protocols::denovo_design::components::StrandPairing Class Reference

#include <SegmentPairing.hh>

Inheritance diagram for protocols::denovo_design::components::StrandPairing:

Public Member Functions
	StrandPairing ()
	StrandPairing (SegmentName const &s1, SegmentName const &s2, StrandOrientation const &orient1, StrandOrientation const &orient2, RegisterShift const &shift)
	~StrandPairing () override
SegmentPairingOP	clone () const override
PairingType	type () const override
std::string	pairing_string (StructureData const &sd) const override
bool	parallel () const
StrandOrientation	orient1 () const
StrandOrientation	orient2 () const
RegisterShift	shift () const
void	set_orient1 (StrandOrientation const orient)
	Sets the orientation for the first strand; used to determine whether the strands are parallel or antiparallel. More...
void	set_orient2 (StrandOrientation const orient)
	Sets the orientation for the second strand; used to determine whether the strands are parallel or antiparallel. More...
void	set_shift (RegisterShift const shift)
	Sets the register shift. More...
Public Member Functions inherited from protocols::denovo_design::components::SegmentPairing
	SegmentPairing ()
	SegmentPairing (SegmentNames const &paired_segments)
	~SegmentPairing () override
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	class_name ()
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
Static Public Member Functions inherited from protocols::denovo_design::components::SegmentPairing
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...

Protected Member Functions
void	parse_tag (utility::tag::Tag const &tag) override
void	to_xml (utility::tag::Tag &tag) const override

Private Member Functions
RegisterShift	nobu_register_shift (StructureData const &sd, protocols::fldsgn::topology::Strand const &s1, protocols::fldsgn::topology::Strand const &s2, RegisterShift const nc_order_shift, StrandOrientation const &nc_order_orient) const

Private Attributes
StrandOrientation	orient1_
StrandOrientation	orient2_
RegisterShift	shift_

Additional Inherited Members
Public Types inherited from protocols::denovo_design::components::SegmentPairing
enum	PairingType { HELIX = 1, STRAND = 2, HELIX_SHEET = 3, UNKNOWN }
Static Public Attributes inherited from protocols::denovo_design::components::SegmentPairing
static std::string	TAG_NAME = "Pairing"
Static Protected Member Functions inherited from protocols::denovo_design::components::SegmentPairing
static void	add_common_xml_elements (utility::tag::XMLSchemaDefinition &xsd, std::string const &class_name, std::string const &description, utility::tag::AttributeList &attlist)

Constructor & Destructor Documentation

protocols::denovo_design::components::StrandPairing::StrandPairing

(

)

protocols::denovo_design::components::StrandPairing::StrandPairing	(	SegmentName const &	s1,
		SegmentName const &	s2,
		StrandOrientation const &	orient1,
		StrandOrientation const &	orient2,
		RegisterShift const &	shift
	)

protocols::denovo_design::components::StrandPairing::~StrandPairing ( )

inlineoverride

Member Function Documentation

static std::string protocols::denovo_design::components::StrandPairing::class_name ( )

inlinestatic

Referenced by protocols::denovo_design::components::SegmentPairing::create(), protocols::denovo_design::architects::CompoundArchitect::define_pairing_group(), provide_xml_schema(), and protocols::denovo_design::components::SegmentPairing::type_to_str().

SegmentPairingOP protocols::denovo_design::components::StrandPairing::clone ( ) const

overridevirtual

Implements protocols::denovo_design::components::SegmentPairing.

RegisterShift protocols::denovo_design::components::StrandPairing::nobu_register_shift ( StructureData const &  sd, protocols::fldsgn::topology::Strand const &  s1, protocols::fldsgn::topology::Strand const &  s2, RegisterShift const  nc_order_shift, StrandOrientation const &  nc_order_orient  ) const

private

References protocols::denovo_design::components::StructureData::abego(), protocols::denovo_design::components::count_bulges(), protocols::denovo_design::components::DOWN, protocols::fldsgn::topology::SS_Base::length(), and protocols::denovo_design::components::UP.

Referenced by pairing_string().

StrandOrientation protocols::denovo_design::components::StrandPairing::orient1

(

)

const

References orient1_.

Referenced by protocols::denovo_design::components::add_paired_residues().

StrandOrientation protocols::denovo_design::components::StrandPairing::orient2

(

)

const

References orient2_.

Referenced by protocols::denovo_design::components::add_paired_residues().

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

overridevirtual

Implements protocols::denovo_design::components::SegmentPairing.

References nobu_register_shift(), orient1_, orient2_, parallel(), protocols::denovo_design::components::Segment::safe(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::SegmentPairing::segments(), shift_, and protocols::denovo_design::components::StructureData::ss().

bool protocols::denovo_design::components::StrandPairing::parallel

(

)

const

References orient1_, and orient2_.

Referenced by pairing_string().

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

overrideprotectedvirtual

Implements protocols::denovo_design::components::SegmentPairing.

References protocols::denovo_design::architects::StrandArchitect::int_to_orientation(), orient1_, orient2_, set_orient1(), set_orient2(), set_shift(), and shift_.

void protocols::denovo_design::components::StrandPairing::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References protocols::denovo_design::components::SegmentPairing::add_common_xml_elements(), and class_name().

Referenced by protocols::denovo_design::architects::CompoundArchitect::define_pairing_group().

void protocols::denovo_design::components::StrandPairing::set_orient1 ( StrandOrientation const  orient )

inline

Sets the orientation for the first strand; used to determine whether the strands are parallel or antiparallel.

References orient1_.

Referenced by parse_tag().

void protocols::denovo_design::components::StrandPairing::set_orient2 ( StrandOrientation const  orient )

inline

Sets the orientation for the second strand; used to determine whether the strands are parallel or antiparallel.

References orient2_.

Referenced by parse_tag().

void protocols::denovo_design::components::StrandPairing::set_shift ( RegisterShift const  shift )

inline

Sets the register shift.

References shift(), and shift_.

Referenced by parse_tag().

RegisterShift protocols::denovo_design::components::StrandPairing::shift

(

)

const

References shift_.

Referenced by protocols::denovo_design::components::add_paired_residues(), and set_shift().

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

overrideprotectedvirtual

Implements protocols::denovo_design::components::SegmentPairing.

References orient1_, orient2_, and shift_.

PairingType protocols::denovo_design::components::StrandPairing::type ( ) const

inlineoverridevirtual

Implements protocols::denovo_design::components::SegmentPairing.

References protocols::denovo_design::components::SegmentPairing::STRAND.

Member Data Documentation

StrandOrientation protocols::denovo_design::components::StrandPairing::orient1_

private

Referenced by orient1(), pairing_string(), parallel(), parse_tag(), set_orient1(), and to_xml().

StrandOrientation protocols::denovo_design::components::StrandPairing::orient2_

private

Referenced by orient2(), pairing_string(), parallel(), parse_tag(), set_orient2(), and to_xml().

RegisterShift protocols::denovo_design::components::StrandPairing::shift_

private

Referenced by pairing_string(), parse_tag(), set_shift(), shift(), and to_xml().

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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