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protocols::forge::remodel::RemodelDesignMover Class Reference

#include <RemodelDesignMover.hh>

Inheritance diagram for protocols::forge::remodel::RemodelDesignMover:
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Collaboration diagram for protocols::forge::remodel::RemodelDesignMover:
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Public Types

typedef core::Real Real
 
typedef core::Size Size
 
typedef core::kinematics::MoveMap MoveMap
 
typedef core::pose::Pose Pose
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::pack::task::PackerTaskOP 
PackerTaskOP
 
typedef
core::pack::task::PackerTask 
PackerTask
 
typedef protocols::moves::MoverOP MoverOP
 
typedef
protocols::forge::remodel::RemodelData 
RemodelData
 
typedef
protocols::forge::remodel::WorkingRemodelSet 
RemodelWorkingSet
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 

Public Member Functions

 RemodelDesignMover ()
 
 RemodelDesignMover (RemodelData const &remodel_data, RemodelWorkingSet const &working_model, ScoreFunctionOP const &sfxn)
 value constructor More...
 
virtual ~RemodelDesignMover ()
 copy constructor More...
 
virtual MoverOP clone () const
 clone this object More...
 
virtual MoverOP fresh_instance () const
 create this type of object More...
 
void mode1_packertask (Pose &pose)
 these are split up for convenience reasons, so one can bypass blueprint setting if needed be More...
 
void mode2_packertask (Pose &pose)
 
void mode3_packertask (Pose &pose)
 
void mode4_packertask (Pose &pose)
 
void mode5_packertask (Pose &pose)
 
void mode6_packertask (Pose &pose)
 
void reduce_task (Pose &pose, PackerTaskOP &task, bool core, bool boundary, bool surface)
 
bool check_state ()
 
void set_state (std::string state_tag)
 
bool find_disulfides_in_the_neighborhood (Pose &pose, utility::vector1< std::pair< Size, Size > > &disulf_partners)
 
void make_disulfide (Pose &pose, utility::vector1< std::pair< Size, Size > > &disulf_partners, core::kinematics::MoveMapOP mm)
 
virtual void apply (Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
core::pack::task::PackerTaskOPtask ()
 
void scorefunction (ScoreFunctionOP const &sfxn)
 
- 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
 
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)
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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
 this function informs 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
 this function informs 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
 

Private Types

typedef protocols::moves::Mover Super
 

Private Attributes

RemodelData remodel_data_
 
RemodelWorkingSet working_model_
 
PackerTaskOP archived_starting_task_
 
utility::vector1< boolnon_default_positions_
 
std::string state_
 
ScoreFunctionOP score_fxn_
 

Additional Inherited Members

- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover ( )

References state_.

Referenced by clone(), and fresh_instance().

protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover ( RemodelData const &  remodel_data,
RemodelWorkingSet const &  working_model,
ScoreFunctionOP const &  sfxn 
)
protocols::forge::remodel::RemodelDesignMover::~RemodelDesignMover ( )
virtual

copy constructor

default destructor

Member Function Documentation

void protocols::forge::remodel::RemodelDesignMover::apply ( Pose pose)
virtual
bool protocols::forge::remodel::RemodelDesignMover::check_state ( )

References state_, and protocols::forge::remodel::TR().

Referenced by apply().

RemodelDesignMover::MoverOP protocols::forge::remodel::RemodelDesignMover::clone ( ) const
virtual

clone this object

Reimplemented from protocols::moves::Mover.

References RemodelDesignMover().

bool protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood ( Pose pose,
utility::vector1< std::pair< Size, Size > > &  disulf_partners 
)
RemodelDesignMover::MoverOP protocols::forge::remodel::RemodelDesignMover::fresh_instance ( ) const
virtual

create this type of object

Reimplemented from protocols::moves::Mover.

References RemodelDesignMover().

std::string protocols::forge::remodel::RemodelDesignMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::forge::remodel::RemodelDesignMover::make_disulfide ( Pose pose,
utility::vector1< std::pair< Size, Size > > &  disulf_partners,
core::kinematics::MoveMapOP  mm 
)
void protocols::forge::remodel::RemodelDesignMover::mode1_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode2_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode3_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode4_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode5_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode6_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::reduce_task ( Pose pose,
PackerTaskOP task,
bool  core,
bool  boundary,
bool  surface 
)
void protocols::forge::remodel::RemodelDesignMover::scorefunction ( ScoreFunctionOP const &  sfxn)
void protocols::forge::remodel::RemodelDesignMover::set_state ( std::string  state_tag)
core::pack::task::PackerTaskOP & protocols::forge::remodel::RemodelDesignMover::task ( )

Member Data Documentation

PackerTaskOP protocols::forge::remodel::RemodelDesignMover::archived_starting_task_
private

Referenced by RemodelDesignMover(), and set_state().

utility::vector1<bool> protocols::forge::remodel::RemodelDesignMover::non_default_positions_
private
RemodelData protocols::forge::remodel::RemodelDesignMover::remodel_data_
private
ScoreFunctionOP protocols::forge::remodel::RemodelDesignMover::score_fxn_
private
std::string protocols::forge::remodel::RemodelDesignMover::state_
private
RemodelWorkingSet protocols::forge::remodel::RemodelDesignMover::working_model_
private

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