#include <ThreadSequenceOperation.hh>

Inheritance diagram for protocols::task_operations::ThreadSequenceOperation:

[legend]

Public Types
typedef RestrictOperationsBase	parent

Public Types inherited from protocols::task_operations::RestrictOperationsBase
typedef core::pack::task::operation::TaskOperation	TaskOperation

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

typedef TaskOperation	parent

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
	ThreadSequenceOperation ()

	ThreadSequenceOperation (std::string const &seq)

	~ThreadSequenceOperation () override

TaskOperationOP	clone () const override
	Create another task operation of the type matching the most-derived version of the class. More...

void	target_sequence (std::string const &seq)

std::string	target_sequence () const

void	apply (core::pose::Pose const &, core::pack::task::PackerTask &) const override
	Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...

void	parse_tag (TagCOP, DataMap &) override
	Used to parse an xml-like tag to load parameters and properties. More...

core::Size	start_res () const

void	start_res (core::Size const s)

bool	allow_design_around () const

void	allow_design_around (bool const b)

core::Size	chain_num () const

void	chain_num (core::Size const s)

bool	filter_non_aas () const

void	filter_non_aas (bool const b)

Public Member Functions inherited from protocols::task_operations::RestrictOperationsBase
	RestrictOperationsBase ()

	~RestrictOperationsBase () override

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

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static void	restrict_aas (core::Size const resi, char const aa, core::pose::Pose const &pose, core::pack::task::PackerTask &task)

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	keyname ()

Private Attributes
std::string	target_sequence_

core::Size	start_res_

bool	allow_design_around_

core::Size	chain_num_

bool	filter_non_aas_

Additional Inherited Members
Protected Member Functions inherited from protocols::task_operations::RestrictOperationsBase
void	run_calculator (core::pose::Pose const &pose, std::string const &calculator, std::string const &calculation, utility::vector1_bool &residues) const
	this is the only real function - it takes a calculator name and calculation, and a PackerTask-compatible vector, and flips booleans in the vector according to the calculator More...

Detailed Description

this class is a TaskOperation to prevent repacking of residues not near an interface.

Member Typedef Documentation

◆ parent

typedef RestrictOperationsBase protocols::task_operations::ThreadSequenceOperation::parent

Constructor & Destructor Documentation

◆ ThreadSequenceOperation() [1/2]

protocols::task_operations::ThreadSequenceOperation::ThreadSequenceOperation ( )

References allow_design_around(), chain_num(), filter_non_aas(), start_res(), and target_sequence().

◆ ThreadSequenceOperation() [2/2]

protocols::task_operations::ThreadSequenceOperation::ThreadSequenceOperation ( std::string const & seq )

References target_sequence().

◆ ~ThreadSequenceOperation()

protocols::task_operations::ThreadSequenceOperation::~ThreadSequenceOperation ( )

overridedefault

Member Function Documentation

◆ allow_design_around() [1/2]

bool protocols::task_operations::ThreadSequenceOperation::allow_design_around ( ) const

inline

References allow_design_around_.

Referenced by protocols::task_operations::DatabaseThread::apply(), apply(), parse_tag(), and ThreadSequenceOperation().

◆ allow_design_around() [2/2]

void protocols::task_operations::ThreadSequenceOperation::allow_design_around ( bool const b )

inline

References allow_design_around_, and protocols::match::upstream::b.

◆ apply()

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

overridevirtual

Change a packer task in some way. The input pose is the one to which the input task will be later applied.

Implements protocols::task_operations::RestrictOperationsBase.

References protocols::cluster::calibur::aa, allow_design_around(), core::pack::task::operation::RestrictResidueToRepacking::apply(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), chain_num(), core::pose::Pose::conformation(), filter_non_aas(), core::pack::task::operation::RestrictResidueToRepacking::include_residue(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue_type(), restrict_aas(), core::pose::Pose::size(), start_res(), target_sequence(), and target_sequence_.

Referenced by protocols::task_operations::AlignedThreadOperation::apply(), and protocols::task_operations::DatabaseThread::apply().

◆ chain_num() [1/2]

core::Size protocols::task_operations::ThreadSequenceOperation::chain_num ( ) const

inline

References chain_num_.

Referenced by apply(), parse_tag(), and ThreadSequenceOperation().

◆ chain_num() [2/2]

void protocols::task_operations::ThreadSequenceOperation::chain_num ( core::Size const s )

inline

References chain_num_.

