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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:
Inheritance graph
[legend]

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< 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)
 
void add_strand_extension (std::string const &strand_name, core::Size const length)
 
- 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

void setup_strand_pairings ()
 
void add_strand (StrandArchitect const &strand)
 
void enumerate_permutations ()
 generates and stores a vector of permutations based on strands More...
 
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
 looks up and returns extension length for a strand 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< 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

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

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 
)

References extensions_.

Referenced by set_strand_extensions().

void protocols::denovo_design::architects::BetaSheetArchitect::check_permutation ( components::StructureData const &  perm_noextend) const
private
static std::string protocols::denovo_design::architects::BetaSheetArchitect::class_name ( )
inlinestatic
BetaSheetArchitect::DeNovoArchitectOP protocols::denovo_design::architects::BetaSheetArchitect::clone ( ) const
overridevirtual
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
void protocols::denovo_design::architects::BetaSheetArchitect::enumerate_permutations ( )
private
core::Size protocols::denovo_design::architects::BetaSheetArchitect::extension_length ( std::string const &  strand) const
private

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
void protocols::denovo_design::architects::BetaSheetArchitect::modify_and_add_permutation ( components::StructureData const &  perm)
private
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
void protocols::denovo_design::architects::BetaSheetArchitect::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
Lengths protocols::denovo_design::architects::BetaSheetArchitect::retrieve_lengths ( components::StructureData const &  perm) const
BetaSheetArchitect::StrandOrientations protocols::denovo_design::architects::BetaSheetArchitect::retrieve_orientations ( components::StructureData const &  perm) const
BetaSheetArchitect::RegisterShifts protocols::denovo_design::architects::BetaSheetArchitect::retrieve_register_shifts ( components::StructureData const &  perm) const
void protocols::denovo_design::architects::BetaSheetArchitect::set_strand_extensions ( std::string const &  extensions_str)

References add_strand_extension().

Referenced by parse_tag().

void protocols::denovo_design::architects::BetaSheetArchitect::setup_strand_pairings ( )
private
void protocols::denovo_design::architects::BetaSheetArchitect::store_sheet_idx ( StructureData sd,
core::Size const  sheet_idx 
) const
private
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
utility::vector1< StrandOrientations > protocols::denovo_design::architects::BetaSheetArchitect::orientations_
private
StructureDataCOPs protocols::denovo_design::architects::BetaSheetArchitect::permutations_
private
components::SheetDBOP protocols::denovo_design::architects::BetaSheetArchitect::sheetdb_
private
utility::vector1< RegisterShifts > protocols::denovo_design::architects::BetaSheetArchitect::shifts_
private
StrandArchitectOPs protocols::denovo_design::architects::BetaSheetArchitect::strands_
private
bool protocols::denovo_design::architects::BetaSheetArchitect::updated_
private
bool protocols::denovo_design::architects::BetaSheetArchitect::use_sheetdb_
private

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