#include <ResidueDepthFilter.hh>

Inheritance diagram for protocols::simple_filters::ResidueDepthFilter:

Public Member Functions
	ResidueDepthFilter ()
	Filter. More...

	~ResidueDepthFilter () override

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

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

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

utility::vector1< core::Real >	get_residue_depth (core::pose::Pose const &pose) const

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...

void	set_report_crd (bool const value)

void	set_niter (core::Size const value)

std::string	name () const override

utility::vector1< core::Real >	get_scdepth_avrg () const

utility::vector1< core::Real >	get_scdepth_sdev () const

utility::vector1< core::Real >	get_scdepth_fvar () const

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

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	initialize ()

void	read_db (std::string const infile)

void	read_GUIP_matrix (std::string const infile)

void	fill_GUIP ()

utility::vector1< core::Size >	get_n8 (core::pose::Pose const &pose) const

utility::vector1< core::Size >	search_close_frags (utility::vector1< core::Vector > const &frag_crd, core::Size const n8, core::Size const npick) const

core::Real	get_residue_similarity (core::conformation::Residue const &rsd, utility::vector1< core::Vector > const &frag_crd, core::Size const n8, utility::vector1< ResidueDepthDataCOP > const context_rdd, utility::vector1< core::Size > const &close_ids, core::Size const n) const

core::Real	get_simscore (core::chemical::AA const aa1, core::chemical::AA const aa2) const

core::Real	compare_by_superposition (utility::vector1< ResidueDepthDataCOP > const &context_rdd, utility::vector1< core::Vector > const &frag_crd, utility::vector1< ResidueDepthDataCOP > const &context_rdd_ref, utility::vector1< core::Vector > const &frag_crd_ref) const

utility::vector1< ResidueDepthDataCOP >	make_context (core::pose::Pose const &pose, core::Size const ires) const

utility::vector1< ResidueDepthDataCOP >	make_context_ref (core::Size const ipdb, core::Size const ires) const

void	fill_neighs (ResidueDepthData &rdd, utility::vector1< ResidueDepthData > const &pdb_rdds) const

Private Attributes
std::string	dbfile_

std::string	GUIP_matrix_file_

ResidueDepthCalculator	RDC_

core::Size	ncandidate1_

core::Size	ncandidate2_

std::string	similarity_mode_

core::Real	gamma_

utility::vector1< utility::vector1< ResidueDepthDataCOP > >	db_

utility::vector1< std::string >	pdbid_

std::map< core::Size, utility::vector1< ResidueDepthFrag > >	frag_db_

utility::vector1< utility::vector1< core::Real > >	GUIP_matrix_

core::select::residue_selector::ResidueSelectorCOP	evalres_

core::Real	maxdist_

core::Real	mindist_

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

Constructor & Destructor Documentation

◆ ResidueDepthFilter()

protocols::simple_filters::ResidueDepthFilter::ResidueDepthFilter ( )

Filter.

References initialize().

◆ ~ResidueDepthFilter()

protocols::simple_filters::ResidueDepthFilter::~ResidueDepthFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::simple_filters::ResidueDepthFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

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

Implements protocols::filters::Filter.

References evalres_, core::chemical::element::F, get_residue_depth(), get_scdepth_avrg(), get_scdepth_fvar(), core::chemical::element::I, maxdist_, mindist_, core::conformation::Residue::name(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::simple_filters::TR().

◆ class_name()

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

static

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

◆ clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ compare_by_superposition()

core::Real protocols::simple_filters::ResidueDepthFilter::compare_by_superposition	(	utility::vector1< ResidueDepthDataCOP > const &	context_rdd,
		utility::vector1< core::Vector > const &	frag_crd,
		utility::vector1< ResidueDepthDataCOP > const &	context_rdd_ref,
		utility::vector1< core::Vector > const &	frag_crd_ref
	)		const

private

References core::scoring::rms, and protocols::simple_filters::TR().

Referenced by get_residue_similarity().

◆ fill_GUIP()

void protocols::simple_filters::ResidueDepthFilter::fill_GUIP ( )

private

◆ fill_neighs()

void protocols::simple_filters::ResidueDepthFilter::fill_neighs	(	ResidueDepthData &	rdd,
		utility::vector1< ResidueDepthData > const &	pdb_rdds
	)		const

private

References protocols::simple_filters::ResidueDepthData::CENcrd, protocols::simple_filters::ResidueDepthData::ires, and protocols::simple_filters::ResidueDepthData::neigh_ress.

◆ fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ get_n8()

utility::vector1< core::Size > protocols::simple_filters::ResidueDepthFilter::get_n8 ( core::pose::Pose const & pose ) const

private

References core::conformation::Residue::is_virtual_residue(), make_context(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by get_SDE_score().

