Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::grafting::simple_movers::ReplaceRegionMover Class Reference

Replace a region of residues with another from a pose piece. Wrapper to grafting utility function. More...

#include <ReplaceRegionMover.hh>

Public Member Functions

 ReplaceRegionMover (bool copy_pdbinfo=false)
 
 ReplaceRegionMover (core::pose::Pose const &src_pose, core::Size const src_pose_start, core::Size const target_pose_start, core::Size const span, bool copy_pdbinfo=false)
 
 ReplaceRegionMover (ReplaceRegionMover const &src)
 
virtual ~ReplaceRegionMover ()
 
virtual void apply (core::pose::Pose &pose)
 
core::Size src_pose_start () const
 
void src_pose_start (core::Size start)
 
core::Size target_pose_start () const
 
void target_pose_start (core::Size start)
 
void src_pose (core::pose::Pose const &from_pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, moves::Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
void set_type (std::string const &setting)
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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
 
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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Attributes

core::Size src_pose_start_
 
core::Size target_pose_start_
 
core::Size span_
 
bool copy_pdbinfo_
 
core::pose::PoseOP src_pose_
 
TagCOP tag_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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...
 
- 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...
 

Detailed Description

Replace a region of residues with another from a pose piece. Wrapper to grafting utility function.

Specify the start residue of the source pose, the residue where replacement will begin, In addition to the number of residues (span) .

Constructor & Destructor Documentation

protocols::grafting::simple_movers::ReplaceRegionMover::ReplaceRegionMover ( bool  copy_pdbinfo = false)

Referenced by clone(), and fresh_instance().

protocols::grafting::simple_movers::ReplaceRegionMover::ReplaceRegionMover ( core::pose::Pose const &  src_pose,
core::Size const  src_pose_start,
core::Size const  target_pose_start,
core::Size const  span,
bool  copy_pdbinfo = false 
)

References src_pose_.

protocols::grafting::simple_movers::ReplaceRegionMover::ReplaceRegionMover ( ReplaceRegionMover const &  src)
protocols::grafting::simple_movers::ReplaceRegionMover::~ReplaceRegionMover ( )
virtual

Member Function Documentation

void protocols::grafting::simple_movers::ReplaceRegionMover::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::grafting::simple_movers::ReplaceRegionMover::clone ( ) const
virtual

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.

References ReplaceRegionMover().

protocols::moves::MoverOP protocols::grafting::simple_movers::ReplaceRegionMover::fresh_instance ( ) const
virtual

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.

References ReplaceRegionMover().

std::string protocols::grafting::simple_movers::ReplaceRegionMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::grafting::simple_movers::ReplaceRegionMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap data,
Filters_map const &  filters,
moves::Movers_map const &  movers,
Pose const &  pose 
)
virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References copy_pdbinfo_, protocols::rosetta_scripts::parse_bogus_res_tag(), protocols::rosetta_scripts::saved_reference_pose(), span_, src_pose_, and tag_.

void protocols::grafting::simple_movers::ReplaceRegionMover::src_pose ( core::pose::Pose const &  from_pose)

References src_pose_.

core::Size protocols::grafting::simple_movers::ReplaceRegionMover::src_pose_start ( ) const

References src_pose_start_.

void protocols::grafting::simple_movers::ReplaceRegionMover::src_pose_start ( core::Size  start)
core::Size protocols::grafting::simple_movers::ReplaceRegionMover::target_pose_start ( ) const

References target_pose_start_.

void protocols::grafting::simple_movers::ReplaceRegionMover::target_pose_start ( core::Size  start)

Member Data Documentation

bool protocols::grafting::simple_movers::ReplaceRegionMover::copy_pdbinfo_
private

Referenced by parse_my_tag().

core::Size protocols::grafting::simple_movers::ReplaceRegionMover::span_
private

Referenced by apply(), and parse_my_tag().

core::pose::PoseOP protocols::grafting::simple_movers::ReplaceRegionMover::src_pose_
private
core::Size protocols::grafting::simple_movers::ReplaceRegionMover::src_pose_start_
private

Referenced by apply(), and src_pose_start().

TagCOP protocols::grafting::simple_movers::ReplaceRegionMover::tag_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::grafting::simple_movers::ReplaceRegionMover::target_pose_start_
private

Referenced by apply(), and target_pose_start().


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