◆ clone()

core::pack::task::operation::TaskOperationOP protocols::task_operations::ThreadSequenceOperation::clone ( ) const

overridevirtual

Create another task operation of the type matching the most-derived version of the class.

Implements protocols::task_operations::RestrictOperationsBase.

◆ filter_non_aas() [1/2]

bool protocols::task_operations::ThreadSequenceOperation::filter_non_aas ( ) const

inline

References filter_non_aas_.

Referenced by apply(), parse_tag(), and ThreadSequenceOperation().

◆ filter_non_aas() [2/2]

void protocols::task_operations::ThreadSequenceOperation::filter_non_aas ( bool const b )

inline

References protocols::match::upstream::b, and filter_non_aas_.

◆ keyname()

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

inlinestatic

Referenced by protocols::task_operations::ThreadSequenceOperationCreator::keyname(), and provide_xml_schema().

◆ parse_tag()

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

overridevirtual

Used to parse an xml-like tag to load parameters and properties.

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

References allow_design_around(), chain_num(), filter_non_aas(), start_res(), target_sequence(), and protocols::task_operations::TR().

◆ provide_xml_schema()

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

static

References keyname(), and core::pack::task::operation::task_op_schema_w_attributes().

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

◆ restrict_aas()

void protocols::task_operations::ThreadSequenceOperation::restrict_aas	(	core::Size const	resi,
		char const	aa,
		core::pose::Pose const &	pose,
		core::pack::task::PackerTask &	task
	)

static

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), core::pack::task::operation::RestrictAbsentCanonicalAAS::include_residue(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), and core::chemical::num_canonical_aas.

Referenced by apply().

◆ start_res() [1/2]

core::Size protocols::task_operations::ThreadSequenceOperation::start_res ( ) const

References start_res_.

Referenced by protocols::task_operations::AlignedThreadOperation::apply(), protocols::task_operations::DatabaseThread::apply(), apply(), parse_tag(), and ThreadSequenceOperation().

◆ start_res() [2/2]

void protocols::task_operations::ThreadSequenceOperation::start_res ( core::Size const s )

References start_res_.

◆ target_sequence() [1/2]

std::string protocols::task_operations::ThreadSequenceOperation::target_sequence ( ) const

References target_sequence_.

Referenced by apply(), parse_tag(), and ThreadSequenceOperation().

◆ target_sequence() [2/2]

void protocols::task_operations::ThreadSequenceOperation::target_sequence ( std::string const & seq )

References target_sequence_.

Referenced by protocols::task_operations::AlignedThreadOperation::apply(), and protocols::task_operations::DatabaseThread::apply().

Member Data Documentation

◆ allow_design_around_

bool protocols::task_operations::ThreadSequenceOperation::allow_design_around_

private

Referenced by allow_design_around().

◆ chain_num_

core::Size protocols::task_operations::ThreadSequenceOperation::chain_num_

private

Referenced by chain_num().

◆ filter_non_aas_

bool protocols::task_operations::ThreadSequenceOperation::filter_non_aas_

private

Referenced by filter_non_aas().

◆ start_res_

core::Size protocols::task_operations::ThreadSequenceOperation::start_res_

private

Referenced by start_res().

◆ target_sequence_

std::string protocols::task_operations::ThreadSequenceOperation::target_sequence_

private

Referenced by apply(), and target_sequence().

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

src/protocols/task_operations/ThreadSequenceOperation.hh
src/protocols/task_operations/ThreadSequenceOperation.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ ThreadSequenceOperation() [1/2]

◆ ThreadSequenceOperation() [2/2]

◆ ~ThreadSequenceOperation()

Member Function Documentation

◆ allow_design_around() [1/2]

◆ allow_design_around() [2/2]

◆ apply()

◆ chain_num() [1/2]

◆ chain_num() [2/2]

◆ clone()

◆ filter_non_aas() [1/2]

◆ filter_non_aas() [2/2]

◆ keyname()

◆ parse_tag()

◆ provide_xml_schema()

◆ restrict_aas()

◆ start_res() [1/2]

◆ start_res() [2/2]

◆ target_sequence() [1/2]

◆ target_sequence() [2/2]

Member Data Documentation

◆ allow_design_around_

◆ chain_num_

◆ filter_non_aas_

◆ start_res_

◆ target_sequence_