◆ get_residue_depth()

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthFilter::get_residue_depth ( core::pose::Pose const & pose ) const

References protocols::simple_filters::ResidueDepthCalculator::estimate_sidechain_depth(), and RDC_.

Referenced by apply().

◆ get_residue_similarity()

core::Real protocols::simple_filters::ResidueDepthFilter::get_residue_similarity	(	core::conformation::Residue const &	rsd,
		utility::vector1< core::Vector > const &	frag_crd,
		core::Size const	n8,
		utility::vector1< ResidueDepthDataCOP > const	context_rdd,
		utility::vector1< core::Size > const &	close_ids,
		core::Size const	n
	)		const

private

References core::conformation::Residue::aa(), protocols::simple_filters::ResidueDepthFrag::aa(), core::chemical::aa_from_oneletter_code(), compare_by_superposition(), db_, frag_db_, gamma_, protocols::simple_filters::ResidueDepthFrag::get_CENcrd(), get_simscore(), protocols::simple_filters::ResidueDepthFrag::ipdb(), protocols::simple_filters::ResidueDepthFrag::ires(), make_context_ref(), protocols::simple_filters::mycomp(), core::chemical::oneletter_code_from_aa(), pdbid_, core::scoring::rms, similarity_mode_, and protocols::simple_filters::TR().

Referenced by get_SDE_score().

◆ get_scdepth_avrg()

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthFilter::get_scdepth_avrg ( ) const

inline

References protocols::simple_filters::ResidueDepthCalculator::get_scdepth_avrg(), and RDC_.

Referenced by apply().

◆ get_scdepth_fvar()

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthFilter::get_scdepth_fvar ( ) const

inline

References protocols::simple_filters::ResidueDepthCalculator::get_scdepth_fvar(), and RDC_.

Referenced by apply().

◆ get_scdepth_sdev()

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthFilter::get_scdepth_sdev ( ) const

inline

References protocols::simple_filters::ResidueDepthCalculator::get_scdepth_sdev(), and RDC_.

◆ get_SDE_score()

core::Real protocols::simple_filters::ResidueDepthFilter::get_SDE_score ( core::pose::Pose const & pose )

References core::chemical::CENTROID, protocols::simple_filters::ResidueDepthCalculator::estimate_sidechain_depth(), frag_db_, get_n8(), get_residue_similarity(), make_context(), ncandidate1_, ncandidate2_, RDC_, core::pose::Pose::residue(), search_close_frags(), protocols::simple_filters::TR(), and core::conformation::Residue::xyz().

◆ get_simscore()

core::Real protocols::simple_filters::ResidueDepthFilter::get_simscore	(	core::chemical::AA const	aa1,
		core::chemical::AA const	aa2
	)		const

private

References GUIP_matrix_, and core::chemical::num_canonical_aas.

Referenced by get_residue_similarity().

◆ initialize()

void protocols::simple_filters::ResidueDepthFilter::initialize ( )

private

References evalres_, gamma_, GUIP_matrix_file_, maxdist_, mindist_, ncandidate1_, ncandidate2_, RDC_, read_GUIP_matrix(), and similarity_mode_.

Referenced by ResidueDepthFilter().

◆ make_context()

utility::vector1< ResidueDepthDataCOP > protocols::simple_filters::ResidueDepthFilter::make_context	(	core::pose::Pose const &	pose,
		core::Size const	ires
	)		const

private

References core::conformation::Residue::aa(), protocols::simple_filters::ResidueDepthCalculator::get_scdepth_avrg(), core::conformation::Residue::is_virtual_residue(), core::chemical::name_from_aa(), RDC_, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by get_n8(), and get_SDE_score().

◆ make_context_ref()

utility::vector1< ResidueDepthDataCOP > protocols::simple_filters::ResidueDepthFilter::make_context_ref	(	core::Size const	ipdb,
		core::Size const	ires
	)		const

private

References db_.

Referenced by get_residue_similarity().

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::simple_filters::ResidueDepthFilter::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 evalres_, maxdist_, mindist_, RDC_, protocols::simple_filters::ResidueDepthCalculator::set_dcut1(), and protocols::simple_filters::ResidueDepthCalculator::set_dcut2().

◆ provide_xml_schema()

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

static

References core::pose::attributes_for_get_resnum_selector(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

◆ read_db()

void protocols::simple_filters::ResidueDepthFilter::read_db ( std::string const infile )

private

References protocols::cluster::calibur::aa, protocols::mean_field::add(), db_, frag_db_, pdbid_, protocols::simple_filters::ResidueDepthFrag::set_rdd(), and protocols::simple_filters::TR().

