protocols::toolbox::task_operations::DatabaseThread Class Reference

#include <DatabaseThread.hh>

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

Public Member Functions
	DatabaseThread ()
virtual	~DatabaseThread ()
virtual TaskOperationOP	clone () const
virtual void	apply (core::pose::Pose const &, core::pack::task::PackerTask &) const
virtual void	parse_tag (TagCOP, DataMap &)
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
Public Member Functions inherited from protocols::toolbox::task_operations::RestrictOperationsBase
	RestrictOperationsBase ()
virtual	~RestrictOperationsBase ()

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_

Additional Inherited Members
Protected Member Functions inherited from protocols::toolbox::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

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

Constructor & Destructor Documentation

protocols::toolbox::task_operations::DatabaseThread::DatabaseThread

(

)

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

Referenced by clone().

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

virtual

Member Function Documentation

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

inline

References allow_design_around_.

Referenced by parse_tag().

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

inline

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

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

virtual

Implements protocols::toolbox::task_operations::RestrictOperationsBase.

References protocols::toolbox::task_operations::ThreadSequenceOperation::allow_design_around(), allow_design_around_, protocols::toolbox::task_operations::ThreadSequenceOperation::apply(), designable_, protocols::rosetta_scripts::find_nearest_res(), leave_as_is_, mark_designable(), mark_leave_as_is(), pick_sequence_from_database(), sequence, start_res(), protocols::toolbox::task_operations::ThreadSequenceOperation::start_res(), protocols::toolbox::task_operations::ThreadSequenceOperation::target_sequence(), target_sequence(), template_pose_, and protocols::toolbox::task_operations::TR.

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

virtual

Implements protocols::toolbox::task_operations::RestrictOperationsBase.

References DatabaseThread().

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

inline

References database_fname_.

Referenced by parse_tag().

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

inline

References database_fname_.

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

inline

References designable_.

Referenced by parse_tag().

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

inline

References designable_.

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

inline

References end_res_.

Referenced by parse_tag().

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

inline

References end_res_.

core::Size protocols::toolbox::task_operations::DatabaseThread::find_length

(

core::pose::Pose const &

pose

)

const

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

Referenced by pick_sequence_from_database().

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

inline

References leave_as_is_.

Referenced by parse_tag().

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

inline

References leave_as_is_.

void protocols::toolbox::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().

void protocols::toolbox::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().

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

virtual

References allow_design_around(), database, database_fname(), database_fname_, designable(), end_res(), full_database_, getline(), leave_as_is(), core::import_pose::pose_from_pdb(), start_res(), utility::string_split(), target_sequence(), template_file(), template_file_, template_pose_, and utility_exit_with_message.

std::string protocols::toolbox::task_operations::DatabaseThread::pick_sequence_from_database

(

core::pose::Pose const &

pose

)

const

References database_fname_, find_length(), full_database_, protocols::RG, protocols::toolbox::task_operations::TR, numeric::random::RandomGenerator::uniform(), and utility_exit_with_message.

Referenced by apply().

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

inline

References start_res_.

Referenced by apply(), and parse_tag().

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

inline

References start_res_.

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

inline

References target_sequence_.

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

inline

Referenced by apply(), and parse_tag().

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

inline

References template_file_.

Referenced by parse_tag().

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

inline

References template_file_.

Member Data Documentation

bool protocols::toolbox::task_operations::DatabaseThread::allow_design_around_

private

Referenced by allow_design_around(), and apply().

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

private

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

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

private

Referenced by DatabaseThread().

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

private

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

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

private

Referenced by end_res().

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

private

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

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

private

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

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

private

Referenced by DatabaseThread().

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

private

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

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

private

Referenced by target_sequence().

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

private

Referenced by parse_tag(), and template_file().

core::pose::PoseOP protocols::toolbox::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/toolbox/task_operations/DatabaseThread.hh
• src/protocols/toolbox/task_operations/DatabaseThread.cc