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protocols::abinitio::abscript::AbscriptStageMover Class Reference

#include <AbscriptStageMover.hh>

Inheritance diagram for protocols::abinitio::abscript::AbscriptStageMover:
Inheritance graph
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Public Member Functions

 AbscriptStageMover (StageID stage, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP score, core::Size cycles)
 
void apply (core::pose::Pose &) override
 Main Method. More...
 
void yield_submovers (MoverSet &set) const
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool setup_stage (core::pose::Pose &pose, core::Real const &progress)
 
void add_submover (ClientMoverOP mover, core::Real weight)
 
void add_preparer (StagePreparerOP mover)
 
void set_cycles_adjust (core::Real in)
 
void set_seq_sep_ramping (core::Real const slope, core::Real const intercept)
 
void set_chainbreak_ramping (core::Real const slope, core::Real const intercept)
 
core::Real const & seq_sep_intercept ()
 
core::scoring::ScoreFunctionCOP scorefxn () const
 
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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 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...
 

Private Types

typedef environment::ClientMoverOP ClientMoverOP
 
typedef std::set< ClientMoverOPMoverSet
 
typedef std::set< StagePreparerOPPreparerSet
 

Private Member Functions

void update_max_seq_sep (core::pose::Pose &pose, core::Real const &progress)
 

Private Attributes

StageID stage_
 
moves::RandomMoverOP random_mover_
 
MoverSet movers_
 
PreparerSet preparers_
 
core::Size const cycles_
 
core::Real cycles_adjust_
 
core::scoring::ScoreFunctionOP score_
 
moves::MonteCarloOP mc_
 
core::Real temperature_
 
core::Real seqsep_slope_
 
core::Real seqsep_intcpt_
 
core::Real chbreak_slope_
 
core::Real chbreak_intcpt_
 
constraints_additional::MaxSeqSepConstraintSetOP constraints_
 

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
 
- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::abinitio::abscript::AbscriptStageMover::AbscriptStageMover ( StageID  stage,
moves::MonteCarloOP  mc,
core::scoring::ScoreFunctionOP  score,
core::Size  cycles 
)

References random_mover_.

Member Function Documentation

void protocols::abinitio::abscript::AbscriptStageMover::add_preparer ( StagePreparerOP  mover)

References preparers_.

void protocols::abinitio::abscript::AbscriptStageMover::add_submover ( ClientMoverOP  mover,
core::Real  weight 
)

References movers_, and random_mover_.

void protocols::abinitio::abscript::AbscriptStageMover::apply ( core::pose::Pose )
overridevirtual
std::string protocols::abinitio::abscript::AbscriptStageMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References stage_, and core::id::to_string().

core::scoring::ScoreFunctionCOP protocols::abinitio::abscript::AbscriptStageMover::scorefxn ( ) const
inline

References score_.

core::Real const& protocols::abinitio::abscript::AbscriptStageMover::seq_sep_intercept ( )
inline

References seqsep_intcpt_.

void protocols::abinitio::abscript::AbscriptStageMover::set_chainbreak_ramping ( core::Real const  slope,
core::Real const  intercept 
)

References chbreak_intcpt_, and chbreak_slope_.

void protocols::abinitio::abscript::AbscriptStageMover::set_cycles_adjust ( core::Real  in)
void protocols::abinitio::abscript::AbscriptStageMover::set_seq_sep_ramping ( core::Real const  slope,
core::Real const  intercept 
)

References seqsep_intcpt_, and seqsep_slope_.

bool protocols::abinitio::abscript::AbscriptStageMover::setup_stage ( core::pose::Pose pose,
core::Real const &  progress 
)
void protocols::abinitio::abscript::AbscriptStageMover::update_max_seq_sep ( core::pose::Pose pose,
core::Real const &  progress 
)
private
void protocols::abinitio::abscript::AbscriptStageMover::yield_submovers ( MoverSet set) const

References movers_, and preparers_.

Member Data Documentation

core::Real protocols::abinitio::abscript::AbscriptStageMover::chbreak_intcpt_
private
core::Real protocols::abinitio::abscript::AbscriptStageMover::chbreak_slope_
private
constraints_additional::MaxSeqSepConstraintSetOP protocols::abinitio::abscript::AbscriptStageMover::constraints_
private

Referenced by update_max_seq_sep().

core::Size const protocols::abinitio::abscript::AbscriptStageMover::cycles_
private

Referenced by apply().

core::Real protocols::abinitio::abscript::AbscriptStageMover::cycles_adjust_
private

Referenced by apply(), and set_cycles_adjust().

moves::MonteCarloOP protocols::abinitio::abscript::AbscriptStageMover::mc_
private
MoverSet protocols::abinitio::abscript::AbscriptStageMover::movers_
private

Referenced by add_submover(), and yield_submovers().

PreparerSet protocols::abinitio::abscript::AbscriptStageMover::preparers_
private
moves::RandomMoverOP protocols::abinitio::abscript::AbscriptStageMover::random_mover_
private
core::scoring::ScoreFunctionOP protocols::abinitio::abscript::AbscriptStageMover::score_
private
core::Real protocols::abinitio::abscript::AbscriptStageMover::seqsep_intcpt_
private
core::Real protocols::abinitio::abscript::AbscriptStageMover::seqsep_slope_
private
StageID protocols::abinitio::abscript::AbscriptStageMover::stage_
private
core::Real protocols::abinitio::abscript::AbscriptStageMover::temperature_
private

Referenced by setup_stage().


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