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protocols::task_operations::DatabaseThread Class Reference

#include <DatabaseThread.hh>

Inheritance diagram for protocols::task_operations::DatabaseThread:
Inheritance graph
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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::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
 
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::Sizedesign_
 
utility::vector1< core::Sizerevert_to_template_
 
utility::vector1< std::string > full_database_
 
utility::vector1< core::Sizedesignable_
 
utility::vector1< core::Sizeleave_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

Constructor & Destructor Documentation

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

Member Function Documentation

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

References allow_design_around_.

Referenced by parse_tag().

void protocols::task_operations::DatabaseThread::allow_design_around ( bool const  b)
inline
void protocols::task_operations::DatabaseThread::apply ( core::pose::Pose const &  ,
core::pack::task::PackerTask  
) const
overridevirtual
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.

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

References database_fname_.

Referenced by parse_tag().

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

References database_fname_.

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

References designable_.

Referenced by parse_tag().

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

References designable_.

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

References end_res_.

Referenced by parse_tag(), and pick_sequence_from_database().

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

References end_res_.

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

References itterative_.

Referenced by parse_tag(), and pick_sequence_from_database().

void protocols::task_operations::DatabaseThread::itterative ( bool const  b)
inline
static std::string protocols::task_operations::DatabaseThread::keyname ( )
inlinestatic
utility::vector1<core::Size> protocols::task_operations::DatabaseThread::leave_as_is ( ) const
inline

References leave_as_is_.

Referenced by parse_tag().

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

References leave_as_is_.

void protocols::task_operations::DatabaseThread::mark_designable ( std::string &  sequence,
core::pose::Pose const &  pose 
) const
void protocols::task_operations::DatabaseThread::mark_leave_as_is ( std::string &  sequence,
core::pose::Pose const &  pose 
) const
void protocols::task_operations::DatabaseThread::parse_tag ( TagCOP  tag,
DataMap  
)
overridevirtual
std::string protocols::task_operations::DatabaseThread::pick_sequence_from_database ( core::pose::Pose const &  pose) const
void protocols::task_operations::DatabaseThread::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Size protocols::task_operations::DatabaseThread::start_res ( ) const
inline

References start_res_.

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

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

References start_res_.

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

References target_sequence_.

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

References target_sequence_.

Referenced by apply(), and parse_tag().

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

References template_file_.

Member Data Documentation

bool protocols::task_operations::DatabaseThread::allow_design_around_
private

Referenced by allow_design_around(), and apply().

core::Size protocols::task_operations::DatabaseThread::count_
mutableprivate
std::string protocols::task_operations::DatabaseThread::database_fname_
private
utility::vector1<core::Size> protocols::task_operations::DatabaseThread::design_
private

Referenced by DatabaseThread().

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

Referenced by end_res().

utility::vector1<std::string> protocols::task_operations::DatabaseThread::full_database_
private
bool protocols::task_operations::DatabaseThread::itterative_ = false
private

Referenced by itterative().

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

Referenced by DatabaseThread().

core::Size protocols::task_operations::DatabaseThread::start_res_
private
std::string protocols::task_operations::DatabaseThread::target_sequence_
private

Referenced by target_sequence().

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

Referenced by parse_tag(), and template_file().

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

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