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

#include <FitnessFilter.hh>

Inheritance diagram for protocols::recon_design::FitnessFilter:

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 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 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

Apply function to run under MPI.

Implements protocols::filters::VectorPoseFilter.

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

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

References core::pose::Pose::clone(), protocols::wum::mpi_rank(), and sfxn_.

Referenced by apply_mpi().

filters::FilterOP protocols::recon_design::FitnessFilter::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

References FitnessFilter().

filters::FilterOP protocols::recon_design::FitnessFilter::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

References FitnessFilter().

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

References protocols::mean_field::max(), core::id::to_string(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::recon_design::FitnessFilterCreator::provide_xml_schema().

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

Referenced by calculate_fitness(), calculate_fitness_mpi(), parse_my_tag(), and sfxn().

core::Real protocols::recon_design::FitnessFilter::threshold_

private

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

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

src/protocols/recon_design/FitnessFilter.hh
src/protocols/recon_design/FitnessFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation