Filter used in 'Principles for designing proteins with cavities formed by curved b-sheets' to control helix geometry. More...

#include <HelixBendFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::HelixBendFilter:

[legend]

Public Member Functions
	HelixBendFilter ()

	~HelixBendFilter () override

void	secstruct (std::string const &ss)
	set secondary structure More...

void	set_secstruct_from_bp (std::string const &bp_file_path)
	set secondary structure using a blueprint file More...

void	threshold (core::Real const r)
	minimum angle for filtering More...

void	helix_id (core::Size const r)
	Strand id number. More...

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

void	compute (core::pose::Pose const &pose) const
	computes filter value More...

core::Real	report_sm (core::pose::Pose const &pose) const override
	required for reporting score values More...

void	report (std::ostream &os, core::pose::Pose const &pose) const override
	allows printing data to a stream More...

std::string	name () const override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Filter in Rosetta Scripts) More...

protocols::filters::FilterOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::filters::FilterOP	clone () const override
	required in the context of the parser/scripting scheme More...

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
std::string	secstruct_

core::Real	threshold_

core::Size	helix_id_

bool	filter_status_

core::Real	filter_val_

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

Detailed Description

Filter used in 'Principles for designing proteins with cavities formed by curved b-sheets' to control helix geometry.

Constructor & Destructor Documentation

◆ HelixBendFilter()

protocols::fldsgn::filters::HelixBendFilter::HelixBendFilter ( )

◆ ~HelixBendFilter()

protocols::fldsgn::filters::HelixBendFilter::~HelixBendFilter ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

returns true if the structure passes the filter, false otherwise

Implements protocols::filters::Filter.

References compute(), filter_status_, secstruct_, core::pose::Pose::size(), and protocols::fldsgn::TR().

◆ class_name()

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

static

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

◆ clone()

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

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ compute()

void protocols::fldsgn::filters::HelixBendFilter::compute ( core::pose::Pose const & pose ) const

computes filter value

References core::conformation::Residue::atom(), protocols::simple_filters::dssp(), core::sequence::end, filter_status_, filter_val_, helix_id_, protocols::mean_field::min(), core::pose::Pose::residue(), secstruct_, threshold_, protocols::fldsgn::TR(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by apply(), and report_sm().

◆ fresh_instance()

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

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ helix_id()

void protocols::fldsgn::filters::HelixBendFilter::helix_id ( core::Size const r )

Strand id number.

References helix_id_.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::fldsgn::filters::HelixBendFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Filter in Rosetta Scripts)

Reimplemented from protocols::filters::Filter.

References helix_id_, secstruct(), set_secstruct_from_bp(), and threshold_.

◆ provide_xml_schema()

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

static

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

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

◆ report()

void protocols::fldsgn::filters::HelixBendFilter::report	(	std::ostream &	os,
		core::pose::Pose const &	pose
	)		const

overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

References filter_status_, filter_val_, threshold_, and protocols::fldsgn::TR().

◆ report_sm()

core::Real protocols::fldsgn::filters::HelixBendFilter::report_sm ( core::pose::Pose const & pose ) const

overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References compute(), filter_status_, filter_val_, threshold_, and protocols::fldsgn::TR().

◆ secstruct()

void protocols::fldsgn::filters::HelixBendFilter::secstruct ( std::string const & ss )

set secondary structure

References secstruct_.

Referenced by parse_my_tag(), and set_secstruct_from_bp().

◆ set_secstruct_from_bp()

void protocols::fldsgn::filters::HelixBendFilter::set_secstruct_from_bp ( std::string const & bp_file_path )

set secondary structure using a blueprint file

set secondary structure from blueprint

This triggers a read from disk; use with caution.

References protocols::parser::BluePrint::secstruct(), and secstruct().

Referenced by parse_my_tag().

◆ threshold()

void protocols::fldsgn::filters::HelixBendFilter::threshold ( core::Real const r )

minimum angle for filtering

References threshold_.

Member Data Documentation

◆ filter_status_

bool protocols::fldsgn::filters::HelixBendFilter::filter_status_

mutableprivate

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

◆ filter_val_

core::Real protocols::fldsgn::filters::HelixBendFilter::filter_val_

mutableprivate

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

◆ helix_id_

core::Size protocols::fldsgn::filters::HelixBendFilter::helix_id_

private

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

◆ secstruct_

std::string protocols::fldsgn::filters::HelixBendFilter::secstruct_

mutableprivate

Referenced by apply(), compute(), and secstruct().

◆ threshold_

core::Real protocols::fldsgn::filters::HelixBendFilter::threshold_

private

Referenced by compute(), parse_my_tag(), report(), report_sm(), and threshold().

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ HelixBendFilter()

◆ ~HelixBendFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ fresh_instance()

◆ helix_id()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ secstruct()

◆ set_secstruct_from_bp()

◆ threshold()

Member Data Documentation

◆ filter_status_

◆ filter_val_

◆ helix_id_

◆ secstruct_

◆ threshold_