Architect that creates a beta strand. More...

#include <StrandArchitect.hh>

Inheritance diagram for protocols::denovo_design::architects::StrandArchitect:

Public Types
typedef std::set< core::Size >	LengthSet

typedef protocols::denovo_design::architects::DeNovoArchitect	DeNovoArchitect

typedef protocols::denovo_design::architects::DeNovoArchitectOP	DeNovoArchitectOP

typedef protocols::denovo_design::components::StructureData	StructureData

typedef protocols::denovo_design::components::StructureDataOP	StructureDataOP

typedef components::RegisterShift	RegisterShift

typedef components::RegisterShifts	RegisterShifts

typedef components::StrandOrientation	StrandOrientation

typedef components::StrandOrientations	StrandOrientations

Public Types inherited from protocols::denovo_design::architects::DeNovoArchitect
typedef components::StructureDataOP	StructureDataOP

Public Member Functions
	StrandArchitect (std::string const &id_value)

	~StrandArchitect () override

std::string	type () const override
	simply returns the name of this type of architect More...

DeNovoArchitectOP	clone () const override

StructureDataOP	design (core::pose::Pose const &pose, core::Real &random) const override

components::StructureDataCOPs::const_iterator	motifs_begin () const

components::StructureDataCOPs::const_iterator	motifs_end () const

void	set_length (std::string const &length_str)

void	set_length (Lengths const &lengths_val)

void	set_bulges (std::string const &bulges_str)

void	set_bulges (AllowedStrandBulges const &bulges)

void	set_extended (std::string const &extended_str)

void	set_extended (AllowedStrandExtended const &extended)

void	enumerate_permutations ()

StrandBulges	retrieve_bulges (StructureData const &sd) const

Public Member Functions inherited from protocols::denovo_design::architects::DeNovoArchitect
	DeNovoArchitect (std::string const &id)

	~DeNovoArchitect () override

components::StructureDataOP	apply (core::pose::Pose const &pose) const

Public Member Functions inherited from protocols::denovo_design::architects::StructureArchitect
	StructureArchitect (std::string const &id)

	~StructureArchitect () override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)

std::string const &	id () const

void	set_id (std::string const &new_id)

Static Public Member Functions
static std::string	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string const	bulge_keyname ()

static StrandOrientation	int_to_orientation (int const integer)

static StrandBulges	retrieve_bulges_s (StructureData const &sd, std::string const &segment_id)

Static Public Member Functions inherited from protocols::denovo_design::architects::DeNovoArchitect
static void	add_common_denovo_architect_attributes (utility::tag::AttributeList &attlist)

Static Public Member Functions inherited from protocols::denovo_design::architects::StructureArchitect
static void	attributes_for_parse_my_tag (utility::tag::AttributeList &attlist)

Protected Member Functions
void	parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Configuration by XML. More...

Private Member Functions
void	store_bulges (StructureData &sd, StrandBulges const &bulge) const

StructureDataOP	create_motif (StrandBulges const &bulges, StrandExtended const &extended, std::string const &secstruct, std::string const &abego) const
	Given a list of bulges, build a motif. More...

void	needs_update ()

void	check_updated () const
	If architect is updated, simply exit without error. If not, exit with an error message. More...

components::StructureDataCOPs	compute_permutations () const

Private Attributes
components::StructureDataCOPs	motifs_

Lengths	lengths_

AllowedStrandBulges	bulges_

AllowedStrandExtended	extended_

bool	updated_

Additional Inherited Members
Static Public Attributes inherited from protocols::denovo_design::architects::DeNovoArchitect
static std::string const	DATA_MAP_NAME = "DeNovoArchitects"

Detailed Description

Architect that creates a beta strand.

Member Typedef Documentation

typedef protocols::denovo_design::architects::DeNovoArchitect protocols::denovo_design::architects::StrandArchitect::DeNovoArchitect

typedef protocols::denovo_design::architects::DeNovoArchitectOP protocols::denovo_design::architects::StrandArchitect::DeNovoArchitectOP

typedef std::set< core::Size > protocols::denovo_design::architects::StrandArchitect::LengthSet

typedef components::RegisterShift protocols::denovo_design::architects::StrandArchitect::RegisterShift

typedef components::RegisterShifts protocols::denovo_design::architects::StrandArchitect::RegisterShifts

typedef components::StrandOrientation protocols::denovo_design::architects::StrandArchitect::StrandOrientation

typedef components::StrandOrientations protocols::denovo_design::architects::StrandArchitect::StrandOrientations

typedef protocols::denovo_design::components::StructureData protocols::denovo_design::architects::StrandArchitect::StructureData

typedef protocols::denovo_design::components::StructureDataOP protocols::denovo_design::architects::StrandArchitect::StructureDataOP

Constructor & Destructor Documentation

protocols::denovo_design::architects::StrandArchitect::StrandArchitect ( std::string const & id_value )

protocols::denovo_design::architects::StrandArchitect::~StrandArchitect ( )

overridedefault

Member Function Documentation

std::string const protocols::denovo_design::architects::StrandArchitect::bulge_keyname ( )

static

Referenced by retrieve_bulges_s(), and store_bulges().

void protocols::denovo_design::architects::StrandArchitect::check_updated ( ) const

private

If architect is updated, simply exit without error. If not, exit with an error message.

References updated_.

Referenced by design(), motifs_begin(), and motifs_end().

static std::string protocols::denovo_design::architects::StrandArchitect::class_name ( )

inlinestatic

Referenced by design(), int_to_orientation(), protocols::denovo_design::architects::StrandArchitectCreator::keyname(), provide_xml_schema(), and type().

