Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::denovo_design::architects::StrandArchitect Class Reference

Architect that creates a beta strand. More...

#include <StrandArchitect.hh>

Inheritance diagram for protocols::denovo_design::architects::StrandArchitect:
Inheritance graph
[legend]

Public Types

typedef std::set< core::SizeLengthSet
 
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

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
StrandArchitect::DeNovoArchitectOP protocols::denovo_design::architects::StrandArchitect::clone ( ) const
overridevirtual
components::StructureDataCOPs protocols::denovo_design::architects::StrandArchitect::compute_permutations ( ) const
private
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]bulgesList of bulge positions to place onto the strand
[in]secstructSecondary structure for the new segment
[in]abegoAbego 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
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
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
void protocols::denovo_design::architects::StrandArchitect::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
StrandBulges protocols::denovo_design::architects::StrandArchitect::retrieve_bulges ( StructureData const &  sd) const
StrandBulges protocols::denovo_design::architects::StrandArchitect::retrieve_bulges_s ( StructureData const &  sd,
std::string const &  segment_id 
)
static
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
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
Lengths protocols::denovo_design::architects::StrandArchitect::lengths_
private

Referenced by compute_permutations(), and set_length().

components::StructureDataCOPs protocols::denovo_design::architects::StrandArchitect::motifs_
private
bool protocols::denovo_design::architects::StrandArchitect::updated_
private

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