protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter Class Reference

#include <RmsdFromResidueSelectorFilter.hh>

Inheritance diagram for protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter:

Public Member Functions
	RmsdFromResidueSelectorFilter ()
	~RmsdFromResidueSelectorFilter () override
protocols::filters::FilterOP	clone () const override
protocols::filters::FilterOP	fresh_instance () const override
void	reference_pose (core::pose::PoseOP const &ref)
void	reference_pose (core::pose::Pose const &ref)
void	threshold (core::Real threshold)
void	CA_only (bool pick)
void	GDT (bool pick)
void	superimpose (bool pick)
void	count_residues (bool pick)
void	reference_selector (core::select::residue_selector::ResidueSelectorCOP const &select)
void	reference_selector (core::select::residue_selector::ResidueSelector const &select)
void	query_selector (core::select::residue_selector::ResidueSelectorCOP const &select)
void	query_selector (core::select::residue_selector::ResidueSelector const &select)
void	selectors (core::select::residue_selector::ResidueSelectorCOP const &reference, core::select::residue_selector::ResidueSelectorCOP const &query)
void	selectors (core::select::residue_selector::ResidueSelector const &reference, core::select::residue_selector::ResidueSelector const &query)
bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...
void	report (std::ostream &out, core::pose::Pose const &pose) const override
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
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...
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)

Static Private Member Functions
static core::Real	default_rmsd_threshold ()
static bool	default_ca_selection ()
static bool	default_gdt_selection ()
static bool	default_superimpose_selection ()
static bool	default_count_residues ()

Private Attributes
core::select::residue_selector::ResidueSelectorCOP	reference_select_
core::select::residue_selector::ResidueSelectorCOP	query_select_
core::Real	threshold_
core::pose::PoseCOP	reference_pose_
core::Real	sensitivity_
bool	CA_only_
bool	gdt_
bool	superimpose_
bool	count_residues_

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

Constructor & Destructor Documentation

RmsdFromResidueSelectorFilter()

protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::RmsdFromResidueSelectorFilter

(

)

~RmsdFromResidueSelectorFilter()

protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::~RmsdFromResidueSelectorFilter ( )

overridedefault

Member Function Documentation

apply()

bool protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::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::fold_from_loops::filters::TR().

CA_only()

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::CA_only ( bool  pick )

inline

References CA_only_.

Referenced by parse_my_tag().

class_name()

static std::string protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::class_name ( )

inlinestatic

Referenced by protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilterCreator::keyname(), name(), parse_my_tag(), and provide_xml_schema().

clone()

protocols::filters::FilterOP protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute

(

core::pose::Pose const &

pose

)

const

References protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::simple_filters::SelectGdtEvaluator::apply(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), CA_only_, count_residues_, core::select::residue_selector::count_selected(), core::pose::Pose::detached_copy(), gdt_, protocols::filters::Filter::get_user_defined_name(), core::scoring::is_protein_CA(), query_select_, reference_pose_, reference_select_, core::pose::Pose::remove_constraints(), core::select::residue_selector::represent_residue_selector(), core::scoring::rmsd_no_super(), sensitivity_, protocols::grafting::simple_movers::DeleteRegionMover::set_residue_selector(), superimpose_, and protocols::fold_from_loops::filters::TR().

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

count_residues()

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::count_residues ( bool  pick )

inline

References count_residues_.

Referenced by parse_my_tag().

default_ca_selection()

static bool protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::default_ca_selection ( )

inlinestaticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

default_count_residues()

static bool protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::default_count_residues ( )

inlinestaticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

default_gdt_selection()

static bool protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::default_gdt_selection ( )

inlinestaticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

default_rmsd_threshold()

static core::Real protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::default_rmsd_threshold ( )

inlinestaticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

default_superimpose_selection()

static bool protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::default_superimpose_selection ( )

inlinestaticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

fresh_instance()

protocols::filters::FilterOP protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

GDT()

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::GDT ( bool  pick )

inline

References gdt_.

Referenced by parse_my_tag().

name()

std::string protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::name ( ) const

inlineoverridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::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 CA_only(), class_name(), count_residues(), default_ca_selection(), default_count_residues(), default_gdt_selection(), default_rmsd_threshold(), default_superimpose_selection(), GDT(), core::select::residue_selector::get_residue_selector(), protocols::rosetta_scripts::legacy_saved_pose_or_input(), query_selector(), reference_pose_, reference_selector(), superimpose(), and threshold().

provide_xml_schema()

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector_when_required(), protocols::rosetta_scripts::attributes_for_saved_reference_pose(), class_name(), default_ca_selection(), default_count_residues(), default_gdt_selection(), default_rmsd_threshold(), default_superimpose_selection(), core::id::to_string(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilterCreator::provide_xml_schema().

query_selector() [1/2]

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::query_selector ( core::select::residue_selector::ResidueSelector const &  select )

inline

References core::select::residue_selector::ResidueSelector::clone(), and query_select_.

query_selector() [2/2]

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::query_selector ( core::select::residue_selector::ResidueSelectorCOP const &  select )

inline

References query_select_.

Referenced by parse_my_tag(), and selectors().

reference_pose() [1/2]

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::reference_pose

(

core::pose::Pose const &

ref

)

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

reference_pose() [2/2]

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::reference_pose

(

core::pose::PoseOP const &

ref

)

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

reference_selector() [1/2]

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::reference_selector ( core::select::residue_selector::ResidueSelector const &  select )

inline

References core::select::residue_selector::ResidueSelector::clone(), and reference_select_.

reference_selector() [2/2]

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::reference_selector ( core::select::residue_selector::ResidueSelectorCOP const &  select )

inline

References reference_select_.

Referenced by parse_my_tag(), and selectors().

report()

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::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::fold_from_loops::filters::RmsdFromResidueSelectorFilter::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().

selectors() [1/2]

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::selectors ( core::select::residue_selector::ResidueSelector const &  reference, core::select::residue_selector::ResidueSelector const &  query  )

inline

References query_selector(), and reference_selector().

selectors() [2/2]

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::selectors ( core::select::residue_selector::ResidueSelectorCOP const &  reference, core::select::residue_selector::ResidueSelectorCOP const &  query  )

inline

References query_selector(), and reference_selector().

superimpose()

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::superimpose ( bool  pick )

inline

References superimpose_.

Referenced by parse_my_tag().

threshold()

void protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::threshold ( core::Real  threshold )

inline

References threshold(), and threshold_.

Referenced by parse_my_tag(), and threshold().

Member Data Documentation

CA_only_

bool protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::CA_only_

private

Referenced by CA_only(), and compute().

count_residues_

bool protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::count_residues_

private

Referenced by compute(), and count_residues().

gdt_

bool protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::gdt_

private

Referenced by compute(), and GDT().

query_select_

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::query_select_

private

Referenced by compute(), and query_selector().

reference_pose_

core::pose::PoseCOP protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::reference_pose_

private

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

reference_select_

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::reference_select_

private

Referenced by compute(), and reference_selector().

sensitivity_

core::Real protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::sensitivity_

private

Referenced by compute().

superimpose_

bool protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::superimpose_

private

Referenced by compute(), and superimpose().

threshold_

core::Real protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::threshold_

private

Referenced by apply(), and threshold().

---

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

• src/protocols/fold_from_loops/filters/RmsdFromResidueSelectorFilter.hh
• src/protocols/fold_from_loops/filters/RmsdFromResidueSelectorFilter.cc