StrandArchitect::DeNovoArchitectOP protocols::denovo_design::architects::StrandArchitect::clone ( ) const

overridevirtual

Implements protocols::denovo_design::architects::DeNovoArchitect.

components::StructureDataCOPs protocols::denovo_design::architects::StrandArchitect::compute_permutations ( ) const

private

References core::scoring::abego, bulges_, create_motif(), extended_, and lengths_.

Referenced by enumerate_permutations().

StrandArchitect::StructureDataOP protocols::denovo_design::architects::StrandArchitect::create_motif	(	StrandBulges const &	bulges,
		StrandExtended const &	extended,
		std::string const &	secstruct,
		std::string const &	abego
	)		const

private

Given a list of bulges, build a motif.

Parameters

[in]	bulges	List of bulge positions to place onto the strand
[in]	secstruct	Secondary structure for the new segment
[in]	abego	Abego for the new segment, without bulges placed

References core::scoring::abego, protocols::denovo_design::abego_str(), protocols::match::upstream::b, and store_bulges().

Referenced by compute_permutations().

StrandArchitect::StructureDataOP protocols::denovo_design::architects::StrandArchitect::design	(	core::pose::Pose const &	pose,
		core::Real &	random
	)		const

overridevirtual

Implements protocols::denovo_design::architects::DeNovoArchitect.

References check_updated(), class_name(), protocols::denovo_design::extract_int(), and motifs_.

void protocols::denovo_design::architects::StrandArchitect::enumerate_permutations ( )

References compute_permutations(), motifs_, and updated_.

Referenced by parse_tag().

StrandArchitect::StrandOrientation protocols::denovo_design::architects::StrandArchitect::int_to_orientation ( int const integer )

static

References class_name(), and protocols::denovo_design::components::ORIENTATIONS_END.

Referenced by protocols::denovo_design::components::StrandPairing::parse_tag().

components::StructureDataCOPs::const_iterator protocols::denovo_design::architects::StrandArchitect::motifs_begin ( ) const

References check_updated(), and motifs_.

components::StructureDataCOPs::const_iterator protocols::denovo_design::architects::StrandArchitect::motifs_end ( ) const

References check_updated(), and motifs_.

void protocols::denovo_design::architects::StrandArchitect::needs_update ( )

private

References updated_.

Referenced by set_bulges(), set_extended(), and set_length().

void protocols::denovo_design::architects::StrandArchitect::parse_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overrideprotectedvirtual

Configuration by XML.

Implements protocols::denovo_design::architects::DeNovoArchitect.

References enumerate_permutations(), set_bulges(), set_extended(), set_length(), and updated_.

void protocols::denovo_design::architects::StrandArchitect::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::denovo_design::architects::DeNovoArchitect::add_common_denovo_architect_attributes(), class_name(), and protocols::denovo_design::architects::DeNovoArchitectFactory::xsd_architect_type_definition_w_attributes().

Referenced by protocols::denovo_design::architects::StrandArchitectCreator::provide_xml_schema(), and protocols::denovo_design::architects::BetaSheetArchitect::provide_xml_schema().

StrandBulges protocols::denovo_design::architects::StrandArchitect::retrieve_bulges ( StructureData const & sd ) const

References retrieve_bulges_s().

Referenced by protocols::denovo_design::architects::bulge_residues().

StrandBulges protocols::denovo_design::architects::StrandArchitect::retrieve_bulges_s	(	StructureData const &	sd,
		std::string const &	segment_id
	)

static

References bulge_keyname(), and protocols::denovo_design::components::StructureData::get_data_str().

Referenced by retrieve_bulges().

void protocols::denovo_design::architects::StrandArchitect::set_bulges ( std::string const & bulges_str )

Referenced by parse_tag().

void protocols::denovo_design::architects::StrandArchitect::set_bulges ( AllowedStrandBulges const & bulges )

References bulges_, and needs_update().

void protocols::denovo_design::architects::StrandArchitect::set_extended ( std::string const & extended_str )

Referenced by parse_tag().

void protocols::denovo_design::architects::StrandArchitect::set_extended ( AllowedStrandExtended const & extended )

References extended_, and needs_update().

void protocols::denovo_design::architects::StrandArchitect::set_length ( std::string const & length_str )

Referenced by parse_tag().

void protocols::denovo_design::architects::StrandArchitect::set_length ( Lengths const & lengths_val )

References lengths_, and needs_update().

void protocols::denovo_design::architects::StrandArchitect::store_bulges	(	StructureData &	sd,
		StrandBulges const &	bulge
	)		const

private

References bulge_keyname(), and protocols::denovo_design::components::StructureData::set_data_str().

Referenced by create_motif().

std::string protocols::denovo_design::architects::StrandArchitect::type ( ) const

overridevirtual

simply returns the name of this type of architect

Implements protocols::denovo_design::architects::DeNovoArchitect.

References class_name().

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

Member Data Documentation

AllowedStrandBulges protocols::denovo_design::architects::StrandArchitect::bulges_

private

Referenced by compute_permutations(), and set_bulges().

AllowedStrandExtended protocols::denovo_design::architects::StrandArchitect::extended_

private

Referenced by compute_permutations(), and set_extended().

Lengths protocols::denovo_design::architects::StrandArchitect::lengths_

private

Referenced by compute_permutations(), and set_length().

components::StructureDataCOPs protocols::denovo_design::architects::StrandArchitect::motifs_

private

Referenced by design(), enumerate_permutations(), motifs_begin(), and motifs_end().

bool protocols::denovo_design::architects::StrandArchitect::updated_

private

Referenced by check_updated(), enumerate_permutations(), needs_update(), and parse_tag().

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

src/protocols/denovo_design/architects/StrandArchitect.hh
src/protocols/denovo_design/architects/StrandArchitect.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation