#include <HSSTripletFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::HSSTripletFilter:

Public Types
typedef protocols::filters::Filter	Super

typedef protocols::filters::Filter	Filter

typedef std::string	String

typedef core::Real	Real

typedef core::Size	Size

typedef protocols::filters::FilterOP	FilterOP

typedef core::pose::Pose	Pose

typedef protocols::fldsgn::topology::SS_Info2	SS_Info2

typedef protocols::fldsgn::topology::HSSTriplet	HSSTriplet

typedef protocols::fldsgn::topology::HSSTriplets	HSSTriplets

typedef protocols::fldsgn::topology::HSSTripletSet	HSSTripletSet

typedef protocols::fldsgn::topology::HSSTripletSetOP	HSSTripletSetOP

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Member Functions
	HSSTripletFilter ()
	default constructor More...

	HSSTripletFilter (HSSTriplets const &hss3s)
	constructor with arguments More...

	HSSTripletFilter (String const &hss3s)
	constructor with arguments More...

	HSSTripletFilter (HSSTripletFilter const &rval)
	copy constructor – required because we clone the hss3set_ pointer More...

	~HSSTripletFilter () override

FilterOP	clone () const override

FilterOP	fresh_instance () const override

void	add_hsstriplets (String const &hss3s)
	add filtered HSSTriplets from string More...

void	add_hsstriplets (HSSTriplets const &hss3s)

void	secstruct (String const &ss)

void	filter_min_dist (Real const r)

void	filter_max_dist (Real const r)
	maximum distance for filtering More...

void	filter_min_angle (Real const r)
	miniimum angle for filtering More...

void	filter_max_angle (Real const r)
	maximum angle for filtering More...

void	output_id (core::Size const i)
	set output id More...

void	output_type (String const &s)
	set output type More...

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

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

Real	compute (Pose const &pose) const

bool	apply (Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. 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
String	get_secstruct (Pose const &pose) const
	computes and returns secondary structure string to use for this filter. More...

HSSTriplets	get_hss3s (Pose const &pose) const
	returns HSSTriplets object to use for this filter More...

bool	check_elements (HSSTriplet const &hss, SS_Info2 const &ss_info) const
	checks secondary structure elements in the triplet, returns false if invalid More...

Real	compute_dist (HSSTriplet const &hss) const
	given an HSS triplet, compute the distance from helix to sheet More...

Real	compute_angle (Real const angle) const
	given an hs-angle, return a valid angle accounting for ignore_helix_direction_ if ignore_helix_direction_ is true, this basically makes angle periodic from -90 to 90 More...

Private Attributes
HSSTripletSetOP	hss3set_
	hsstriplet More...

String	secstruct_
	if value is empty, dssp will run for ss definition ( default is emptry ) More...

Real	filter_min_dist_
	filtered min distance between helix and sheet More...

Real	filter_max_dist_
	filtered max distance between helix and sheet More...

Real	filter_min_angle_
	filtered min angle between helix and sheet More...

Real	filter_max_angle_
	filtered max angle between helix and sheet More...

core::Size	output_id_
	output id of HSSTriplet More...

String	output_type_
	output type, dist or angle More...

bool	ignore_helix_direction_
	if set, the filter will ignore the direction of the helix and return an angle between -90 and 90 instead of -180 and 180 More...

bool	use_dssp_
	if set, and secstruct_ is empty, secondary structure will be determined by dssp. Otherwise, it will be taken from the pose. More...

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

Member Typedef Documentation

◆ DataMap

typedef basic::datacache::DataMap protocols::fldsgn::filters::HSSTripletFilter::DataMap

◆ Filter

typedef protocols::filters::Filter protocols::fldsgn::filters::HSSTripletFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::fldsgn::filters::HSSTripletFilter::FilterOP

◆ HSSTriplet

typedef protocols::fldsgn::topology::HSSTriplet protocols::fldsgn::filters::HSSTripletFilter::HSSTriplet

◆ HSSTriplets

typedef protocols::fldsgn::topology::HSSTriplets protocols::fldsgn::filters::HSSTripletFilter::HSSTriplets

