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protocols::noesy_assign::DistanceScoreMover Class Reference

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:
Inheritance graph
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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 Stringsinfo ()
 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

CrossPeakListcross_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

count for each peak how many decoys have violated

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::noesy_assign::DistanceScoreMover::apply ( core::pose::Pose pose)
overridevirtual
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().

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

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

Implements protocols::moves::Mover.

void protocols::noesy_assign::DistanceScoreMover::prepare_scoring ( bool  use_for_calibration = false)
void protocols::noesy_assign::DistanceScoreMover::set_dcut ( core::Real  setting)
inline

References dcut_.

Member Data Documentation

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

Referenced by apply().

AllStructureDistanceBoundVector protocols::noesy_assign::DistanceScoreMover::all_dist_buf_
private
SingleConstraints protocols::noesy_assign::DistanceScoreMover::constraints_
private

Referenced by apply(), and DistanceScoreMover().

core::Size protocols::noesy_assign::DistanceScoreMover::count_decoys_
private
CrossPeakList& protocols::noesy_assign::DistanceScoreMover::cross_peaks_
private
core::Real protocols::noesy_assign::DistanceScoreMover::dcut_
private

Referenced by apply(), and set_dcut().

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

Referenced by apply().

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

Referenced by DistanceScoreMover().

PeakViolationCounts protocols::noesy_assign::DistanceScoreMover::peak_violation_counts_
private

Referenced by apply(), and prepare_scoring().

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

Referenced by apply(), and prepare_scoring().

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

cumulative sum of peak_violation_counts_;

Referenced by apply(), and prepare_scoring().

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: