#include <RmsdFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::RmsdFilter:

Public Member Functions
	RmsdFilter ()

	RmsdFilter (utility::vector1< core::Size > const selection, bool const superimpose, core::Real const threshold, core::pose::PoseOP reference_pose)

bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...

protocols::filters::FilterOP	clone () const override

protocols::filters::FilterOP	fresh_instance () const override

void	report (std::ostream &out, core::pose::Pose const &pose) const override

void	reference_pose (core::pose::PoseOP ref)

void	set_selection (core::select::residue_selector::ResidueSelectorOP const &sele)
	Resets the selection to the given ResidueSelector. More...

void	add_selector (core::select::residue_selector::ResidueSelectorOP const &sele)
	Adds the given ResidueSelector to the selection. (As in all residues in both selections.) More...

void	superimpose (bool s)

bool	superimpose () const

core::Real	report_sm (core::pose::Pose const &pose) const override
	used to report filter internals through a score or silent file More...

core::Real	compute (core::pose::Pose const &pose) const

	~RmsdFilter () override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data_map) override
	Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...

void	superimpose_on_all (bool const b)

bool	superimpose_on_all () const

void	by_aln (bool s)

bool	by_aln () const

std::string	name () const override

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string 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 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	class_name ()

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

Private Attributes
core::select::residue_selector::ResidueSelectorOP	selection_

bool	superimpose_

bool	symmetry_

core::Real	threshold_

core::pose::PoseCOP	reference_pose_

bool	selection_from_segment_cache_

bool	superimpose_on_all_

bool	specify_both_spans_

bool	CA_only_

core::Size	begin_native_

core::Size	end_native_

core::Size	begin_pose_

core::Size	end_pose_

bool	by_aln_

utility::vector1< std::string >	aln_files_

utility::vector1< std::string >	template_names_

utility::vector1< std::string >	query_names_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Constructor & Destructor Documentation

◆ RmsdFilter() [1/2]

protocols::protein_interface_design::filters::RmsdFilter::RmsdFilter ( )

References aln_files_, query_names_, and template_names_.

◆ RmsdFilter() [2/2]

protocols::protein_interface_design::filters::RmsdFilter::RmsdFilter	(	utility::vector1< core::Size > const	selection,
		bool const	superimpose,
		core::Real const	threshold,
		core::pose::PoseOP	reference_pose
	)

References aln_files_, query_names_, and template_names_.

◆ ~RmsdFilter()

protocols::protein_interface_design::filters::RmsdFilter::~RmsdFilter ( )

overridedefault

Member Function Documentation

◆ add_selector()

void protocols::protein_interface_design::filters::RmsdFilter::add_selector ( core::select::residue_selector::ResidueSelectorOP const & sele )

Adds the given ResidueSelector to the selection. (As in all residues in both selections.)

References core::select::residue_selector::OR_combine(), and selection_.

Referenced by parse_my_tag().

◆ apply()

bool protocols::protein_interface_design::filters::RmsdFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), threshold_, and protocols::protein_interface_design::filters::TR().

◆ by_aln() [1/2]

bool protocols::protein_interface_design::filters::RmsdFilter::by_aln ( ) const

inline

References by_aln_.

◆ by_aln() [2/2]

void protocols::protein_interface_design::filters::RmsdFilter::by_aln ( bool s )

inline

References by_aln_.

◆ class_name()

std::string protocols::protein_interface_design::filters::RmsdFilter::class_name ( )

static

Referenced by protocols::protein_interface_design::filters::RmsdFilterCreator::keyname(), name(), parse_my_tag(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::protein_interface_design::filters::RmsdFilter::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::protein_interface_design::filters::RmsdFilter::compute ( core::pose::Pose const & pose ) const

References aln_files_, protocols::toolbox::apply_superposition_transform(), begin_native_, begin_pose_, by_aln_, protocols::protein_interface_design::filters::Ca_coords(), CA_only_, core::scoring::calpha_superimpose_pose(), end_native_, core::scoring::is_protein_CA(), query_names_, reference_pose_, protocols::protein_interface_design::filters::res_rmsd(), core::scoring::rmsd_no_super_subset(), core::scoring::rmsd_with_super_subset(), selection_, selection_from_segment_cache_, core::pose::datacache::SpecialSegmentsObserver::set_farray_from_sso(), core::pose::Pose::size(), specify_both_spans_, superimpose_, superimpose_on_all(), protocols::seeded_abinitio::superposition_transform(), core::scoring::sym_rmsd_with_super_subset(), symmetry_, template_names_, protocols::protein_interface_design::filters::TR(), and core::pose::Pose::xyz().

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

◆ fresh_instance()

protocols::filters::FilterOP protocols::protein_interface_design::filters::RmsdFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ name()

std::string protocols::protein_interface_design::filters::RmsdFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::protein_interface_design::filters::RmsdFilter::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 add_selector(), aln_files_, begin_native_, begin_pose_, by_aln_, CA_only_, class_name(), core::sequence::end, end_native_, end_pose_, core::pose::get_resnum_string(), protocols::rosetta_scripts::legacy_saved_pose_or_input(), query_names_, reference_pose_, selection_, selection_from_segment_cache_, specify_both_spans_, superimpose_, superimpose_on_all(), symmetry_, template_names_, threshold_, and protocols::protein_interface_design::filters::TR().

◆ provide_xml_schema()

void protocols::protein_interface_design::filters::RmsdFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::attributes_for_saved_reference_pose(), class_name(), and protocols::filters::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::protein_interface_design::filters::RmsdFilterCreator::provide_xml_schema().

◆ reference_pose()

void protocols::protein_interface_design::filters::RmsdFilter::reference_pose ( core::pose::PoseOP ref )

inline

References core::scoring::ref, and reference_pose_.

Referenced by protocols::enzdes::RemoveLigandFilter::report_sm().

◆ report()

void protocols::protein_interface_design::filters::RmsdFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and core::conformation::membrane::out.

◆ report_sm()

core::Real protocols::protein_interface_design::filters::RmsdFilter::report_sm ( core::pose::Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

◆ set_selection()

void protocols::protein_interface_design::filters::RmsdFilter::set_selection ( core::select::residue_selector::ResidueSelectorOP const & sele )

Resets the selection to the given ResidueSelector.

References selection_.

◆ superimpose() [1/2]

bool protocols::protein_interface_design::filters::RmsdFilter::superimpose ( ) const

inline

References superimpose_.

◆ superimpose() [2/2]

void protocols::protein_interface_design::filters::RmsdFilter::superimpose ( bool s )

inline

References superimpose_.

◆ superimpose_on_all() [1/2]

bool protocols::protein_interface_design::filters::RmsdFilter::superimpose_on_all ( ) const

inline

References superimpose_on_all_.

Referenced by compute(), and parse_my_tag().

◆ superimpose_on_all() [2/2]

void protocols::protein_interface_design::filters::RmsdFilter::superimpose_on_all ( bool const b )

inline

References protocols::match::upstream::b, and superimpose_on_all_.

Member Data Documentation

◆ aln_files_

utility::vector1<std::string> protocols::protein_interface_design::filters::RmsdFilter::aln_files_

private

Referenced by compute(), parse_my_tag(), and RmsdFilter().

◆ begin_native_

core::Size protocols::protein_interface_design::filters::RmsdFilter::begin_native_

private

Referenced by compute(), and parse_my_tag().

◆ begin_pose_

core::Size protocols::protein_interface_design::filters::RmsdFilter::begin_pose_

private

Referenced by compute(), and parse_my_tag().

◆ by_aln_

bool protocols::protein_interface_design::filters::RmsdFilter::by_aln_

private

Referenced by by_aln(), compute(), and parse_my_tag().

◆ CA_only_

bool protocols::protein_interface_design::filters::RmsdFilter::CA_only_

private

Referenced by compute(), and parse_my_tag().

◆ end_native_

core::Size protocols::protein_interface_design::filters::RmsdFilter::end_native_

private

Referenced by compute(), and parse_my_tag().

◆ end_pose_

core::Size protocols::protein_interface_design::filters::RmsdFilter::end_pose_

private

Referenced by parse_my_tag().

◆ query_names_

utility::vector1<std::string> protocols::protein_interface_design::filters::RmsdFilter::query_names_

private

Referenced by compute(), parse_my_tag(), and RmsdFilter().

◆ reference_pose_

core::pose::PoseCOP protocols::protein_interface_design::filters::RmsdFilter::reference_pose_

private

Referenced by compute(), parse_my_tag(), and reference_pose().

◆ selection_

core::select::residue_selector::ResidueSelectorOP protocols::protein_interface_design::filters::RmsdFilter::selection_

private

Referenced by add_selector(), compute(), parse_my_tag(), and set_selection().

◆ selection_from_segment_cache_

bool protocols::protein_interface_design::filters::RmsdFilter::selection_from_segment_cache_

private

Referenced by compute(), and parse_my_tag().

◆ specify_both_spans_

bool protocols::protein_interface_design::filters::RmsdFilter::specify_both_spans_

private

Referenced by compute(), and parse_my_tag().

◆ superimpose_

bool protocols::protein_interface_design::filters::RmsdFilter::superimpose_

private

Referenced by compute(), parse_my_tag(), and superimpose().

◆ superimpose_on_all_

bool protocols::protein_interface_design::filters::RmsdFilter::superimpose_on_all_

private

Referenced by superimpose_on_all().

◆ symmetry_

bool protocols::protein_interface_design::filters::RmsdFilter::symmetry_

private

Referenced by compute(), and parse_my_tag().

◆ template_names_

utility::vector1<std::string> protocols::protein_interface_design::filters::RmsdFilter::template_names_

private

Referenced by compute(), parse_my_tag(), and RmsdFilter().

◆ threshold_

core::Real protocols::protein_interface_design::filters::RmsdFilter::threshold_

private

Referenced by apply(), and parse_my_tag().

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

src/protocols/protein_interface_design/filters/RmsdFilter.hh
src/protocols/protein_interface_design/filters/RmsdFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ RmsdFilter() [1/2]

◆ RmsdFilter() [2/2]

◆ ~RmsdFilter()

Member Function Documentation

◆ add_selector()

◆ apply()

◆ by_aln() [1/2]

◆ by_aln() [2/2]

◆ class_name()

◆ clone()

◆ compute()

◆ fresh_instance()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ reference_pose()

◆ report()

◆ report_sm()

◆ set_selection()

◆ superimpose() [1/2]

◆ superimpose() [2/2]

◆ superimpose_on_all() [1/2]

◆ superimpose_on_all() [2/2]

Member Data Documentation

◆ aln_files_

◆ begin_native_

◆ begin_pose_

◆ by_aln_

◆ CA_only_

◆ end_native_

◆ end_pose_

◆ query_names_

◆ reference_pose_

◆ selection_

◆ selection_from_segment_cache_

◆ specify_both_spans_

◆ superimpose_

◆ superimpose_on_all_

◆ symmetry_

◆ template_names_

◆ threshold_