#include <HelixKinkFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::HelixKinkFilter:

Public Types
typedef protocols::filters::Filter	Super

typedef protocols::filters::Filter	Filter

typedef protocols::filters::FilterOP	FilterOP

typedef std::string	String

typedef core::Real	Real

typedef core::Size	Size

typedef core::pose::Pose	Pose

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Member Functions
	HelixKinkFilter ()

	~HelixKinkFilter () override

FilterOP	clone () const override

FilterOP	fresh_instance () const override

void	set_bend_angle (Real const bend_angle)
	Set the helix bend angle. More...

void	set_secstruct (String const &secstruct)
	Set the secondary structure string. More...

void	set_resnums (String const &resnums="")
	Set the resnums (comma-separated string to be evaluated) More...

void	set_helix_range (core::Size const helix_start, core::Size const helix_end)
	Set helix_start_, helix_end_, and select_range_. More...

void	set_select_range (bool const select_range)
	Set select_range_. More...

Real	get_bend_angle () const
	Get the helix bend angle. More...

String	get_secstruct () const
	Get the secondary structure string. More...

String	get_string_resnums () const
	Get the resnum string. More...

bool	get_select_resnums () const
	Get select_resnums_. More...

core::Size	get_helix_start () const
	Get helix_start_. More...

core::Size	get_helix_end () const
	Get helix_end_. More...

bool	get_select_range () const
	Get select_range_. More...

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

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 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 Attributes
Real	bend_angle_

String	secstruct_

String	string_resnums_

bool	select_resnums_

bool	select_range_

core::Size	helix_start_

core::Size	helix_end_

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

Member Typedef Documentation

◆ DataMap

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

◆ Filter

typedef protocols::filters::Filter protocols::fldsgn::filters::HelixKinkFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::fldsgn::filters::HelixKinkFilter::FilterOP

◆ Pose

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

◆ Real

typedef core::Real protocols::fldsgn::filters::HelixKinkFilter::Real

◆ Size

typedef core::Size protocols::fldsgn::filters::HelixKinkFilter::Size

◆ String

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

◆ Super

typedef protocols::filters::Filter protocols::fldsgn::filters::HelixKinkFilter::Super

◆ TagCOP

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

Constructor & Destructor Documentation

◆ HelixKinkFilter()

protocols::fldsgn::filters::HelixKinkFilter::HelixKinkFilter ( )

◆ ~HelixKinkFilter()

protocols::fldsgn::filters::HelixKinkFilter::~HelixKinkFilter ( )

inlineoverride

Member Function Documentation

◆ apply()

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

overridevirtual

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

Implements protocols::filters::Filter.

References bend_angle_, core::pose::Pose::chain(), protocols::fldsgn::topology::check_kink_helix(), core::scoring::Energies::data(), core::sequence::end, core::pose::Pose::energies(), core::pose::get_resnum_list_ordered(), core::scoring::EnergiesCacheableDataType::HBOND_SET, helix_end_, helix_start_, core::conformation::Residue::is_lower_terminus(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), secstruct_, select_range_, select_resnums_, core::pose::Pose::size(), string_resnums_, and protocols::fldsgn::TR().

◆ class_name()

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

static

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

◆ clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ get_bend_angle()

core::Real protocols::fldsgn::filters::HelixKinkFilter::get_bend_angle ( ) const

Get the helix bend angle.

References bend_angle_.

◆ get_helix_end()

core::Size protocols::fldsgn::filters::HelixKinkFilter::get_helix_end ( ) const

Get helix_end_.

References helix_end_.

◆ get_helix_start()

core::Size protocols::fldsgn::filters::HelixKinkFilter::get_helix_start ( ) const

Get helix_start_.

References helix_start_.

◆ get_secstruct()

std::string protocols::fldsgn::filters::HelixKinkFilter::get_secstruct ( ) const

Get the secondary structure string.

References secstruct_.

◆ get_select_range()

bool protocols::fldsgn::filters::HelixKinkFilter::get_select_range ( ) const

Get select_range_.

