protocols::denovo_design::components::SegmentPairing Class Reference

#include <SegmentPairing.hh>

Inheritance diagram for protocols::denovo_design::components::SegmentPairing:

Public Types
enum	PairingType { HELIX = 1 , STRAND = 2 , HELIX_SHEET = 3 , UNKNOWN }

Public Member Functions
	SegmentPairing ()
	SegmentPairing (SegmentNames const &paired_segments)
	~SegmentPairing () override
virtual SegmentPairingOP	clone () const =0
virtual PairingType	type () const =0
virtual std::string	pairing_string (StructureData const &sd) const =0
void	parse_my_tag (utility::tag::Tag const &tag)
bool	has_segment (std::string const &segment) const
SegmentNames const &	segments () const
void	set_segments (std::string const &segments_str)
void	set_segments (SegmentNames const &segments)

Static Public Member Functions
static std::string	complex_type_name_for_pairing (std::string const &pairing_name)
static SegmentPairingOP	create (std::string const &type_name)
static std::string	get_strand_pairings (StructureData const &sd)
	Gets string for all strand pairings from a StructureData. More...
static std::string	get_helix_pairings (StructureData const &sd)
	Gets string for all helix pairings from a StructureData. More...
static std::string	get_hss_triplets (StructureData const &sd)
	Gets string for all helix-strand-strand triplets in a StructureData. More...
static ResiduePairs	get_strand_residue_pairs (StructureData const &sd)
	Gets pairs of residues involved in strand pairing. More...

Static Public Attributes
static std::string	TAG_NAME = "Pairing"

Protected Member Functions
virtual void	parse_tag (utility::tag::Tag const &tag)=0
virtual void	to_xml (utility::tag::Tag &tag) const =0

Static Protected Member Functions
static void	add_common_xml_elements (utility::tag::XMLSchemaDefinition &xsd, std::string const &class_name, std::string const &description, utility::tag::AttributeList &attlist)

Static Private Member Functions
static std::string	type_to_str (PairingType const &type)
static SegmentPairingCOPs	get_pairings (StructureData const &sd, PairingType const &type)
static std::string	get_pairing_str (StructureData const &sd, PairingType const &type)

Private Attributes
SegmentNames	segments_

Friends
std::ostream &	operator<< (std::ostream &os, SegmentPairing const &pairing)

Member Enumeration Documentation

PairingType

enum protocols::denovo_design::components::SegmentPairing::PairingType

Enumerator
HELIX
STRAND
HELIX_SHEET
UNKNOWN

Constructor & Destructor Documentation

SegmentPairing() [1/2]

protocols::denovo_design::components::SegmentPairing::SegmentPairing

(

)

SegmentPairing() [2/2]

protocols::denovo_design::components::SegmentPairing::SegmentPairing

(

SegmentNames const &

paired_segments

)

~SegmentPairing()

protocols::denovo_design::components::SegmentPairing::~SegmentPairing ( )

inlineoverride

Member Function Documentation

add_common_xml_elements()

void protocols::denovo_design::components::SegmentPairing::add_common_xml_elements ( utility::tag::XMLSchemaDefinition &  xsd, std::string const &  class_name, std::string const &  description, utility::tag::AttributeList &  attlist  )

staticprotected

References complex_type_name_for_pairing().

Referenced by protocols::denovo_design::components::HelixPairing::provide_xml_schema(), protocols::denovo_design::components::StrandPairing::provide_xml_schema(), and protocols::denovo_design::components::HelixSheetPairing::provide_xml_schema().

clone()

virtual SegmentPairingOP protocols::denovo_design::components::SegmentPairing::clone ( ) const

pure virtual

Implemented in protocols::denovo_design::components::HelixSheetPairing, protocols::denovo_design::components::StrandPairing, and protocols::denovo_design::components::HelixPairing.

complex_type_name_for_pairing()

std::string protocols::denovo_design::components::SegmentPairing::complex_type_name_for_pairing ( std::string const &  pairing_name )

static

Referenced by add_common_xml_elements(), and protocols::denovo_design::architects::CompoundArchitect::define_pairing_group().

create()

SegmentPairingOP protocols::denovo_design::components::SegmentPairing::create ( std::string const &  type_name )

static

References protocols::denovo_design::components::HelixPairing::class_name(), protocols::denovo_design::components::StrandPairing::class_name(), and protocols::denovo_design::components::HelixSheetPairing::class_name().

Referenced by protocols::denovo_design::architects::CompoundArchitect::parse_pairing_tag(), and protocols::denovo_design::components::StructureData::parse_subtag().

get_helix_pairings()

std::string protocols::denovo_design::components::SegmentPairing::get_helix_pairings ( StructureData const &  sd )

static

Gets string for all helix pairings from a StructureData.

References get_pairing_str(), and HELIX.

get_hss_triplets()

std::string protocols::denovo_design::components::SegmentPairing::get_hss_triplets ( StructureData const &  sd )

static

Gets string for all helix-strand-strand triplets in a StructureData.

