#include <HelixPairingFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::HelixPairingFilter:

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::HelixPairing	HelixPairing

typedef protocols::fldsgn::topology::HelixPairings	HelixPairings

typedef protocols::fldsgn::topology::HelixPairingSet	HelixPairingSet

typedef protocols::fldsgn::topology::HelixPairingSetOP	HelixPairingSetOP

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Member Functions
	HelixPairingFilter ()

	HelixPairingFilter (String const &hf)

	HelixPairingFilter (HelixPairings const &hpairs)

	HelixPairingFilter (HelixPairingFilter const &rval)

	~HelixPairingFilter () override

FilterOP	clone () const override

FilterOP	fresh_instance () const override

void	helix_pairings (String const &hpairs)

void	helix_pairings (HelixPairings const &hpairs)

void	secstruct (String const &ss)

void	dist (Real const dist_val)
	sets distance cutoff More...

void	bend_angle (Real const bend_angle_val)
	sets max helix bend More...

void	cross_angle (Real const cross_angle_val)
	sets max cross angle More...

void	align_angle (Real const align_angle_val)
	sets max alignment angle 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
std::string	secstruct (core::pose::Pose const &pose) const
	returns secondary structure to be used for finding helices More...

topology::HelixPairingSet	compute_helix_pairing_set (core::pose::Pose const &pose) const
	Returns the Helix pairing set to filter based on. More...

std::set< core::Size >	find_missing_helices (topology::SS_Info2 const &ss_info, topology::HelixPairings const &hpairs) const
	Returns set of helix IDs that were not found in the pose. Set is empty if all helices are present. More...

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

Real	dist_cutoff_

Real	bend_angle_

Real	cross_angle_

Real	align_angle_

HelixPairingSetOP	hpairset_
	helix pairings More...

core::Size	output_id_
	HelixPairing id for output. More...

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

bool	use_dssp_
	if true, and secstruct_ is empty, DSSP will be used to determine secondary structure of 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::HelixPairingFilter::DataMap

◆ Filter

typedef protocols::filters::Filter protocols::fldsgn::filters::HelixPairingFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::fldsgn::filters::HelixPairingFilter::FilterOP

◆ HelixPairing

typedef protocols::fldsgn::topology::HelixPairing protocols::fldsgn::filters::HelixPairingFilter::HelixPairing

◆ HelixPairings

typedef protocols::fldsgn::topology::HelixPairings protocols::fldsgn::filters::HelixPairingFilter::HelixPairings

◆ HelixPairingSet

typedef protocols::fldsgn::topology::HelixPairingSet protocols::fldsgn::filters::HelixPairingFilter::HelixPairingSet

◆ HelixPairingSetOP

typedef protocols::fldsgn::topology::HelixPairingSetOP protocols::fldsgn::filters::HelixPairingFilter::HelixPairingSetOP

◆ Pose

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

◆ Real

typedef core::Real protocols::fldsgn::filters::HelixPairingFilter::Real

◆ Size

typedef core::Size protocols::fldsgn::filters::HelixPairingFilter::Size

◆ String

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

◆ Super

typedef protocols::filters::Filter protocols::fldsgn::filters::HelixPairingFilter::Super

◆ TagCOP

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

Constructor & Destructor Documentation

◆ HelixPairingFilter() [1/4]

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter ( )

◆ HelixPairingFilter() [2/4]

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter ( String const & hf )

◆ HelixPairingFilter() [3/4]

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter ( HelixPairings const & hpairs )

◆ HelixPairingFilter() [4/4]

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

References hpairset_.

◆ ~HelixPairingFilter()

protocols::fldsgn::filters::HelixPairingFilter::~HelixPairingFilter ( )

inlineoverride

Member Function Documentation

◆ align_angle()

void protocols::fldsgn::filters::HelixPairingFilter::align_angle ( Real const align_angle_val )

sets max alignment angle

References align_angle_.

◆ apply()

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

overridevirtual

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

Implements protocols::filters::Filter.

◆ bend_angle()

void protocols::fldsgn::filters::HelixPairingFilter::bend_angle ( Real const bend_angle_val )

sets max helix bend

References bend_angle_.

◆ class_name()

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

static

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

◆ clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ compute()

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

References protocols::fldsgn::topology::HelixPairingSet::calc_geometry(), compute_helix_pairing_set(), find_missing_helices(), protocols::fldsgn::topology::HelixPairingSet::helix_pairing(), protocols::fldsgn::topology::HelixPairingSet::helix_pairings(), helix_pairings(), output_id_, output_type_, secstruct(), core::pose::Pose::size(), and protocols::fldsgn::TR().

Referenced by report_sm().

◆ compute_helix_pairing_set()

topology::HelixPairingSet protocols::fldsgn::filters::HelixPairingFilter::compute_helix_pairing_set ( core::pose::Pose const & pose ) const

private

Returns the Helix pairing set to filter based on.

If hpairset_ is set, returns that. Otherwise, look up the pairing set using the StructureData cached in the pose

References hpairset_, and protocols::fldsgn::TR().

Referenced by apply(), and compute().

◆ cross_angle()

void protocols::fldsgn::filters::HelixPairingFilter::cross_angle ( Real const cross_angle_val )

sets max cross angle

References cross_angle_.

◆ dist()

void protocols::fldsgn::filters::HelixPairingFilter::dist ( Real const dist_val )

sets distance cutoff

References dist_cutoff_.

◆ find_missing_helices()

std::set< core::Size > protocols::fldsgn::filters::HelixPairingFilter::find_missing_helices	(	topology::SS_Info2 const &	ss_info,
		topology::HelixPairings const &	hpairs
	)		const

private

Returns set of helix IDs that were not found in the pose. Set is empty if all helices are present.

References protocols::antibody::h1, protocols::antibody::h2, and protocols::fldsgn::topology::SS_Info2::helices().

Referenced by apply(), and compute().

◆ fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ helix_pairings() [1/2]

void protocols::fldsgn::filters::HelixPairingFilter::helix_pairings ( HelixPairings const & hpairs )

References hpairset_.

◆ helix_pairings() [2/2]

void protocols::fldsgn::filters::HelixPairingFilter::helix_pairings ( String const & hpairs )

References hpairset_.

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

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

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

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References align_angle_, bend_angle_, cross_angle_, dist_cutoff_, helix_pairings(), output_id_, output_type_, secstruct_, protocols::fldsgn::TR(), and use_dssp_.

◆ provide_xml_schema()

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

static

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

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

◆ report_sm()

HelixPairingFilter::Real protocols::fldsgn::filters::HelixPairingFilter::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() [1/2]

std::string protocols::fldsgn::filters::HelixPairingFilter::secstruct ( core::pose::Pose const & pose ) const

private

returns secondary structure to be used for finding helices

If secstruct_ is set, returns that. If use_dssp_ is true, returns secstruct from DSSP Otherwise, returns the pose.secstruct()

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

◆ secstruct() [2/2]

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

References secstruct_.

Referenced by apply(), and compute().

Member Data Documentation

◆ align_angle_

Real protocols::fldsgn::filters::HelixPairingFilter::align_angle_

private

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

◆ bend_angle_

Real protocols::fldsgn::filters::HelixPairingFilter::bend_angle_

private

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

◆ cross_angle_

Real protocols::fldsgn::filters::HelixPairingFilter::cross_angle_

private

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

◆ dist_cutoff_

Real protocols::fldsgn::filters::HelixPairingFilter::dist_cutoff_

private

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

◆ hpairset_

HelixPairingSetOP protocols::fldsgn::filters::HelixPairingFilter::hpairset_

private

helix pairings

Referenced by compute_helix_pairing_set(), helix_pairings(), and HelixPairingFilter().

◆ output_id_

core::Size protocols::fldsgn::filters::HelixPairingFilter::output_id_

private

HelixPairing id for output.

Referenced by compute(), and parse_my_tag().

◆ output_type_

String protocols::fldsgn::filters::HelixPairingFilter::output_type_

private

output type, dist or angle

Referenced by compute(), and parse_my_tag().

◆ secstruct_

String protocols::fldsgn::filters::HelixPairingFilter::secstruct_

private

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

Referenced by parse_my_tag(), and secstruct().

◆ use_dssp_

bool protocols::fldsgn::filters::HelixPairingFilter::use_dssp_

private

if true, and secstruct_ is empty, DSSP will be used to determine secondary structure of the pose

Referenced by parse_my_tag(), and secstruct().

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

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

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ DataMap

◆ Filter

◆ FilterOP

◆ HelixPairing

◆ HelixPairings

◆ HelixPairingSet

◆ HelixPairingSetOP

◆ Pose

◆ Real

◆ Size

◆ String

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ HelixPairingFilter() [1/4]

◆ HelixPairingFilter() [2/4]

◆ HelixPairingFilter() [3/4]

◆ HelixPairingFilter() [4/4]

◆ ~HelixPairingFilter()

Member Function Documentation

◆ align_angle()

◆ apply()

◆ bend_angle()

◆ class_name()

◆ clone()

◆ compute()

◆ compute_helix_pairing_set()

◆ cross_angle()

◆ dist()

◆ find_missing_helices()

◆ fresh_instance()

◆ helix_pairings() [1/2]

◆ helix_pairings() [2/2]

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report_sm()

◆ secstruct() [1/2]

◆ secstruct() [2/2]

Member Data Documentation

◆ align_angle_

◆ bend_angle_

◆ cross_angle_

◆ dist_cutoff_

◆ hpairset_

◆ output_id_

◆ output_type_

◆ secstruct_

◆ use_dssp_