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protocols::recon_design::FitnessFilter Class Reference

Returns the sum of energy of input poses. Only accessible through recon application. More...

#include <FitnessFilter.hh>

Inheritance diagram for protocols::recon_design::FitnessFilter:
Inheritance graph
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Public Member Functions

 FitnessFilter ()
 empty constructor More...
 
 ~FitnessFilter () override
 
bool apply (core::pose::Pose const &pose) const override
 Movers derived from VectorPoseFilter must define two apply methods: apply and apply_mpi, depending on whether the protocol is run in MPI or not Running in MPI will distribute each pose to a separate node, so the mover will operate on one pose. More...
 
bool apply_mpi (core::pose::Pose const &pose) const override
 Apply function to run under MPI. More...
 
void report (std::ostream &, core::pose::Pose const &) const override
 NOTE: report and report_sm are not implemented for use with the VectorPoseJobDistributor and the recon application. More...
 
core::Real report_sm (core::pose::Pose const &) const override
 NOTE: report and report_sm are not implemented for use with the VectorPoseJobDistributor and the recon application. More...
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
core::Real calculate_fitness (core::pose::Pose const &) const
 Internal functions to get the fitness over all poses. More...
 
core::Real calculate_fitness_mpi (core::pose::Pose const &pose) const
 
core::Real threshold () const
 
void threshold (core::Real)
 
core::scoring::ScoreFunctionOP sfxn () const
 
void sfxn (core::scoring::ScoreFunctionOP)
 
- Public Member Functions inherited from protocols::filters::VectorPoseFilter
 VectorPoseFilter ()
 Constructor. More...
 
 ~VectorPoseFilter () override
 
 VectorPoseFilter (std::string const &name)
 
 VectorPoseFilter (VectorPoseFilter const &other)
 
void set_poses (utility::vector1< core::pose::PoseOP > const &poses)
 Set the vector of poses for the mover to act upon. More...
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
virtual std::string get_type () const
 
std::string get_user_defined_name () const
 
void set_user_defined_name (std::string const &name)
 
virtual void clear ()
 used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual std::string name () const
 
virtual bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

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

Private Attributes

core::scoring::ScoreFunctionOP sfxn_
 
bool output_to_scorefile_
 
core::Real threshold_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::VectorPoseFilter
utility::vector1
< core::pose::PoseOP
poses_
 
- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Detailed Description

Returns the sum of energy of input poses. Only accessible through recon application.

Constructor & Destructor Documentation

protocols::recon_design::FitnessFilter::FitnessFilter ( )

empty constructor

Referenced by clone(), and fresh_instance().

protocols::recon_design::FitnessFilter::~FitnessFilter ( )
override

Member Function Documentation

bool protocols::recon_design::FitnessFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

Movers derived from VectorPoseFilter must define two apply methods: apply and apply_mpi, depending on whether the protocol is run in MPI or not Running in MPI will distribute each pose to a separate node, so the mover will operate on one pose.

Implements protocols::filters::VectorPoseFilter.

References calculate_fitness(), protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), output_to_scorefile_, and threshold_.

bool protocols::recon_design::FitnessFilter::apply_mpi ( core::pose::Pose const &  pose) const
overridevirtual
core::Real protocols::recon_design::FitnessFilter::calculate_fitness ( core::pose::Pose const &  ) const

Internal functions to get the fitness over all poses.

References protocols::filters::VectorPoseFilter::poses_, and sfxn_.

Referenced by apply(), report(), and report_sm().

core::Real protocols::recon_design::FitnessFilter::calculate_fitness_mpi ( core::pose::Pose const &  pose) const
filters::FilterOP protocols::recon_design::FitnessFilter::clone ( ) const
overridevirtual
filters::FilterOP protocols::recon_design::FitnessFilter::fresh_instance ( ) const
overridevirtual
void protocols::recon_design::FitnessFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References protocols::mean_field::max(), output_to_scorefile_, sfxn_, and threshold_.

void protocols::recon_design::FitnessFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::recon_design::FitnessFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

NOTE: report and report_sm are not implemented for use with the VectorPoseJobDistributor and the recon application.

Reimplemented from protocols::filters::Filter.

References calculate_fitness().

core::Real protocols::recon_design::FitnessFilter::report_sm ( core::pose::Pose const &  pose) const
overridevirtual

NOTE: report and report_sm are not implemented for use with the VectorPoseJobDistributor and the recon application.

Reimplemented from protocols::filters::Filter.

References calculate_fitness().

core::scoring::ScoreFunctionOP protocols::recon_design::FitnessFilter::sfxn ( ) const

References sfxn_.

Referenced by sfxn().

void protocols::recon_design::FitnessFilter::sfxn ( core::scoring::ScoreFunctionOP  sfxn)

References sfxn(), and sfxn_.

core::Real protocols::recon_design::FitnessFilter::threshold ( ) const

References threshold_.

void protocols::recon_design::FitnessFilter::threshold ( core::Real  thresh)

References threshold_.

Member Data Documentation

bool protocols::recon_design::FitnessFilter::output_to_scorefile_
private

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

core::scoring::ScoreFunctionOP protocols::recon_design::FitnessFilter::sfxn_
private
core::Real protocols::recon_design::FitnessFilter::threshold_
private

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