protocols::fldsgn::filters::HelixPairingFilter Class Reference

#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 (Filter 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

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

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

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

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

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

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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter

(

)

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter

(

String const &

hf

)

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter

(

HelixPairings const &

hpairs

)

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter

(

HelixPairingFilter const &

rval

)

References hpairset_.

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

inlineoverride

Member Function Documentation

void protocols::fldsgn::filters::HelixPairingFilter::align_angle

(

Real const

align_angle_val

)

sets max alignment angle

References align_angle_.

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.

References protocols::fldsgn::topology::HelixPairing::align_angle(), align_angle_, bend_angle_, compute_helix_pairing_set(), protocols::fldsgn::topology::HelixPairing::cross_angle(), cross_angle_, protocols::fldsgn::topology::HelixPairing::dist(), dist_cutoff_, find_missing_helices(), protocols::fldsgn::topology::HelixPairing::h1(), protocols::fldsgn::topology::HelixPairing::h2(), helix_pairings(), secstruct(), core::pose::Pose::size(), and protocols::fldsgn::TR().

void protocols::fldsgn::filters::HelixPairingFilter::bend_angle

(

Real const

bend_angle_val

)

sets max helix bend

References bend_angle_.

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

static

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

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

inlineoverridevirtual

Implements protocols::filters::Filter.

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(), helix_pairings(), protocols::fldsgn::topology::HelixPairingSet::helix_pairings(), output_id_, output_type_, secstruct(), core::pose::Pose::size(), and protocols::fldsgn::TR().

Referenced by report_sm().

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().

void protocols::fldsgn::filters::HelixPairingFilter::cross_angle

(

Real const

cross_angle_val

)

sets max cross angle

References cross_angle_.

void protocols::fldsgn::filters::HelixPairingFilter::dist

(

Real const

dist_val

)

sets distance cutoff

References dist_cutoff_.

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().

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

inlineoverridevirtual

Implements protocols::filters::Filter.

void protocols::fldsgn::filters::HelixPairingFilter::helix_pairings

(

String const &

hpairs

)

References hpairset_.

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

void protocols::fldsgn::filters::HelixPairingFilter::helix_pairings

(

HelixPairings const &

hpairs

)

References hpairset_.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

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_.

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().

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().

void protocols::fldsgn::filters::HelixPairingFilter::secstruct

(

String const &

ss

)

References secstruct_.

Referenced by apply(), and compute().

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_.

Member Data Documentation

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

private

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

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

private

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

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

private

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

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

private

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

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

private

helix pairings

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

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

private

HelixPairing id for output.

Referenced by compute(), and parse_my_tag().

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

private

output type, dist or angle

Referenced by compute(), and parse_my_tag().

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().

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