◆ HSSTripletSet

typedef protocols::fldsgn::topology::HSSTripletSet protocols::fldsgn::filters::HSSTripletFilter::HSSTripletSet

◆ HSSTripletSetOP

typedef protocols::fldsgn::topology::HSSTripletSetOP protocols::fldsgn::filters::HSSTripletFilter::HSSTripletSetOP

◆ Pose

typedef core::pose::Pose protocols::fldsgn::filters::HSSTripletFilter::Pose

◆ Real

typedef core::Real protocols::fldsgn::filters::HSSTripletFilter::Real

◆ Size

typedef core::Size protocols::fldsgn::filters::HSSTripletFilter::Size

◆ SS_Info2

typedef protocols::fldsgn::topology::SS_Info2 protocols::fldsgn::filters::HSSTripletFilter::SS_Info2

◆ String

typedef std::string protocols::fldsgn::filters::HSSTripletFilter::String

◆ Super

typedef protocols::filters::Filter protocols::fldsgn::filters::HSSTripletFilter::Super

◆ TagCOP

typedef utility::tag::TagCOP protocols::fldsgn::filters::HSSTripletFilter::TagCOP

Constructor & Destructor Documentation

◆ HSSTripletFilter() [1/4]

protocols::fldsgn::filters::HSSTripletFilter::HSSTripletFilter ( )

default constructor

◆ HSSTripletFilter() [2/4]

protocols::fldsgn::filters::HSSTripletFilter::HSSTripletFilter ( HSSTriplets const & hss3s )

constructor with arguments

◆ HSSTripletFilter() [3/4]

protocols::fldsgn::filters::HSSTripletFilter::HSSTripletFilter ( String const & hss3s )

constructor with arguments

◆ HSSTripletFilter() [4/4]

protocols::fldsgn::filters::HSSTripletFilter::HSSTripletFilter ( HSSTripletFilter const & rval )

copy constructor – required because we clone the hss3set_ pointer

References hss3set_.

◆ ~HSSTripletFilter()

protocols::fldsgn::filters::HSSTripletFilter::~HSSTripletFilter ( )

inlineoverride

Member Function Documentation

◆ add_hsstriplets() [1/2]

void protocols::fldsgn::filters::HSSTripletFilter::add_hsstriplets ( HSSTriplets const & hss3s )

References hss3set_.

◆ add_hsstriplets() [2/2]

void protocols::fldsgn::filters::HSSTripletFilter::add_hsstriplets ( String const & hss3s )

add filtered HSSTriplets from string

set filtered HSSTriplets from string

References protocols::fldsgn::topology::HSSTripletSet::hss_triplets().

Referenced by parse_my_tag().

◆ apply()

bool protocols::fldsgn::filters::HSSTripletFilter::apply ( Pose const & pose ) const

overridevirtual

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

Implements protocols::filters::Filter.

References protocols::fldsgn::topology::HSSTriplet::calc_geometry(), check_elements(), compute_angle(), compute_dist(), filter_max_angle_, filter_max_dist_, filter_min_dist_, get_hss3s(), get_secstruct(), protocols::fldsgn::topology::HSSTriplet::hs1_dist(), protocols::fldsgn::topology::HSSTriplet::hs2_dist(), protocols::fldsgn::topology::HSSTriplet::hs_angle(), secstruct(), core::pose::Pose::size(), and protocols::fldsgn::TR().

◆ check_elements()

bool protocols::fldsgn::filters::HSSTripletFilter::check_elements	(	topology::HSSTriplet const &	hss,
		topology::SS_Info2 const &	ss_info
	)		const

private

checks secondary structure elements in the triplet, returns false if invalid

If the pose doesn't contain the helix or strands, returns false If the length of the helix is < 5, returns false If the length of either strand is < 2, returns false

References protocols::fldsgn::topology::SS_Info2::helices(), protocols::fldsgn::topology::HSSTriplet::helix(), protocols::fldsgn::topology::HSSTriplet::strand1(), protocols::fldsgn::topology::HSSTriplet::strand2(), protocols::fldsgn::topology::SS_Info2::strands(), and protocols::fldsgn::TR().

