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protocols::denovo_design::architects::BetaSheetArchitect Class Reference

Architect that creates a beta sheet. More...

#include <BetaSheetArchitect.hh>

Inheritance diagram for protocols::denovo_design::architects::BetaSheetArchitect:
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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::StructureDataCOPStructureDataCOPs
 
typedef utility::vector1< StrandArchitectOPStrandArchitectOPs
 
typedef std::pair< std::string, core::SizeStrandExtension
 
typedef std::map< std::string, core::SizeStrandExtensionsMap
 
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::StrandPairingCOPPairingsInfo
 
typedef std::vector< PairingsInfoPairingsInfoVector
 
- 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< StrandOrientationsorientations_
 
utility::vector1< RegisterShiftsshifts_
 
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

◆ DeNovoArchitect

◆ DeNovoArchitectOP

◆ PairingsInfo

◆ PairingsInfoVector

◆ RegisterShift

◆ RegisterShifts

◆ ResidueVector

◆ StrandArchitectOPs

◆ StrandExtension

◆ StrandExtensionsMap

◆ StrandOrientation

◆ StrandOrientations

◆ StructureData

◆ StructureDataCOPs

◆ StructureDataOP

Constructor & Destructor Documentation

◆ BetaSheetArchitect()

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

◆ ~BetaSheetArchitect()

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

Member Function Documentation

◆ add_orientations()

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

◆ add_pairings()

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

◆ add_register_shifts()

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, protocols::TR(), and protocols::hybridization::val.

Referenced by parse_tag().

◆ add_strand()

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

Adds a strand to the sheet definition.

References needs_update(), protocols::loops::loop_closure::ccd::strand, and strands_.

Referenced by parse_tag().

◆ add_strand_extension()

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().

◆ check_permutation()

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

◆ class_name()

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

◆ clear_all_strand_data()

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().

◆ clone()

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

◆ combine_permutations()

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().

◆ 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().

◆ design()

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

◆ enumerate_permutations()

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

◆ extension_length()

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_, and protocols::loops::loop_closure::ccd::strand.

◆ filter_permutations()

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

◆ modify_and_add_permutation()

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

◆ needs_update()

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

References updated_.

Referenced by add_strand().

◆ parse_tag()

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

◆ provide_xml_schema()

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

◆ retrieve_lengths()

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

◆ retrieve_orientations()

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

◆ retrieve_register_shifts()

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

◆ set_sheet_db_path()

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().

◆ set_strand_extensions()

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().

◆ store_sheet_idx()

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

◆ type()

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

◆ extensions_

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

◆ orientations_

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

◆ permutations_

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

◆ sheetdb_

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

◆ shifts_

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

◆ strands_

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

◆ updated_

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

◆ use_sheetdb_

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

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