#include <ShapeComplementarityFilter.hh>

Inheritance diagram for protocols::simple_filters::ShapeComplementarityFilter:

Public Types
typedef protocols::filters::Filter	Super

typedef protocols::filters::Filter	Filter

typedef protocols::filters::FilterOP	FilterOP

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

typedef core::scoring::sc::ShapeComplementarityCalculator	ShapeComplementarityCalculator

typedef core::scoring::sc::RESULTS	ShapeComplementarityCalculatorResults

Public Member Functions
	ShapeComplementarityFilter ()

	ShapeComplementarityFilter (Real const &filtered_sc, Real const &filtered_area, core::Size const &jump_id, bool const quick, bool const verbose, bool const use_rosetta_radii=false, Real const &filtered_median_distance=1000.0f)

	~ShapeComplementarityFilter () override=default

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

void	filtered_sc (Real const &filtered_sc)

void	filtered_area (Real const &filtered_area)

void	filtered_median_distance (Real const &filtered_d_median)

void	quick (bool const quick)

void	verbose (bool const verbose)

void	use_rosetta_radii (bool const use_rosetta_radii)

void	residues1 (std::string const &res_string)

void	residues2 (std::string const &res_string)

void	sym_dof_name (std::string const &sym_dof_name)

std::string	sym_dof_name () const

void	write_int_area (bool write_int_area)

bool	write_int_area () const

void	write_median_distance (bool write_median_distance)

bool	write_median_distance () const

void	multicomp (bool multicomp)

bool	multicomp () const

void	selector1 (core::select::residue_selector::ResidueSelectorCOP selector1)

void	selector2 (core::select::residue_selector::ResidueSelectorCOP selector2)

void	jump_id (core::Size jump_id)

void	set_jump_selector (core::select::jump_selector::JumpSelectorCOP sele)

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	parse xml More...

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

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

ShapeComplementarityCalculatorResults	compute (Pose const &pose) const
	calc shape complementarity, returns results of the ShapeComplementarityCalculator More...

std::string	name () const override

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

	Filter (std::string const &)

	~Filter () override

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

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 Member Functions
void	setup_from_selectors (Pose const &pose, ShapeComplementarityCalculator &scc) const
	Uses residue selectors to set up the ShapeComplementarityCalculator. More...

void	setup_multi_component_symm (Pose const &pose, ShapeComplementarityCalculator &scc, core::Real &nsubs_scalefactor) const
	Uses multi-component symmetric interfaces to set up the ShapeComplementarityCalculator. More...

void	setup_single_component_symm (Pose const &pose, ShapeComplementarityCalculator &scc, core::Real &nsubs_scalefactor) const
	Uses single-component symmetric interfaces to set up the ShapeComplementarityCalculator. More...

void	print_sc_results (std::ostream &tr, ShapeComplementarityCalculatorResults const &r, core::Real const nsubs_scalefactor) const
	prints results to given tracer in a human-readable format More...

void	write_area (Pose const &pose, core::Real const area_val) const
	writes area value to current jd2 job More...

void	write_median_distance (Pose const &pose, core::Real const d_median) const
	writes median distance value to current jd2 job More...

Private Attributes
Real	filtered_sc_

Real	filtered_area_

Real	filtered_d_median_

bool	quick_ = false

bool	verbose_ = false

bool	use_rosetta_radii_ = false

core::select::residue_selector::ResidueSelectorCOP	selector1_

core::select::residue_selector::ResidueSelectorCOP	selector2_

bool	write_int_area_

bool	write_d_median_

core::Size	jump_id_ = 1

core::select::jump_selector::JumpSelectorCOP	jump_selector_ = nullptr

bool	multicomp_

std::string	sym_dof_name_

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

Member Typedef Documentation

◆ DataMap

typedef basic::datacache::DataMap protocols::simple_filters::ShapeComplementarityFilter::DataMap

◆ Filter

typedef protocols::filters::Filter protocols::simple_filters::ShapeComplementarityFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::simple_filters::ShapeComplementarityFilter::FilterOP

◆ Pose

typedef core::pose::Pose protocols::simple_filters::ShapeComplementarityFilter::Pose

◆ Real

typedef core::Real protocols::simple_filters::ShapeComplementarityFilter::Real

◆ ShapeComplementarityCalculator

typedef core::scoring::sc::ShapeComplementarityCalculator protocols::simple_filters::ShapeComplementarityFilter::ShapeComplementarityCalculator

◆ ShapeComplementarityCalculatorResults

typedef core::scoring::sc::RESULTS protocols::simple_filters::ShapeComplementarityFilter::ShapeComplementarityCalculatorResults

◆ Super

typedef protocols::filters::Filter protocols::simple_filters::ShapeComplementarityFilter::Super

◆ TagCOP

typedef utility::tag::TagCOP protocols::simple_filters::ShapeComplementarityFilter::TagCOP

Constructor & Destructor Documentation

◆ ShapeComplementarityFilter() [1/2]

protocols::simple_filters::ShapeComplementarityFilter::ShapeComplementarityFilter ( )

◆ ShapeComplementarityFilter() [2/2]

protocols::simple_filters::ShapeComplementarityFilter::ShapeComplementarityFilter	(	Real const &	filtered_sc,
		Real const &	filtered_area,
		core::Size const &	jump_id,
		bool const	quick,
		bool const	verbose,
		bool const	use_rosetta_radii = `false`,
		Real const &	filtered_median_distance = `1000.0f`
	)

◆ ~ShapeComplementarityFilter()

protocols::simple_filters::ShapeComplementarityFilter::~ShapeComplementarityFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::simple_filters::ShapeComplementarityFilter::apply ( Pose const & pose ) const

overridevirtual

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

Implements protocols::filters::Filter.

References core::scoring::sc::_RESULTS::area, compute(), core::scoring::sc::_RESULTS::distance, filtered_area_, filtered_d_median_, filtered_sc_, core::scoring::sc::_RESULTS::sc, and protocols::simple_filters::tr().

◆ class_name()

std::string protocols::simple_filters::ShapeComplementarityFilter::class_name ( )

static

Referenced by protocols::simple_filters::ShapeComplementarityFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

filters::FilterOP protocols::simple_filters::ShapeComplementarityFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ compute()

ShapeComplementarityFilter::ShapeComplementarityCalculatorResults protocols::simple_filters::ShapeComplementarityFilter::compute ( Pose const & pose ) const

calc shape complementarity, returns results of the ShapeComplementarityCalculator

Parameters

[in] pose Pose to be analyzed

Exceptions

EXCN_CalcInitFailed	Thrown if calculator couldn't be initialized
EXCN_ResultsInvalid	Thrown if computed results are invalid

Returns: ShapeComplementarityCalculator::RESULTS object

References core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::scoring::sc::MolecularSurfaceCalculator::density, core::scoring::sc::MolecularSurfaceCalculator::GetResults(), core::scoring::sc::MolecularSurfaceCalculator::Init(), core::pose::symmetry::is_symmetric(), jump_id(), jump_id_, jump_selector_, multicomp_, print_sc_results(), quick_, core::scoring::sc::MolecularSurfaceCalculator::Reset(), selector1_, selector2_, core::scoring::sc::MolecularSurfaceCalculator::settings, setup_from_selectors(), setup_multi_component_symm(), setup_single_component_symm(), protocols::simple_filters::tr(), core::scoring::sc::MolecularSurfaceCalculator::use_rosetta_radii, use_rosetta_radii_, and verbose_.

Referenced by apply(), and report_sm().

◆ filtered_area()

void protocols::simple_filters::ShapeComplementarityFilter::filtered_area ( Real const & filtered_area )

References filtered_area_.

◆ filtered_median_distance()

void protocols::simple_filters::ShapeComplementarityFilter::filtered_median_distance ( Real const & filtered_d_median )

References filtered_d_median_.

◆ filtered_sc()

void protocols::simple_filters::ShapeComplementarityFilter::filtered_sc ( Real const & filtered_sc )

References filtered_sc_.

◆ fresh_instance()

filters::FilterOP protocols::simple_filters::ShapeComplementarityFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ jump_id()

void protocols::simple_filters::ShapeComplementarityFilter::jump_id ( core::Size jump_id )

References jump_id_.

Referenced by compute(), and parse_my_tag().

◆ multicomp() [1/2]

bool protocols::simple_filters::ShapeComplementarityFilter::multicomp ( ) const

References multicomp_.

Referenced by multicomp(), and parse_my_tag().

◆ multicomp() [2/2]

void protocols::simple_filters::ShapeComplementarityFilter::multicomp ( bool multicomp )

References multicomp(), and multicomp_.

◆ name()

std::string protocols::simple_filters::ShapeComplementarityFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

◆ print_sc_results()

void protocols::simple_filters::ShapeComplementarityFilter::print_sc_results	(	std::ostream &	tr,
		ShapeComplementarityCalculatorResults const &	r,
		core::Real const	nsubs_scalefactor
	)		const

private

prints results to given tracer in a human-readable format

Parameters

[out]	tr	std::ostream object to write to
[in]	r	ShapeComplementarityCalculatorResults object containing results

Referenced by compute().

◆ provide_xml_schema()

void protocols::simple_filters::ShapeComplementarityFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::simple_filters::ShapeComplementarityFilterCreator::provide_xml_schema().

◆ quick()

void protocols::simple_filters::ShapeComplementarityFilter::quick ( bool const quick )

References quick_.

◆ report_sm()

core::Real protocols::simple_filters::ShapeComplementarityFilter::report_sm ( Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References core::scoring::sc::_RESULTS::area, compute(), core::scoring::sc::_RESULTS::distance, core::scoring::sc::_RESULTS::sc, protocols::simple_filters::tr(), write_area(), write_d_median_, write_int_area_, and write_median_distance().

◆ residues1()

void protocols::simple_filters::ShapeComplementarityFilter::residues1 ( std::string const & res_string )

References selector1_.

Referenced by parse_my_tag(), and setup_from_selectors().

◆ residues2()

void protocols::simple_filters::ShapeComplementarityFilter::residues2 ( std::string const & res_string )

References selector2_.

Referenced by parse_my_tag(), and setup_from_selectors().

◆ selector1()

void protocols::simple_filters::ShapeComplementarityFilter::selector1 ( core::select::residue_selector::ResidueSelectorCOP selector1 )

References selector1_.

◆ selector2()

void protocols::simple_filters::ShapeComplementarityFilter::selector2 ( core::select::residue_selector::ResidueSelectorCOP selector2 )

References selector2_.

◆ set_jump_selector()

void protocols::simple_filters::ShapeComplementarityFilter::set_jump_selector ( core::select::jump_selector::JumpSelectorCOP sele )

inline

References jump_selector_.

Referenced by parse_my_tag().

◆ setup_from_selectors()

void protocols::simple_filters::ShapeComplementarityFilter::setup_from_selectors	(	Pose const &	pose,
		ShapeComplementarityCalculator &	scc
	)		const

private

Uses residue selectors to set up the ShapeComplementarityCalculator.

Parameters

[in]	pose	Pose to be analyzed
[out]	scc	Initialized, empty ShapeComplementarityCalculator, to which pose residues are added

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::pose::Pose::residue(), residues1(), residues2(), selector1_, selector2_, and protocols::simple_filters::tr().

Referenced by compute().

◆ setup_multi_component_symm()

void protocols::simple_filters::ShapeComplementarityFilter::setup_multi_component_symm	(	Pose const &	pose,
		ShapeComplementarityCalculator &	scc,
		core::Real &	nsubs_scalefactor
	)		const

private

Uses multi-component symmetric interfaces to set up the ShapeComplementarityCalculator.

Parameters

[in]	pose	Pose to be analyzed
[out]	scc	Initialized, empty ShapeComplementarityCalculator, to which pose residues are added
[out]	nsubs_scalefactor	Writes number of subunits, to be used as scaling factor for sc calculations

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::pose::symmetry::get_full_intracomponent_neighbor_resis(), core::pose::symmetry::get_full_intracomponent_resis(), core::pose::symmetry::get_jump_name_to_subunits(), core::pose::symmetry::intracomponent_contact(), core::pose::Pose::residue(), sym_dof_name(), and protocols::simple_filters::tr().

Referenced by compute().

◆ setup_single_component_symm()

void protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm	(	Pose const &	pose,
		ShapeComplementarityCalculator &	scc,
		core::Real &	nsubs_scalefactor
	)		const

private

Uses single-component symmetric interfaces to set up the ShapeComplementarityCalculator.

Parameters

[in]	pose	Pose to be analyzed
[out]	scc	Initialized, empty ShapeComplementarityCalculator, to which pose residues are added
[out]	nsubs_scalefactor	Writes number of subunits, to be used as scaling factor for sc calculations

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::pose::Pose::fold_tree(), core::pose::symmetry::get_sym_aware_jump_num(), core::pose::symmetry::partition_by_symm_jumps(), core::pose::Pose::residue(), core::pose::Pose::size(), core::pose::symmetry::sym_dof_jump_num(), sym_dof_name(), and core::pose::symmetry::symmetry_info().

Referenced by compute().

◆ sym_dof_name() [1/2]

std::string protocols::simple_filters::ShapeComplementarityFilter::sym_dof_name ( ) const

References sym_dof_name_.

Referenced by parse_my_tag(), setup_multi_component_symm(), setup_single_component_symm(), sym_dof_name(), and write_area().

◆ sym_dof_name() [2/2]

void protocols::simple_filters::ShapeComplementarityFilter::sym_dof_name ( std::string const & sym_dof_name )

References sym_dof_name(), and sym_dof_name_.

◆ use_rosetta_radii()

void protocols::simple_filters::ShapeComplementarityFilter::use_rosetta_radii ( bool const use_rosetta_radii )

References use_rosetta_radii_.

◆ verbose()

void protocols::simple_filters::ShapeComplementarityFilter::verbose ( bool const verbose )

References verbose_.

◆ write_area()

void protocols::simple_filters::ShapeComplementarityFilter::write_area	(	Pose const &	pose,
		core::Real const	area_val
	)		const

private

writes area value to current jd2 job

Parameters

[in]	pose	Pose being analyzed
[in]	area_val	Area to be reported, before correcting for symmetry. If area < 0, the uncorrected value will be reported. If the pose isn't symmetric, the uncorrected value will be reported.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::jd2::add_string_real_pair_to_current_job(), core::pose::Pose::fold_tree(), core::pose::symmetry::get_jump_name_to_subunits(), core::pose::symmetry::get_sym_aware_jump_num(), protocols::filters::Filter::get_user_defined_name(), core::pose::symmetry::is_symmetric(), multicomp_, core::pose::symmetry::partition_by_symm_jumps(), core::pose::Pose::residue(), core::pose::Pose::size(), core::pose::symmetry::sym_dof_jump_num(), sym_dof_name(), and core::pose::symmetry::symmetry_info().

Referenced by report_sm().

◆ write_int_area() [1/2]

bool protocols::simple_filters::ShapeComplementarityFilter::write_int_area ( ) const

References write_int_area_.

Referenced by write_int_area().

◆ write_int_area() [2/2]

void protocols::simple_filters::ShapeComplementarityFilter::write_int_area ( bool write_int_area )

References write_int_area(), and write_int_area_.

◆ write_median_distance() [1/3]

bool protocols::simple_filters::ShapeComplementarityFilter::write_median_distance ( ) const

References write_d_median_.

Referenced by report_sm(), and write_median_distance().

◆ write_median_distance() [2/3]

void protocols::simple_filters::ShapeComplementarityFilter::write_median_distance ( bool write_median_distance )

References write_d_median_, and write_median_distance().

