Architect that creates a beta sheet. More...

#include <BetaSheetArchitect.hh>

Inheritance diagram for protocols::denovo_design::architects::BetaSheetArchitect:

Public Types
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 utility::vector1 < components::StructureDataCOP >	StructureDataCOPs

typedef utility::vector1 < StrandArchitectOP >	StrandArchitectOPs

typedef std::pair< std::string, core::Size >	StrandExtension

typedef std::map< std::string, core::Size >	StrandExtensionsMap

typedef components::StrandOrientation	StrandOrientation

typedef components::StrandOrientations	StrandOrientations

typedef components::RegisterShift	RegisterShift

typedef components::RegisterShifts	RegisterShifts

typedef core::select::residue_selector::ResidueVector	ResidueVector

typedef std::vector < components::StrandPairingCOP >	PairingsInfo

typedef std::vector< PairingsInfo >	PairingsInfoVector

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

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

	~BetaSheetArchitect () 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

Lengths	retrieve_lengths (components::StructureData const &perm) const
	given a permutation, returns Lengths More...

StrandOrientations	retrieve_orientations (components::StructureData const &perm) const
	given a permutation, returns Orientations More...

RegisterShifts	retrieve_register_shifts (components::StructureData const &perm) const
	given a permutation, returns register shifts More...

void	set_strand_extensions (std::string const &extensions_str)
	Informs the SheetArchitect that another architect will enlongate one of the strands using a string as input. More...

void	add_strand_extension (std::string const &strand_name, core::Size const length)
	Informs the SheetArchitect that another architect will enlongate one of the strands. More...

void	clear_all_strand_data ()
	Clears the lists of strands/orientations/register shifts. More...

void	add_strand (StrandArchitect const &strand)
	Adds a strand to the sheet definition. More...

void	set_sheet_db_path (std::string const &sheet_db_path)
	Sets the path to the sheet database. More...

void	enumerate_permutations ()
	generates and stores a vector of permutations based on strands More...

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 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
StructureDataOP	combine_permutations (components::StructureDataCOPs const &chain) const
	merges a list of permutations More...

void	combine_permutations_rec (components::StructureDataCOPs const &chain, utility::vector1< components::StructureDataCOPs > const &plist)
	combines the given set of permutations with the current set More...

void	modify_and_add_permutation (StructureData const &perm)
	modifies/stores data into a permutation and adds it More...

void	check_permutation (StructureData const &perm) const
	checks permutations More...

core::Size	extension_length (std::string const &strand) const
	gets the length that a given strand will be elongated by using a different architect More...

void	needs_update ()

void	store_sheet_idx (StructureData &sd, core::Size const sheet_idx) const

void	add_register_shifts (std::string const &val)
	set allowed register shifts from a string More...

void	add_orientations (std::string const &orientations_str)

components::StructureDataCOPs	filter_permutations (components::StructureDataCOPs const &perms) const

components::StructureDataCOPs	add_pairings (components::StructureDataCOPs const &perms) const

Private Attributes
StructureDataCOPs	permutations_

StrandArchitectOPs	strands_

utility::vector1 < StrandOrientations >	orientations_

utility::vector1< RegisterShifts >	shifts_

StrandExtensionsMap	extensions_

components::SheetDBOP	sheetdb_

bool	use_sheetdb_

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 sheet.

Member Typedef Documentation

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

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

typedef std::vector< components::StrandPairingCOP > protocols::denovo_design::architects::BetaSheetArchitect::PairingsInfo

typedef std::vector< PairingsInfo > protocols::denovo_design::architects::BetaSheetArchitect::PairingsInfoVector

typedef components::RegisterShift protocols::denovo_design::architects::BetaSheetArchitect::RegisterShift

typedef components::RegisterShifts protocols::denovo_design::architects::BetaSheetArchitect::RegisterShifts

typedef core::select::residue_selector::ResidueVector protocols::denovo_design::architects::BetaSheetArchitect::ResidueVector

typedef utility::vector1< StrandArchitectOP > protocols::denovo_design::architects::BetaSheetArchitect::StrandArchitectOPs

typedef std::pair< std::string, core::Size > protocols::denovo_design::architects::BetaSheetArchitect::StrandExtension

typedef std::map< std::string, core::Size > protocols::denovo_design::architects::BetaSheetArchitect::StrandExtensionsMap

typedef components::StrandOrientation protocols::denovo_design::architects::BetaSheetArchitect::StrandOrientation

typedef components::StrandOrientations protocols::denovo_design::architects::BetaSheetArchitect::StrandOrientations

typedef protocols::denovo_design::components::StructureData protocols::denovo_design::architects::BetaSheetArchitect::StructureData

typedef utility::vector1< components::StructureDataCOP > protocols::denovo_design::architects::BetaSheetArchitect::StructureDataCOPs

typedef protocols::denovo_design::components::StructureDataOP protocols::denovo_design::architects::BetaSheetArchitect::StructureDataOP

Constructor & Destructor Documentation

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

protocols::denovo_design::architects::BetaSheetArchitect::~BetaSheetArchitect ( )

overridedefault

Member Function Documentation

void protocols::denovo_design::architects::BetaSheetArchitect::add_orientations ( std::string const & orientations_str )

private

References protocols::denovo_design::components::DOWN, orientations_, protocols::TR(), and protocols::denovo_design::components::UP.