References select_range_.

◆ get_select_resnums()

bool protocols::fldsgn::filters::HelixKinkFilter::get_select_resnums ( ) const

Get select_resnums_.

References select_resnums_.

◆ get_string_resnums()

std::string protocols::fldsgn::filters::HelixKinkFilter::get_string_resnums ( ) const

Get the resnum string.

References string_resnums_.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

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

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References bend_angle_, protocols::parser::BluePrint::secstruct(), secstruct_, select_range_, select_resnums_, set_helix_range(), and set_resnums().

◆ provide_xml_schema()

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

static

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

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

◆ set_bend_angle()

void protocols::fldsgn::filters::HelixKinkFilter::set_bend_angle ( Real const bend_angle )

Set the helix bend angle.

References bend_angle_.

◆ set_helix_range()

void protocols::fldsgn::filters::HelixKinkFilter::set_helix_range	(	core::Size const	helix_start,
		core::Size const	helix_end
	)

Set helix_start_, helix_end_, and select_range_.

This function sets helix_start_, helix_end_, and sets select_range_ to true

References helix_end_, helix_start_, select_range_, and protocols::fldsgn::TR().

Referenced by parse_my_tag().

◆ set_resnums()

void protocols::fldsgn::filters::HelixKinkFilter::set_resnums ( String const & resnums = "" )

Set the resnums (comma-separated string to be evaluated)

This function sets string_resnums_ and select_resnums_. select_resnums_ will be set to arguments' value. If an empty string is passed (default), select_resnums_ will be set to false. Otherwise, select_resnums_ will be set to true.

References select_resnums_, string_resnums_, and protocols::fldsgn::TR().

Referenced by parse_my_tag().

◆ set_secstruct()

void protocols::fldsgn::filters::HelixKinkFilter::set_secstruct ( String const & secstruct )

Set the secondary structure string.

References secstruct_.

◆ set_select_range()

void protocols::fldsgn::filters::HelixKinkFilter::set_select_range ( bool const select_range )

Set select_range_.

References select_range_.

Member Data Documentation

◆ bend_angle_

Real protocols::fldsgn::filters::HelixKinkFilter::bend_angle_

private

Referenced by apply(), get_bend_angle(), parse_my_tag(), and set_bend_angle().

◆ helix_end_

core::Size protocols::fldsgn::filters::HelixKinkFilter::helix_end_

private

Referenced by apply(), get_helix_end(), and set_helix_range().

◆ helix_start_

core::Size protocols::fldsgn::filters::HelixKinkFilter::helix_start_

private

Referenced by apply(), get_helix_start(), and set_helix_range().

◆ secstruct_

String protocols::fldsgn::filters::HelixKinkFilter::secstruct_

private

Referenced by apply(), get_secstruct(), parse_my_tag(), and set_secstruct().

◆ select_range_

bool protocols::fldsgn::filters::HelixKinkFilter::select_range_

private

Referenced by apply(), get_select_range(), parse_my_tag(), set_helix_range(), and set_select_range().

◆ select_resnums_

bool protocols::fldsgn::filters::HelixKinkFilter::select_resnums_

private

Referenced by apply(), get_select_resnums(), parse_my_tag(), and set_resnums().

◆ string_resnums_

String protocols::fldsgn::filters::HelixKinkFilter::string_resnums_

private

Referenced by apply(), get_string_resnums(), and set_resnums().

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

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

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ Size

◆ String

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ HelixKinkFilter()

◆ ~HelixKinkFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ fresh_instance()

◆ get_bend_angle()

◆ get_helix_end()

◆ get_helix_start()

◆ get_secstruct()

◆ get_select_range()

◆ get_select_resnums()

◆ get_string_resnums()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_bend_angle()

◆ set_helix_range()

◆ set_resnums()

◆ set_secstruct()

◆ set_select_range()

Member Data Documentation

◆ bend_angle_

◆ helix_end_

◆ helix_start_

◆ secstruct_

◆ select_range_

◆ select_resnums_

◆ string_resnums_