◆ write_median_distance() [3/3]

void protocols::simple_filters::ShapeComplementarityFilter::write_median_distance	(	Pose const &	pose,
		core::Real const	d_median
	)		const

private

writes median distance value to current jd2 job

Parameters

[in]	pose	Pose being analyzed
[in]	d_median	Median distance to be reported

References protocols::jd2::add_string_real_pair_to_current_job(), and protocols::filters::Filter::get_user_defined_name().

Member Data Documentation

◆ filtered_area_

Real protocols::simple_filters::ShapeComplementarityFilter::filtered_area_

private

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

◆ filtered_d_median_

Real protocols::simple_filters::ShapeComplementarityFilter::filtered_d_median_

private

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

◆ filtered_sc_

Real protocols::simple_filters::ShapeComplementarityFilter::filtered_sc_

private

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

◆ jump_id_

core::Size protocols::simple_filters::ShapeComplementarityFilter::jump_id_ = 1

private

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

◆ jump_selector_

core::select::jump_selector::JumpSelectorCOP protocols::simple_filters::ShapeComplementarityFilter::jump_selector_ = nullptr

private

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

◆ multicomp_

bool protocols::simple_filters::ShapeComplementarityFilter::multicomp_

private

Referenced by compute(), multicomp(), and write_area().

◆ quick_

bool protocols::simple_filters::ShapeComplementarityFilter::quick_ = false

private

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

◆ selector1_

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ShapeComplementarityFilter::selector1_

private

Referenced by compute(), parse_my_tag(), residues1(), selector1(), and setup_from_selectors().

◆ selector2_

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ShapeComplementarityFilter::selector2_

private

Referenced by compute(), parse_my_tag(), residues2(), selector2(), and setup_from_selectors().

◆ sym_dof_name_

std::string protocols::simple_filters::ShapeComplementarityFilter::sym_dof_name_

private

Referenced by sym_dof_name().

◆ use_rosetta_radii_

bool protocols::simple_filters::ShapeComplementarityFilter::use_rosetta_radii_ = false

private

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

◆ verbose_

bool protocols::simple_filters::ShapeComplementarityFilter::verbose_ = false

private

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

◆ write_d_median_

bool protocols::simple_filters::ShapeComplementarityFilter::write_d_median_

private

Referenced by parse_my_tag(), report_sm(), and write_median_distance().

◆ write_int_area_

bool protocols::simple_filters::ShapeComplementarityFilter::write_int_area_

private

Referenced by parse_my_tag(), report_sm(), and write_int_area().

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

src/protocols/simple_filters/ShapeComplementarityFilter.hh
src/protocols/simple_filters/ShapeComplementarityFilter.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ ShapeComplementarityCalculator

◆ ShapeComplementarityCalculatorResults

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ ShapeComplementarityFilter() [1/2]

◆ ShapeComplementarityFilter() [2/2]

◆ ~ShapeComplementarityFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ filtered_area()

◆ filtered_median_distance()

◆ filtered_sc()

◆ fresh_instance()

◆ jump_id()

◆ multicomp() [1/2]

◆ multicomp() [2/2]

◆ name()

◆ parse_my_tag()

◆ print_sc_results()

◆ provide_xml_schema()

◆ quick()

◆ report_sm()

◆ residues1()

◆ residues2()

◆ selector1()

◆ selector2()

◆ set_jump_selector()

◆ setup_from_selectors()

◆ setup_multi_component_symm()

◆ setup_single_component_symm()

◆ sym_dof_name() [1/2]

◆ sym_dof_name() [2/2]

◆ use_rosetta_radii()

◆ verbose()

◆ write_area()

◆ write_int_area() [1/2]

◆ write_int_area() [2/2]

◆ write_median_distance() [1/3]

◆ write_median_distance() [2/3]

◆ write_median_distance() [3/3]

Member Data Documentation

◆ filtered_area_

◆ filtered_d_median_

◆ filtered_sc_

◆ jump_id_

◆ jump_selector_

◆ multicomp_

◆ quick_

◆ selector1_

◆ selector2_

◆ sym_dof_name_

◆ use_rosetta_radii_

◆ verbose_

◆ write_d_median_

◆ write_int_area_