Referenced by parse_tag().

components::StructureDataCOPs protocols::denovo_design::architects::BetaSheetArchitect::add_pairings ( components::StructureDataCOPs const & perms ) const

private

References protocols::denovo_design::architects::fill_orientation_info(), orientations_, core::scoring::pair, shifts_, strands_, and protocols::TR().

Referenced by enumerate_permutations().

void protocols::denovo_design::architects::BetaSheetArchitect::add_register_shifts ( std::string const & val )

private

set allowed register shifts from a string

References core::sequence::end, shifts_, protocols::loops::start, and protocols::TR().

Referenced by parse_tag().

void protocols::denovo_design::architects::BetaSheetArchitect::add_strand ( StrandArchitect const & strand )

Adds a strand to the sheet definition.

References needs_update(), and strands_.

Referenced by parse_tag().

void protocols::denovo_design::architects::BetaSheetArchitect::add_strand_extension	(	std::string const &	strand_name,
		core::Size const	length
	)

Informs the SheetArchitect that another architect will enlongate one of the strands.

References extensions_.

Referenced by set_strand_extensions().

void protocols::denovo_design::architects::BetaSheetArchitect::check_permutation ( components::StructureData const & perm_noextend ) const

private

checks permutations

checks whether the given permutation forms a valid sheet

Exceptions

EXCN_PreFilterFailed if something goes wrong

Referenced by filter_permutations().

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

inlinestatic

Referenced by protocols::denovo_design::architects::BetaSheetArchitectCreator::keyname(), provide_xml_schema(), retrieve_orientations(), and type().

void protocols::denovo_design::architects::BetaSheetArchitect::clear_all_strand_data ( )

Clears the lists of strands/orientations/register shifts.

References orientations_, shifts_, and strands_.

Referenced by parse_tag().

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

overridevirtual

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

components::StructureDataOP protocols::denovo_design::architects::BetaSheetArchitect::combine_permutations ( components::StructureDataCOPs const & chain ) const

private

merges a list of permutations

References strands_.

Referenced by combine_permutations_rec().

void protocols::denovo_design::architects::BetaSheetArchitect::combine_permutations_rec	(	components::StructureDataCOPs const &	chain,
		utility::vector1< components::StructureDataCOPs > const &	plist
	)

private

combines the given set of permutations with the current set

References combine_permutations(), permutations_, and protocols::TR().

Referenced by enumerate_permutations().

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

overridevirtual

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

References protocols::denovo_design::extract_int(), permutations_, protocols::TR(), type(), and updated_.

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

generates and stores a vector of permutations based on strands

References add_pairings(), combine_permutations_rec(), core::kinematics::distance(), filter_permutations(), modify_and_add_permutation(), orientations_, permutations_, shifts_, strands_, protocols::TR(), and updated_.

Referenced by parse_tag().

core::Size protocols::denovo_design::architects::BetaSheetArchitect::extension_length ( std::string const & strand ) const

private

gets the length that a given strand will be elongated by using a different architect

looks up and returns extension length for a strand

References extensions_.

components::StructureDataCOPs protocols::denovo_design::architects::BetaSheetArchitect::filter_permutations ( components::StructureDataCOPs const & perms ) const

private

References check_permutation(), and protocols::TR().

Referenced by enumerate_permutations().

void protocols::denovo_design::architects::BetaSheetArchitect::modify_and_add_permutation ( components::StructureData const & perm )

private

modifies/stores data into a permutation and adds it

References permutations_, protocols::denovo_design::components::StructureData::pose_length(), retrieve_lengths(), retrieve_orientations(), retrieve_register_shifts(), sheetdb_, protocols::loops::start, store_sheet_idx(), protocols::loops::loop_closure::ccd::strand, strands_, protocols::TR(), and use_sheetdb_.

Referenced by enumerate_permutations().

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

private

References updated_.

Referenced by add_strand().

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

overrideprotectedvirtual

Configuration by XML.

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

References add_orientations(), add_register_shifts(), add_strand(), clear_all_strand_data(), enumerate_permutations(), protocols::denovo_design::architects::StructureArchitect::id(), protocols::denovo_design::architects::StructureArchitect::parse_my_tag(), set_sheet_db_path(), set_strand_extensions(), protocols::TR(), protocols::denovo_design::architects::StrandArchitect::type(), and updated_.

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

static

References protocols::denovo_design::architects::DeNovoArchitect::add_common_denovo_architect_attributes(), class_name(), protocols::denovo_design::architects::DeNovoArchitectFactory::complex_type_name_for_architect(), and protocols::denovo_design::architects::StrandArchitect::provide_xml_schema().

Referenced by protocols::denovo_design::architects::BetaSheetArchitectCreator::provide_xml_schema().

Lengths protocols::denovo_design::architects::BetaSheetArchitect::retrieve_lengths ( components::StructureData const & perm ) const

given a permutation, returns Lengths

References protocols::denovo_design::components::StructureData::segment(), protocols::loops::loop_closure::ccd::strand, and strands_.

Referenced by check_permutation(), and modify_and_add_permutation().

BetaSheetArchitect::StrandOrientations protocols::denovo_design::architects::BetaSheetArchitect::retrieve_orientations ( components::StructureData const & perm ) const

given a permutation, returns Orientations

References class_name(), protocols::denovo_design::components::StructureData::pairings_begin(), protocols::denovo_design::components::StructureData::pairings_end(), protocols::denovo_design::components::SegmentPairing::STRAND, and strands_.

Referenced by check_permutation(), and modify_and_add_permutation().

BetaSheetArchitect::RegisterShifts protocols::denovo_design::architects::BetaSheetArchitect::retrieve_register_shifts ( components::StructureData const & perm ) const

given a permutation, returns register shifts

References core::pack::dunbrack::c, core::scoring::pair, protocols::denovo_design::components::StructureData::pairing(), and strands_.

Referenced by check_permutation(), and modify_and_add_permutation().

void protocols::denovo_design::architects::BetaSheetArchitect::set_sheet_db_path ( std::string const & sheet_db_path )

Sets the path to the sheet database.

References sheetdb_, and use_sheetdb_.

Referenced by parse_tag().

void protocols::denovo_design::architects::BetaSheetArchitect::set_strand_extensions ( std::string const & extensions_str )

Informs the SheetArchitect that another architect will enlongate one of the strands using a string as input.

References add_strand_extension().

Referenced by parse_tag().

void protocols::denovo_design::architects::BetaSheetArchitect::store_sheet_idx	(	StructureData &	sd,
		core::Size const	sheet_idx
	)		const

private

References protocols::denovo_design::components::StructureData::set_data_int().

Referenced by modify_and_add_permutation().

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

overridevirtual

simply returns the name of this type of architect

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

References class_name().

Referenced by design().

Member Data Documentation

StrandExtensionsMap protocols::denovo_design::architects::BetaSheetArchitect::extensions_

private

Referenced by add_strand_extension(), check_permutation(), and extension_length().

utility::vector1< StrandOrientations > protocols::denovo_design::architects::BetaSheetArchitect::orientations_

private

Referenced by add_orientations(), add_pairings(), clear_all_strand_data(), and enumerate_permutations().

StructureDataCOPs protocols::denovo_design::architects::BetaSheetArchitect::permutations_

private

Referenced by combine_permutations_rec(), design(), enumerate_permutations(), and modify_and_add_permutation().

components::SheetDBOP protocols::denovo_design::architects::BetaSheetArchitect::sheetdb_

private

Referenced by check_permutation(), modify_and_add_permutation(), and set_sheet_db_path().

utility::vector1< RegisterShifts > protocols::denovo_design::architects::BetaSheetArchitect::shifts_

private

Referenced by add_pairings(), add_register_shifts(), clear_all_strand_data(), and enumerate_permutations().

StrandArchitectOPs protocols::denovo_design::architects::BetaSheetArchitect::strands_

private

Referenced by add_pairings(), add_strand(), check_permutation(), clear_all_strand_data(), combine_permutations(), enumerate_permutations(), modify_and_add_permutation(), retrieve_lengths(), retrieve_orientations(), and retrieve_register_shifts().

bool protocols::denovo_design::architects::BetaSheetArchitect::updated_

private

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

bool protocols::denovo_design::architects::BetaSheetArchitect::use_sheetdb_

private

Referenced by check_permutation(), modify_and_add_permutation(), and set_sheet_db_path().

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

src/protocols/denovo_design/architects/BetaSheetArchitect.hh
src/protocols/denovo_design/architects/BetaSheetArchitect.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