Referenced by apply(), and compute().

◆ class_name()

std::string protocols::fldsgn::filters::HSSTripletFilter::class_name ( )

static

Referenced by protocols::fldsgn::filters::HSSTripletFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

FilterOP protocols::fldsgn::filters::HSSTripletFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ compute()

HSSTripletFilter::Real protocols::fldsgn::filters::HSSTripletFilter::compute ( Pose const & pose ) const

References protocols::fldsgn::topology::HSSTriplet::calc_geometry(), check_elements(), compute_angle(), get_hss3s(), get_secstruct(), protocols::fldsgn::topology::HSSTriplet::hs_angle(), protocols::fldsgn::topology::HSSTriplet::hsheet_dist(), output_id_, output_type_, secstruct(), core::pose::Pose::size(), and protocols::fldsgn::TR().

Referenced by report_sm().

◆ compute_angle()

HSSTripletFilter::Real protocols::fldsgn::filters::HSSTripletFilter::compute_angle ( core::Real const angle ) const

private

given an hs-angle, return a valid angle accounting for ignore_helix_direction_ if ignore_helix_direction_ is true, this basically makes angle periodic from -90 to 90

References ignore_helix_direction_.

Referenced by apply(), and compute().

◆ compute_dist()

HSSTripletFilter::Real protocols::fldsgn::filters::HSSTripletFilter::compute_dist ( HSSTriplet const & hss ) const

private

given an HSS triplet, compute the distance from helix to sheet

References protocols::fldsgn::topology::HSSTriplet::hs1_dist(), and protocols::fldsgn::topology::HSSTriplet::hs2_dist().

Referenced by apply().

◆ filter_max_angle()

void protocols::fldsgn::filters::HSSTripletFilter::filter_max_angle ( Real const r )

maximum angle for filtering

References filter_max_angle_.

◆ filter_max_dist()

void protocols::fldsgn::filters::HSSTripletFilter::filter_max_dist ( Real const r )

maximum distance for filtering

References filter_max_dist_.

◆ filter_min_angle()

void protocols::fldsgn::filters::HSSTripletFilter::filter_min_angle ( Real const r )

miniimum angle for filtering

References filter_min_angle_.

◆ filter_min_dist()

void protocols::fldsgn::filters::HSSTripletFilter::filter_min_dist ( Real const r )

References filter_min_dist_.

◆ fresh_instance()

FilterOP protocols::fldsgn::filters::HSSTripletFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ get_hss3s()

HSSTripletFilter::HSSTriplets protocols::fldsgn::filters::HSSTripletFilter::get_hss3s ( Pose const & pose ) const

private

returns HSSTriplets object to use for this filter

if hss triplets are given prior to apply time, returns those otherwise, look for HSS info in the pose's StructureData and return that

References protocols::denovo_design::components::StructureDataFactory::get_from_const_pose(), hss3set_, protocols::fldsgn::topology::HSSTripletSet::hss_triplets(), and protocols::fldsgn::TR().

Referenced by apply(), and compute().

◆ get_secstruct()

HSSTripletFilter::String protocols::fldsgn::filters::HSSTripletFilter::get_secstruct ( Pose const & pose ) const

private

computes and returns secondary structure string to use for this filter.

if secstruct_ is non-empty, returns that if use_dssp_ is true, use DSSP to compute secstruct otherwise, use secstruct stored in the pose

References protocols::simple_filters::dssp(), core::pose::Pose::secstruct(), secstruct_, and use_dssp_.

Referenced by apply(), and compute().

◆ name()

std::string protocols::fldsgn::filters::HSSTripletFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ output_id()

void protocols::fldsgn::filters::HSSTripletFilter::output_id ( core::Size const i )

set output id

maximum angle for filtering

References output_id_.

◆ output_type()

void protocols::fldsgn::filters::HSSTripletFilter::output_type ( String const & s )

set output type

References output_type_.

◆ parse_my_tag()

void protocols::fldsgn::filters::HSSTripletFilter::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References add_hsstriplets(), filter_max_angle_, filter_max_dist_, filter_min_angle_, filter_min_dist_, hss3set_, ignore_helix_direction_, output_id_, output_type_, secstruct_, protocols::fldsgn::TR(), and use_dssp_.

◆ provide_xml_schema()

void protocols::fldsgn::filters::HSSTripletFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::fldsgn::filters::HSSTripletFilterCreator::provide_xml_schema().

◆ report_sm()

HSSTripletFilter::Real protocols::fldsgn::filters::HSSTripletFilter::report_sm ( Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

◆ secstruct()

void protocols::fldsgn::filters::HSSTripletFilter::secstruct ( String const & ss )

References secstruct_.

Referenced by apply(), and compute().

Member Data Documentation

◆ filter_max_angle_

Real protocols::fldsgn::filters::HSSTripletFilter::filter_max_angle_

private

filtered max angle between helix and sheet

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

◆ filter_max_dist_

Real protocols::fldsgn::filters::HSSTripletFilter::filter_max_dist_

private

filtered max distance between helix and sheet

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

◆ filter_min_angle_

Real protocols::fldsgn::filters::HSSTripletFilter::filter_min_angle_

private

filtered min angle between helix and sheet

Referenced by filter_min_angle(), and parse_my_tag().

◆ filter_min_dist_

Real protocols::fldsgn::filters::HSSTripletFilter::filter_min_dist_

private

filtered min distance between helix and sheet

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

◆ hss3set_

HSSTripletSetOP protocols::fldsgn::filters::HSSTripletFilter::hss3set_

private

hsstriplet

Referenced by add_hsstriplets(), get_hss3s(), HSSTripletFilter(), and parse_my_tag().

◆ ignore_helix_direction_

bool protocols::fldsgn::filters::HSSTripletFilter::ignore_helix_direction_

private

if set, the filter will ignore the direction of the helix and return an angle between -90 and 90 instead of -180 and 180

Referenced by compute_angle(), and parse_my_tag().

◆ output_id_

core::Size protocols::fldsgn::filters::HSSTripletFilter::output_id_

private

output id of HSSTriplet

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

◆ output_type_

String protocols::fldsgn::filters::HSSTripletFilter::output_type_

private

output type, dist or angle

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

◆ secstruct_

String protocols::fldsgn::filters::HSSTripletFilter::secstruct_

private

if value is empty, dssp will run for ss definition ( default is emptry )

Referenced by get_secstruct(), parse_my_tag(), and secstruct().

◆ use_dssp_

bool protocols::fldsgn::filters::HSSTripletFilter::use_dssp_

private

if set, and secstruct_ is empty, secondary structure will be determined by dssp. Otherwise, it will be taken from the pose.

Referenced by get_secstruct(), and parse_my_tag().

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

src/protocols/fldsgn/filters/HSSTripletFilter.hh
src/protocols/fldsgn/filters/HSSTripletFilter.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ DataMap

◆ Filter

◆ FilterOP

◆ HSSTriplet

◆ HSSTriplets

◆ HSSTripletSet

◆ HSSTripletSetOP

◆ Pose

◆ Real

◆ Size

◆ SS_Info2

◆ String

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ HSSTripletFilter() [1/4]

◆ HSSTripletFilter() [2/4]

◆ HSSTripletFilter() [3/4]

◆ HSSTripletFilter() [4/4]

◆ ~HSSTripletFilter()

Member Function Documentation

◆ add_hsstriplets() [1/2]

◆ add_hsstriplets() [2/2]

◆ apply()

◆ check_elements()

◆ class_name()

◆ clone()

◆ compute()

◆ compute_angle()

◆ compute_dist()

◆ filter_max_angle()

◆ filter_max_dist()

◆ filter_min_angle()

◆ filter_min_dist()

◆ fresh_instance()

◆ get_hss3s()

◆ get_secstruct()

◆ name()

◆ output_id()

◆ output_type()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report_sm()

◆ secstruct()

Member Data Documentation

◆ filter_max_angle_

◆ filter_max_dist_

◆ filter_min_angle_

◆ filter_min_dist_

◆ hss3set_

◆ ignore_helix_direction_

◆ output_id_

◆ output_type_

◆ secstruct_

◆ use_dssp_