◆ read_GUIP_matrix()

void protocols::simple_filters::ResidueDepthFilter::read_GUIP_matrix ( std::string const infile )

private

References GUIP_matrix_, and protocols::hybridization::val.

Referenced by initialize().

◆ search_close_frags()

utility::vector1< core::Size > protocols::simple_filters::ResidueDepthFilter::search_close_frags	(	utility::vector1< core::Vector > const &	frag_crd,
		core::Size const	n8,
		core::Size const	npick
	)		const

private

References frag_db_, protocols::simple_filters::ResidueDepthFrag::get_CAcrd(), and protocols::simple_filters::TR().

Referenced by get_SDE_score().

◆ set_niter()

void protocols::simple_filters::ResidueDepthFilter::set_niter ( core::Size const value )

inline

References protocols::simple_filters::ResidueDepthCalculator::niter(), and RDC_.

◆ set_report_crd()

void protocols::simple_filters::ResidueDepthFilter::set_report_crd ( bool const value )

inline

References RDC_, and protocols::simple_filters::ResidueDepthCalculator::report_crd().

Member Data Documentation

◆ db_

utility::vector1< utility::vector1< ResidueDepthDataCOP > > protocols::simple_filters::ResidueDepthFilter::db_

private

Referenced by get_residue_similarity(), make_context_ref(), and read_db().

◆ dbfile_

std::string protocols::simple_filters::ResidueDepthFilter::dbfile_

private

◆ evalres_

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ResidueDepthFilter::evalres_

private

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

◆ frag_db_

std::map< core::Size, utility::vector1<ResidueDepthFrag> > protocols::simple_filters::ResidueDepthFilter::frag_db_

private

Referenced by get_residue_similarity(), get_SDE_score(), read_db(), and search_close_frags().

◆ gamma_

core::Real protocols::simple_filters::ResidueDepthFilter::gamma_

private

Referenced by get_residue_similarity(), and initialize().

◆ GUIP_matrix_

utility::vector1< utility::vector1< core::Real > > protocols::simple_filters::ResidueDepthFilter::GUIP_matrix_

private

Referenced by get_simscore(), and read_GUIP_matrix().

◆ GUIP_matrix_file_

std::string protocols::simple_filters::ResidueDepthFilter::GUIP_matrix_file_

private

Referenced by initialize().

◆ maxdist_

core::Real protocols::simple_filters::ResidueDepthFilter::maxdist_

private

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

◆ mindist_

core::Real protocols::simple_filters::ResidueDepthFilter::mindist_

private

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

◆ ncandidate1_

core::Size protocols::simple_filters::ResidueDepthFilter::ncandidate1_

private

Referenced by get_SDE_score(), and initialize().

◆ ncandidate2_

core::Size protocols::simple_filters::ResidueDepthFilter::ncandidate2_

private

Referenced by get_SDE_score(), and initialize().

◆ pdbid_

utility::vector1< std::string > protocols::simple_filters::ResidueDepthFilter::pdbid_

private

Referenced by get_residue_similarity(), and read_db().

◆ RDC_

ResidueDepthCalculator protocols::simple_filters::ResidueDepthFilter::RDC_

private

Referenced by get_residue_depth(), get_scdepth_avrg(), get_scdepth_fvar(), get_scdepth_sdev(), get_SDE_score(), initialize(), make_context(), parse_my_tag(), set_niter(), and set_report_crd().

◆ similarity_mode_

std::string protocols::simple_filters::ResidueDepthFilter::similarity_mode_

private

Referenced by get_residue_similarity(), and initialize().

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

src/protocols/simple_filters/ResidueDepthFilter.hh
src/protocols/simple_filters/ResidueDepthFilter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ResidueDepthFilter()

◆ ~ResidueDepthFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compare_by_superposition()

◆ fill_GUIP()

◆ fill_neighs()

◆ fresh_instance()

◆ get_n8()

◆ get_residue_depth()

◆ get_residue_similarity()

◆ get_scdepth_avrg()

◆ get_scdepth_fvar()

◆ get_scdepth_sdev()

◆ get_SDE_score()

◆ get_simscore()

◆ initialize()

◆ make_context()

◆ make_context_ref()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ read_db()

◆ read_GUIP_matrix()

◆ search_close_frags()

◆ set_niter()

◆ set_report_crd()

Member Data Documentation

◆ db_

◆ dbfile_

◆ evalres_

◆ frag_db_

◆ gamma_

◆ GUIP_matrix_

◆ GUIP_matrix_file_

◆ maxdist_

◆ mindist_

◆ ncandidate1_

◆ ncandidate2_

◆ pdbid_

◆ RDC_

◆ similarity_mode_