#include <DatabaseThread.hh>

Inheritance diagram for protocols::task_operations::DatabaseThread:

[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
	DatabaseThread ()

	~DatabaseThread () override

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

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	find_length (core::pose::Pose const &pose) const

std::string	pick_sequence_from_database (core::pose::Pose const &pose) const

void	mark_designable (std::string &sequence, core::pose::Pose const &) const

void	mark_leave_as_is (std::string &sequence, core::pose::Pose const &) const

std::string	template_file () const

void	template_file (std::string const &s)

core::Size	start_res () const

void	start_res (core::Size const s)

core::Size	end_res () const

void	end_res (core::Size const s)

bool	allow_design_around () const

void	allow_design_around (bool const b)

std::string	database_fname () const

void	database_fname (std::string const &d)

utility::vector1< core::Size >	designable () const

void	designable (utility::vector1< core::Size > const &vector)

utility::vector1< core::Size >	leave_as_is () const

void	leave_as_is (utility::vector1< core::Size > const &vector)

void	target_sequence (std::string const &seq)

std::string	target_sequence () const

bool	itterative () const

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

static std::string	keyname ()

Private Attributes
std::string	target_sequence_

std::string	template_file_

std::string	database_fname_

core::pose::PoseOP	template_pose_

core::Size	start_res_

core::Size	end_res_

bool	allow_design_around_

utility::vector1< core::Size >	design_

utility::vector1< core::Size >	revert_to_template_

utility::vector1< std::string >	full_database_

utility::vector1< core::Size >	designable_

utility::vector1< core::Size >	leave_as_is_

bool	itterative_ = false

core::Size	count_

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 thread sequences from a database.

Member Typedef Documentation

◆ parent

typedef RestrictOperationsBase protocols::task_operations::DatabaseThread::parent

Constructor & Destructor Documentation

◆ DatabaseThread()

protocols::task_operations::DatabaseThread::DatabaseThread ( )

References count_, design_, designable_, full_database_, leave_as_is_, and revert_to_template_.

◆ ~DatabaseThread()

protocols::task_operations::DatabaseThread::~DatabaseThread ( )

overridedefault

Member Function Documentation

◆ allow_design_around() [1/2]

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

inline

References allow_design_around_.

Referenced by parse_tag().

◆ allow_design_around() [2/2]

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

inline

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

◆ apply()

void protocols::task_operations::DatabaseThread::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::task_operations::ThreadSequenceOperation::allow_design_around(), allow_design_around_, protocols::task_operations::ThreadSequenceOperation::apply(), designable_, protocols::rosetta_scripts::find_nearest_res(), leave_as_is_, mark_designable(), mark_leave_as_is(), pick_sequence_from_database(), core::pose::Pose::size(), start_res(), protocols::task_operations::ThreadSequenceOperation::start_res(), target_sequence(), protocols::task_operations::ThreadSequenceOperation::target_sequence(), template_file(), template_pose_, and protocols::task_operations::TR().

◆ clone()

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

overridevirtual

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

Implements protocols::task_operations::RestrictOperationsBase.

◆ database_fname() [1/2]

std::string protocols::task_operations::DatabaseThread::database_fname ( ) const

inline

References database_fname_.

Referenced by parse_tag().

◆ database_fname() [2/2]

void protocols::task_operations::DatabaseThread::database_fname ( std::string const & d )

inline

References database_fname_.

◆ designable() [1/2]

utility::vector1<core::Size> protocols::task_operations::DatabaseThread::designable ( ) const

inline

References designable_.

Referenced by parse_tag().

◆ designable() [2/2]

void protocols::task_operations::DatabaseThread::designable ( utility::vector1< core::Size > const & vector )

inline

References designable_.

◆ end_res() [1/2]

core::Size protocols::task_operations::DatabaseThread::end_res ( ) const

inline

References end_res_.

Referenced by parse_tag(), and pick_sequence_from_database().

◆ end_res() [2/2]

void protocols::task_operations::DatabaseThread::end_res ( core::Size const s )

inline

References end_res_.

◆ find_length()

core::Size protocols::task_operations::DatabaseThread::find_length ( core::pose::Pose const & pose ) const

References protocols::rosetta_scripts::find_nearest_res(), and protocols::task_operations::TR().

Referenced by pick_sequence_from_database().

◆ itterative() [1/2]

bool protocols::task_operations::DatabaseThread::itterative ( ) const

inline

References itterative_.

Referenced by parse_tag(), and pick_sequence_from_database().

◆ itterative() [2/2]

void protocols::task_operations::DatabaseThread::itterative ( bool const b )

inline

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

◆ keyname()

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

inlinestatic

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

◆ leave_as_is() [1/2]

utility::vector1<core::Size> protocols::task_operations::DatabaseThread::leave_as_is ( ) const

inline

References leave_as_is_.

Referenced by parse_tag().

◆ leave_as_is() [2/2]

void protocols::task_operations::DatabaseThread::leave_as_is ( utility::vector1< core::Size > const & vector )

inline

References leave_as_is_.

◆ mark_designable()

void protocols::task_operations::DatabaseThread::mark_designable	(	std::string &	sequence,
		core::pose::Pose const &	pose
	)		const

References designable_, protocols::rosetta_scripts::find_nearest_res(), start_res_, and template_pose_.

