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protocols::splice::RBInMover Class Reference

#include <RBInMover.hh>

Inheritance diagram for protocols::splice::RBInMover:
Inheritance graph
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Public Member Functions

 RBInMover ()
 
 ~RBInMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string RBDatabase_fname () const
 
void RBDatabase_fname (std::string const &s)
 
void RB_dbase (std::string const &s)
 
std::string RB_dbase () const
 
core::Size from_entry () const
 
void from_entry (core::Size const s)
 
void to_entry (core::Size const s)
 
core::Size to_entry () const
 
bool randomize () const
 
void randomize (bool const b)
 
utility::vector1< std::pair
< std::string,
core::kinematics::Jump > > 
jump_library () const
 
void jump_library (utility::vector1< std::pair< std::string, core::kinematics::Jump > > j)
 
void checkpointing_file (std::string const &s)
 
std::string checkpointing_file () const
 
void set_fold_tree (core::pose::Pose &pose)
 
void modify_foldtree (bool const m)
 
bool modify_foldtree () const
 
void find_disulfide_postions (core::pose::Pose const &pose, utility::vector1< core::Size > &cys_pos)
 
core::Size find_vl_vh_cut (core::pose::Pose pose) const
 
utility::vector1< std::array
< int, 3 > > 
set_fold_tree_nodes (core::pose::Pose const &pose, utility::vector1< core::Size > &cys_pos, core::Size vl_vh_cut)
 
void db_entry (std::string s)
 
std::string db_entry ()
 
void select_entry_by_name ()
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Member Functions

void init ()
 
bool checkpoint_recovery ()
 sets the entry order; if the jump_library is already populated returns without doing anything More...
 
bool checkpoint () const
 recover from checkpointing. If checkpointing is off, does nothing. Returns true if recovered from checkpoint More...
 

Private Attributes

std::string RB_dbase_
 
core::Size from_entry_
 
core::Size to_entry_
 
core::Size current_entry_
 
bool randomize_
 
utility::vector1< std::pair
< std::string,
core::kinematics::Jump > > 
jump_library_
 
std::string checkpointing_file_
 
bool modify_foldtree_
 
std::string db_entry_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Constructor & Destructor Documentation

protocols::splice::RBInMover::RBInMover ( )

References jump_library_.

protocols::splice::RBInMover::~RBInMover ( )
overridedefault

Member Function Documentation

void protocols::splice::RBInMover::apply ( core::pose::Pose )
overridevirtual
bool protocols::splice::RBInMover::checkpoint ( ) const
private

recover from checkpointing. If checkpointing is off, does nothing. Returns true if recovered from checkpoint

References checkpointing_file(), checkpointing_file_, current_entry_, jump_library(), core::conformation::membrane::out, and protocols::splice::TR().

Referenced by apply(), and init().

bool protocols::splice::RBInMover::checkpoint_recovery ( )
private

sets the entry order; if the jump_library is already populated returns without doing anything

Referenced by init().

void protocols::splice::RBInMover::checkpointing_file ( std::string const &  s)
inline

References checkpointing_file_.

std::string protocols::splice::RBInMover::checkpointing_file ( ) const
inline

References checkpointing_file_.

Referenced by checkpoint(), and parse_my_tag().

moves::MoverOP protocols::splice::RBInMover::clone ( ) const
overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

void protocols::splice::RBInMover::db_entry ( std::string  s)
inline

References db_entry_.

std::string protocols::splice::RBInMover::db_entry ( )
inline

References db_entry_.

Referenced by parse_my_tag(), and select_entry_by_name().

void protocols::splice::RBInMover::find_disulfide_postions ( core::pose::Pose const &  pose,
utility::vector1< core::Size > &  cys_pos 
)
core::Size protocols::splice::RBInMover::find_vl_vh_cut ( core::pose::Pose  pose) const
moves::MoverOP protocols::splice::RBInMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

core::Size protocols::splice::RBInMover::from_entry ( ) const
inline

References from_entry_.

Referenced by init(), and parse_my_tag().

void protocols::splice::RBInMover::from_entry ( core::Size const  s)
inline

References from_entry_.

std::string protocols::splice::RBInMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

void protocols::splice::RBInMover::init ( void  )
private
utility::vector1< std::pair< std::string, core::kinematics::Jump > > protocols::splice::RBInMover::jump_library ( ) const

References jump_library_.

Referenced by checkpoint().

void protocols::splice::RBInMover::jump_library ( utility::vector1< std::pair< std::string, core::kinematics::Jump > >  j)

References jump_library_.

void protocols::splice::RBInMover::modify_foldtree ( bool const  m)
inline

References modify_foldtree_.

bool protocols::splice::RBInMover::modify_foldtree ( ) const
inline

References modify_foldtree_.

Referenced by apply(), and parse_my_tag().

std::string protocols::splice::RBInMover::mover_name ( )
static
void protocols::splice::RBInMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References checkpointing_file(), db_entry(), from_entry(), init(), modify_foldtree(), randomize(), RB_dbase(), and to_entry().

void protocols::splice::RBInMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
bool protocols::splice::RBInMover::randomize ( ) const
inline

References randomize_.

Referenced by init(), and parse_my_tag().

void protocols::splice::RBInMover::randomize ( bool const  b)
inline
void protocols::splice::RBInMover::RB_dbase ( std::string const &  s)
inline

References RB_dbase_.

std::string protocols::splice::RBInMover::RB_dbase ( ) const
inline

References RB_dbase_.

Referenced by parse_my_tag().

std::string protocols::splice::RBInMover::RBDatabase_fname ( ) const
inline

References RB_dbase_.

void protocols::splice::RBInMover::RBDatabase_fname ( std::string const &  s)
inline

References RB_dbase_.

void protocols::splice::RBInMover::select_entry_by_name ( )

References current_entry_, db_entry(), db_entry_, and jump_library_.

Referenced by apply().

void protocols::splice::RBInMover::set_fold_tree ( core::pose::Pose pose)
utility::vector1< std::array< int, 3 > > protocols::splice::RBInMover::set_fold_tree_nodes ( core::pose::Pose const &  pose,
utility::vector1< core::Size > &  cys_pos,
core::Size  vl_vh_cut 
)
void protocols::splice::RBInMover::to_entry ( core::Size const  s)
inline

References to_entry_.

core::Size protocols::splice::RBInMover::to_entry ( ) const
inline

References to_entry_.

Referenced by init(), and parse_my_tag().

Member Data Documentation

std::string protocols::splice::RBInMover::checkpointing_file_
private

Referenced by checkpoint(), and checkpointing_file().

core::Size protocols::splice::RBInMover::current_entry_
private
std::string protocols::splice::RBInMover::db_entry_
private

Referenced by db_entry(), and select_entry_by_name().

core::Size protocols::splice::RBInMover::from_entry_
private

Referenced by from_entry().

utility::vector1< std::pair <std::string,core::kinematics::Jump> > protocols::splice::RBInMover::jump_library_
private
bool protocols::splice::RBInMover::modify_foldtree_
private

Referenced by modify_foldtree().

bool protocols::splice::RBInMover::randomize_
private

Referenced by randomize().

std::string protocols::splice::RBInMover::RB_dbase_
private

Referenced by init(), RB_dbase(), and RBDatabase_fname().

core::Size protocols::splice::RBInMover::to_entry_
private

Referenced by to_entry().


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