References get_pairing_str(), and HELIX_SHEET.

get_pairing_str()

std::string protocols::denovo_design::components::SegmentPairing::get_pairing_str ( StructureData const &  sd, PairingType const &  type  )

staticprivate

References get_pairings(), and type().

Referenced by get_helix_pairings(), get_hss_triplets(), and get_strand_pairings().

get_pairings()

SegmentPairingCOPs protocols::denovo_design::components::SegmentPairing::get_pairings ( StructureData const &  sd, PairingType const &  type  )

staticprivate

References protocols::denovo_design::components::StructureData::pairings_begin(), protocols::denovo_design::components::StructureData::pairings_end(), and type().

Referenced by get_pairing_str(), and get_strand_residue_pairs().

get_strand_pairings()

std::string protocols::denovo_design::components::SegmentPairing::get_strand_pairings ( StructureData const &  sd )

static

Gets string for all strand pairings from a StructureData.

References get_pairing_str(), and STRAND.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::get_filtered_sheet_topology(), and protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::get_sheet_topology().

get_strand_residue_pairs()

ResiduePairs protocols::denovo_design::components::SegmentPairing::get_strand_residue_pairs ( StructureData const &  sd )

static

Gets pairs of residues involved in strand pairing.

References protocols::denovo_design::components::add_paired_residues(), get_pairings(), protocols::denovo_design::components::StructureData::ss(), and STRAND.

Referenced by protocols::denovo_design::architects::BetaSheetArchitect::check_permutation().

has_segment()

bool protocols::denovo_design::components::SegmentPairing::has_segment

(

std::string const &

segment

)

const

References segments_.

pairing_string()

virtual std::string protocols::denovo_design::components::SegmentPairing::pairing_string ( StructureData const &  sd ) const

pure virtual

Implemented in protocols::denovo_design::components::HelixSheetPairing, protocols::denovo_design::components::StrandPairing, and protocols::denovo_design::components::HelixPairing.

parse_my_tag()

void protocols::denovo_design::components::SegmentPairing::parse_my_tag

(

utility::tag::Tag const &

tag

)

References parse_tag(), and set_segments().

parse_tag()

virtual void protocols::denovo_design::components::SegmentPairing::parse_tag ( utility::tag::Tag const &  tag )

protectedpure virtual

Implemented in protocols::denovo_design::components::HelixSheetPairing, protocols::denovo_design::components::StrandPairing, and protocols::denovo_design::components::HelixPairing.

Referenced by parse_my_tag().

segments()

SegmentNames const & protocols::denovo_design::components::SegmentPairing::segments

(

)

const

References segments_.

Referenced by protocols::denovo_design::components::add_paired_residues(), protocols::denovo_design::components::HelixPairing::pairing_string(), protocols::denovo_design::components::StrandPairing::pairing_string(), protocols::denovo_design::components::HelixSheetPairing::pairing_string(), protocols::denovo_design::components::HelixPairing::parse_tag(), and set_segments().

set_segments() [1/2]

void protocols::denovo_design::components::SegmentPairing::set_segments

(

SegmentNames const &

segments

)

References segments(), and segments_.

set_segments() [2/2]

void protocols::denovo_design::components::SegmentPairing::set_segments

(

std::string const &

segments_str

)

References segments().

Referenced by parse_my_tag().

to_xml()

virtual void protocols::denovo_design::components::SegmentPairing::to_xml ( utility::tag::Tag &  tag ) const

protectedpure virtual

Implemented in protocols::denovo_design::components::HelixSheetPairing, protocols::denovo_design::components::StrandPairing, and protocols::denovo_design::components::HelixPairing.

type()

virtual PairingType protocols::denovo_design::components::SegmentPairing::type ( ) const

pure virtual

Implemented in protocols::denovo_design::components::HelixSheetPairing, protocols::denovo_design::components::StrandPairing, and protocols::denovo_design::components::HelixPairing.

Referenced by get_pairing_str(), get_pairings(), and type_to_str().

type_to_str()

std::string protocols::denovo_design::components::SegmentPairing::type_to_str ( PairingType const &  type )

staticprivate

References protocols::denovo_design::components::HelixPairing::class_name(), protocols::denovo_design::components::StrandPairing::class_name(), protocols::denovo_design::components::HelixSheetPairing::class_name(), HELIX, HELIX_SHEET, STRAND, and type().

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  os, SegmentPairing const &  pairing  )

friend

Member Data Documentation

segments_

SegmentNames protocols::denovo_design::components::SegmentPairing::segments_

private

Referenced by has_segment(), segments(), and set_segments().

TAG_NAME

std::string protocols::denovo_design::components::SegmentPairing::TAG_NAME = "Pairing"

static

Referenced by protocols::denovo_design::components::StructureData::parse_subtag().

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

• src/protocols/denovo_design/components/SegmentPairing.hh
• src/protocols/denovo_design/components/SegmentPairing.cc