Referenced by apply().

◆ mark_leave_as_is()

void protocols::task_operations::DatabaseThread::mark_leave_as_is	(	std::string &	sequence,
		core::pose::Pose const &	pose
	)		const

References protocols::rosetta_scripts::find_nearest_res(), leave_as_is_, start_res_, and template_pose_.

Referenced by apply().

◆ parse_tag()

void protocols::task_operations::DatabaseThread::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(), database_fname(), database_fname_, designable(), end_res(), full_database_, itterative(), leave_as_is(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), start_res(), target_sequence(), template_file(), template_file_, and template_pose_.

◆ pick_sequence_from_database()

std::string protocols::task_operations::DatabaseThread::pick_sequence_from_database ( core::pose::Pose const & pose ) const

References count_, database_fname_, end_res(), find_length(), full_database_, itterative(), core::scoring::rg, start_res(), template_file(), and protocols::task_operations::TR().

Referenced by apply().

◆ provide_xml_schema()

void protocols::task_operations::DatabaseThread::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::DatabaseThreadCreator::provide_xml_schema().

◆ start_res() [1/2]

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

inline

References start_res_.

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

◆ start_res() [2/2]

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

inline

References start_res_.

◆ target_sequence() [1/2]

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

inline

References target_sequence_.

Referenced by apply(), and parse_tag().

◆ target_sequence() [2/2]

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

inline

References target_sequence_.

◆ template_file() [1/2]

std::string protocols::task_operations::DatabaseThread::template_file ( ) const

inline

References template_file_.

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

◆ template_file() [2/2]

void protocols::task_operations::DatabaseThread::template_file ( std::string const & s )

inline

References template_file_.

Member Data Documentation

◆ allow_design_around_

bool protocols::task_operations::DatabaseThread::allow_design_around_

private

Referenced by allow_design_around(), and apply().

◆ count_

core::Size protocols::task_operations::DatabaseThread::count_

mutableprivate

Referenced by DatabaseThread(), and pick_sequence_from_database().

◆ database_fname_

std::string protocols::task_operations::DatabaseThread::database_fname_

private

Referenced by database_fname(), parse_tag(), and pick_sequence_from_database().

◆ design_

utility::vector1<core::Size> protocols::task_operations::DatabaseThread::design_

private

Referenced by DatabaseThread().

◆ designable_

utility::vector1<core::Size> protocols::task_operations::DatabaseThread::designable_

private

Referenced by apply(), DatabaseThread(), designable(), and mark_designable().

◆ end_res_

core::Size protocols::task_operations::DatabaseThread::end_res_

private

Referenced by end_res().

◆ full_database_

utility::vector1<std::string> protocols::task_operations::DatabaseThread::full_database_

private

Referenced by DatabaseThread(), parse_tag(), and pick_sequence_from_database().

◆ itterative_

bool protocols::task_operations::DatabaseThread::itterative_ = false

private

Referenced by itterative().

◆ leave_as_is_

utility::vector1<core::Size> protocols::task_operations::DatabaseThread::leave_as_is_

private

Referenced by apply(), DatabaseThread(), leave_as_is(), and mark_leave_as_is().

◆ revert_to_template_

utility::vector1<core::Size> protocols::task_operations::DatabaseThread::revert_to_template_

private

Referenced by DatabaseThread().

◆ start_res_

core::Size protocols::task_operations::DatabaseThread::start_res_

private

Referenced by mark_designable(), mark_leave_as_is(), and start_res().

◆ target_sequence_

std::string protocols::task_operations::DatabaseThread::target_sequence_

private

Referenced by target_sequence().

◆ template_file_

std::string protocols::task_operations::DatabaseThread::template_file_

private

Referenced by parse_tag(), and template_file().

◆ template_pose_

core::pose::PoseOP protocols::task_operations::DatabaseThread::template_pose_

private

Referenced by apply(), mark_designable(), mark_leave_as_is(), and parse_tag().

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

src/protocols/task_operations/DatabaseThread.hh
src/protocols/task_operations/DatabaseThread.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ DatabaseThread()

◆ ~DatabaseThread()

Member Function Documentation

◆ allow_design_around() [1/2]

◆ allow_design_around() [2/2]

◆ apply()

◆ clone()

◆ database_fname() [1/2]

◆ database_fname() [2/2]

◆ designable() [1/2]

◆ designable() [2/2]

◆ end_res() [1/2]

◆ end_res() [2/2]

◆ find_length()

◆ itterative() [1/2]

◆ itterative() [2/2]

◆ keyname()

◆ leave_as_is() [1/2]

◆ leave_as_is() [2/2]

◆ mark_designable()

◆ mark_leave_as_is()

◆ parse_tag()

◆ pick_sequence_from_database()

◆ provide_xml_schema()

◆ start_res() [1/2]

◆ start_res() [2/2]

◆ target_sequence() [1/2]

◆ target_sequence() [2/2]

◆ template_file() [1/2]

◆ template_file() [2/2]

Member Data Documentation

◆ allow_design_around_

◆ count_

◆ database_fname_

◆ design_

◆ designable_

◆ end_res_

◆ full_database_

◆ itterative_

◆ leave_as_is_

◆ revert_to_template_

◆ start_res_

◆ target_sequence_

◆ template_file_

◆ template_pose_