Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Attributes | List of all members
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::Sizedesignable () const
 
void designable (utility::vector1< core::Size > const vector)
 
utility::vector1< core::Sizeleave_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::Sizedesign_
 
utility::vector1< core::Sizerevert_to_template_
 
utility::vector1< std::stringfull_database_
 
utility::vector1< core::Sizedesignable_
 
utility::vector1< core::Sizeleave_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

Constructor & Destructor Documentation

protocols::toolbox::task_operations::DatabaseThread::DatabaseThread ( )
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
void protocols::toolbox::task_operations::DatabaseThread::apply ( core::pose::Pose const &  pose,
core::pack::task::PackerTask task 
) const
virtual
core::pack::task::operation::TaskOperationOP protocols::toolbox::task_operations::DatabaseThread::clone ( ) const
virtual
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
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
void protocols::toolbox::task_operations::DatabaseThread::mark_leave_as_is ( std::string sequence,
core::pose::Pose const &  pose 
) const
void protocols::toolbox::task_operations::DatabaseThread::parse_tag ( TagCOP  tag,
DataMap  
)
virtual
std::string protocols::toolbox::task_operations::DatabaseThread::pick_sequence_from_database ( core::pose::Pose const &  pose) const
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
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
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
utility::vector1<core::Size> protocols::toolbox::task_operations::DatabaseThread::leave_as_is_
private
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
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

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