protocols::denovo_design::architects::BlueprintArchitect Class Reference

Designs a structure using a Blueprint file. More...

#include <BlueprintArchitect.hh>

Inheritance diagram for protocols::denovo_design::architects::BlueprintArchitect:

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

Public Member Functions
	BlueprintArchitect (std::string const &id_value)
	~BlueprintArchitect () 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
void	set_blueprint (protocols::parser::BluePrint const &bp)
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	set_template_segments (StructureData &sd, core::pose::Pose const &pose) const
	add templated segments from pose. These are designated by a residue number in the blueprint instead of 0 More...
SegmentNames	get_template_segments (StructureData const &sd) const
	gets names of templated segments from pose. These are designated by a residue number in the blueprint instead of 0. All residues in the segment must be sequential and not built denovo More...
void	set_helix_pairings (StructureData &sd) const
	Adds helix pairings to the given SD using the HHPAIR line of the blueprint. More...
void	get_helix_pairings (std::string const &hhpair_str, core::Size &h1, core::Size &h2, char &orientation) const
	Converts HHPAIR data in the blueprint into usable information. More...

Private Attributes
protocols::parser::BluePrintCOP	blueprint_

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

Detailed Description

Designs a structure using a Blueprint file.

Member Typedef Documentation

typedef components::StructureData protocols::denovo_design::architects::BlueprintArchitect::StructureData

Constructor & Destructor Documentation

protocols::denovo_design::architects::BlueprintArchitect::BlueprintArchitect

(

std::string const &

id_value

)

protocols::denovo_design::architects::BlueprintArchitect::~BlueprintArchitect ( )

overridedefault

Member Function Documentation

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

inlinestatic

Referenced by get_template_segments(), protocols::denovo_design::architects::BlueprintArchitectCreator::keyname(), provide_xml_schema(), and type().

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

overridevirtual

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

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

overridevirtual

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

References protocols::denovo_design::abego_str(), protocols::denovo_design::components::add_segments_for_chain(), blueprint_, set_helix_pairings(), and set_template_segments().

void protocols::denovo_design::architects::BlueprintArchitect::get_helix_pairings ( std::string const &  hhpair_str, core::Size &  h1, core::Size &  h2, char &  orientation  ) const

private

Converts HHPAIR data in the blueprint into usable information.

Parameters

[in]	hhpair_str	Blueprint HHPAIR string
[out]	h1	Helix number (N–>C ordering) for first paired helix
[out]	h2	Helix number (N–>C ordering) for first paired helix
[out]	orientation	Orientation of the helices (P or A)

References protocols::denovo_design::architects::invalid_hhpair().

Referenced by set_helix_pairings().

SegmentNames protocols::denovo_design::architects::BlueprintArchitect::get_template_segments ( StructureData const &  sd ) const

private

gets names of templated segments from pose. These are designated by a residue number in the blueprint instead of 0. All residues in the segment must be sequential and not built denovo

Parameters

[in]

sd

StructureData to be scanned

Returns

SegmentNameSet of segments with templates

References blueprint_, class_name(), protocols::denovo_design::components::Segment::length(), protocols::denovo_design::components::Segment::lower(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_begin(), protocols::denovo_design::components::StructureData::segments_end(), and protocols::denovo_design::components::Segment::upper().

Referenced by set_template_segments().

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

overrideprotectedvirtual

Configuration by XML.

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

References set_blueprint().

void protocols::denovo_design::architects::BlueprintArchitect::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::BlueprintArchitectCreator::provide_xml_schema().

void protocols::denovo_design::architects::BlueprintArchitect::set_blueprint

(

protocols::parser::BluePrint const &

bp

)

References blueprint_.

Referenced by parse_tag().

void protocols::denovo_design::architects::BlueprintArchitect::set_helix_pairings ( StructureData &  sd ) const

private

Adds helix pairings to the given SD using the HHPAIR line of the blueprint.

Parameters

[in,out]

sd

StructureData object to be modified

References blueprint_, get_helix_pairings(), protocols::antibody::h1, protocols::antibody::h2, and protocols::TR().

Referenced by design().

void protocols::denovo_design::architects::BlueprintArchitect::set_template_segments ( StructureData &  sd, core::pose::Pose const &  pose  ) const

private

add templated segments from pose. These are designated by a residue number in the blueprint instead of 0

Parameters

[in,out]	sd	StructureData to be modified
[in]	pose	Pose containing template residues

References blueprint_, get_template_segments(), protocols::denovo_design::components::Segment::lower(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::set_template_pose(), protocols::TR(), and protocols::denovo_design::components::Segment::upper().

Referenced by design().

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

overridevirtual

simply returns the name of this type of architect

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

References class_name().

Member Data Documentation

protocols::parser::BluePrintCOP protocols::denovo_design::architects::BlueprintArchitect::blueprint_

private

Referenced by design(), get_template_segments(), set_blueprint(), set_helix_pairings(), and set_template_segments().

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

• src/protocols/denovo_design/architects/BlueprintArchitect.hh
• src/protocols/denovo_design/architects/BlueprintArchitect.cc