TaskOperation that can be used to restrict AAs allowed at each position based on DSSP-assigned secondary structure. More...

#include <DsspDesignOperation.hh>

Inheritance diagram for protocols::task_operations::DsspDesignOperation:

[legend]

Public Types
typedef core::pack::task::operation::TaskOperation	parent

typedef core::pack::task::operation::TaskOperationOP	TaskOperationOP

typedef protocols::parser::BluePrint	BluePrint

typedef protocols::parser::BluePrintOP	BluePrintOP

typedef std::map< std::string, std::string >	SecStructResidues

typedef std::pair< std::string, std::string >	SecStruct

Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

typedef pose::Pose	Pose

Public Member Functions
	DsspDesignOperation ()
	default constructor More...

	DsspDesignOperation (DsspDesignOperation const &rval)
	copy constructor More...

	~DsspDesignOperation () override
	destructor More...

TaskOperationOP	clone () const override
	make clone More...

void	set_blueprint (BluePrintOP const bp)
	define secondary structure from a blueprint More...

void	set_restrictions_aa (std::string const &sse, std::string const &aas)
	define allowed residues for some SSE More...

void	set_restrictions_append (std::string const &sse, std::string const &aas)
	append allowed residues for some SSE More...

void	set_restrictions_exclude (std::string const &sse, std::string const &aas)
	exclude allowed residues for some SSE More...

void	parse_tag (TagCOP tag, DataMap &) override
	parse RosettaScripts XML More...

void	apply (Pose const &pose, core::pack::task::PackerTask &task) const override
	apply More...

Public Member Functions inherited from core::pack::task::operation::TaskOperation
	~TaskOperation () override

virtual bool	task_operation_provides_citation_info () const
	Does this task operation provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	task_operation_is_unpublished () const
	Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	keyname ()

Private Member Functions
void	set_default_sse_residues ()
	initialize allowed residue sets with defaults More...

utility::vector1< bool >	get_restrictions (std::string const &ss_type) const
	get the set of allowed residues for some secondary structure element More...

Private Attributes
SecStructResidues	sse_residues_
	map sets of allowed residues to secondary structure elements More...

BluePrintOP	blueprint_

std::string	pose_secstruct_

Friends
class	::DsspDesignOperationTests

Detailed Description

TaskOperation that can be used to restrict AAs allowed at each position based on DSSP-assigned secondary structure.

Member Typedef Documentation

typedef protocols::parser::BluePrint protocols::task_operations::DsspDesignOperation::BluePrint

typedef protocols::parser::BluePrintOP protocols::task_operations::DsspDesignOperation::BluePrintOP

typedef core::pack::task::operation::TaskOperation protocols::task_operations::DsspDesignOperation::parent

typedef std::pair< std::string, std::string > protocols::task_operations::DsspDesignOperation::SecStruct

typedef std::map< std::string, std::string > protocols::task_operations::DsspDesignOperation::SecStructResidues

typedef core::pack::task::operation::TaskOperationOP protocols::task_operations::DsspDesignOperation::TaskOperationOP

Constructor & Destructor Documentation

protocols::task_operations::DsspDesignOperation::DsspDesignOperation ( )

default constructor

protocols::task_operations::DsspDesignOperation::DsspDesignOperation ( DsspDesignOperation const & rval )

default

copy constructor

protocols::task_operations::DsspDesignOperation::~DsspDesignOperation ( )

overridedefault

destructor

Member Function Documentation

void protocols::task_operations::DsspDesignOperation::apply	(	Pose const &	pose,
		core::pack::task::PackerTask &	task
	)		const

overridevirtual

apply

Implements core::pack::task::operation::TaskOperation.

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), core::pose::symmetry::extract_asymmetric_unit(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::is_upper_terminus(), core::pack::task::PackerTask::nonconst_residue_task(), core::pose::Pose::residue(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pose::Pose::size(), and protocols::task_operations::TR().

TaskOperationOP protocols::task_operations::DsspDesignOperation::clone ( ) const

overridevirtual

make clone

Implements core::pack::task::operation::TaskOperation.

utility::vector1< bool > protocols::task_operations::DsspDesignOperation::get_restrictions ( std::string const & ss_type ) const

private

get the set of allowed residues for some secondary structure element

References core::chemical::aa_from_oneletter_code(), and core::chemical::num_canonical_aas.

static std::string protocols::task_operations::DsspDesignOperation::keyname ( )

inlinestatic

Referenced by protocols::task_operations::DsspDesignOperationCreator::keyname().

void protocols::task_operations::DsspDesignOperation::parse_tag	(	TagCOP	tag,
		DataMap &
	)

overridevirtual

parse RosettaScripts XML

Reimplemented from core::pack::task::operation::TaskOperation.

References protocols::task_operations::TR().

void protocols::task_operations::DsspDesignOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::operation::complex_type_name_for_task_op(), and protocols::task_operations::dsspdo_subelement_ct_name().

Referenced by protocols::task_operations::DsspDesignOperationCreator::provide_xml_schema().

void protocols::task_operations::DsspDesignOperation::set_blueprint ( BluePrintOP const bp )

define secondary structure from a blueprint

void protocols::task_operations::DsspDesignOperation::set_default_sse_residues ( )

private

initialize allowed residue sets with defaults

References protocols::task_operations::TR().

void protocols::task_operations::DsspDesignOperation::set_restrictions_aa	(	std::string const &	sse,
		std::string const &	aas
	)

define allowed residues for some SSE

void protocols::task_operations::DsspDesignOperation::set_restrictions_append	(	std::string const &	sse,
		std::string const &	aas
	)

append allowed residues for some SSE

void protocols::task_operations::DsspDesignOperation::set_restrictions_exclude	(	std::string const &	sse,
		std::string const &	aas
	)

exclude allowed residues for some SSE

References protocols::cluster::calibur::aa.

Friends And Related Function Documentation

friend class ::DsspDesignOperationTests

friend

Member Data Documentation

BluePrintOP protocols::task_operations::DsspDesignOperation::blueprint_

private

std::string protocols::task_operations::DsspDesignOperation::pose_secstruct_

private

SecStructResidues protocols::task_operations::DsspDesignOperation::sse_residues_

private

map sets of allowed residues to secondary structure elements

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

src/protocols/task_operations/DsspDesignOperation.hh
src/protocols/task_operations/DsspDesignOperation.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation