreMover::dcut_

private

Referenced by apply(), and set_dcut().

◆ final_dist_power_

core::Real protocols::noesy_assign::DistanceScoreMover::final_dist_power_

private

Referenced by apply().

◆ nr_assignments_

core::Size protocols::noesy_assign::DistanceScoreMover::nr_assignments_

private

Referenced by DistanceScoreMover().

◆ peak_violation_counts_

PeakViolationCounts protocols::noesy_assign::DistanceScoreMover::peak_violation_counts_

private

Referenced by apply(), and prepare_scoring().

◆ total_assigned_distances_

core::Real protocols::noesy_assign::DistanceScoreMover::total_assigned_distances_

private

Referenced by apply(), and prepare_scoring().

◆ total_violation_count_

core::Size protocols::noesy_assign::DistanceScoreMover::total_violation_count_

private

cumulative sum of peak_violation_counts_;

Referenced by apply(), and prepare_scoring().

◆ used_for_calibration_

bool protocols::noesy_assign::DistanceScoreMover::used_for_calibration_

private

Referenced by apply(), and prepare_scoring().

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

src/protocols/noesy_assign/DistanceScoreMover.hh
src/protocols/noesy_assign/DistanceScoreMover.cc

Public Types

Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ AllStructureDistanceBoundVector

◆ DistanceBoundVector

◆ PeakViolationCounts

◆ PoseVector

◆ SingleConstraints

Constructor & Destructor Documentation

◆ DistanceScoreMover()

Member Function Documentation

◆ apply()

◆ finalize_scoring()

◆ get_name()

◆ prepare_scoring()

◆ set_dcut()

Member Data Documentation

◆ active_peaks_

◆ all_dist_buf_

◆ constraints_

◆ count_decoys_

◆ cross_peaks_

◆ dcut_

◆ final_dist_power_

◆ nr_assignments_

◆ peak_violation_counts_

◆ total_assigned_distances_

◆ total_violation_count_

◆ used_for_calibration_