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protocols::abinitio::Stage1Sampler Class Reference
Inheritance diagram for protocols::abinitio::Stage1Sampler:
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Public Member Functions

 Stage1Sampler (core::fragment::FragSetCOP fragset_large, core::kinematics::MoveMapCOP movemap)
 
 Stage1Sampler (protocols::simple_moves::FragmentMoverOP brute_move_large)
 
virtual void apply (core::pose::Pose &pose)
 
- Public Member Functions inherited from protocols::abinitio::ClassicAbinitio
 ClassicAbinitio (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int)
 This constructor does not work – Fix it before using it. More...
 
 ClassicAbinitio (core::fragment::FragSetCOP fragset_small, core::fragment::FragSetCOP fragset_large, core::kinematics::MoveMapCOP movemap)
 constructor: supply fragsets for large and small fragment moves More...
 
 ClassicAbinitio (ClassicAbinitio const &src)
 Explicit copy constructor since this class contains OPs of other classes. More...
 
 ~ClassicAbinitio ()
 Explicit destructor since this class contains OPs of other classes. More...
 
virtual void init (core::pose::Pose const &pose)
 setup moves, mc-object, scores More...
 
virtual moves::MoverOP clone () const
 ClassicAbinitio has virtual functions... use this to obtain a new instance. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
simple_moves::FragmentMoverOP smooth_move_small ()
 
simple_moves::FragmentMoverOP brute_move_small ()
 
simple_moves::FragmentMoverOP brute_move_large ()
 
virtual void set_movemap (core::kinematics::MoveMapCOP mm)
 
core::kinematics::MoveMapCOP movemap ()
 
void set_moves (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small)
 
void set_mc (moves::MonteCarloOP)
 
moves::MonteCarlomc ()
 
moves::MonteCarlo const & mc () const
 
virtual void set_cycles (core::Real increase_cycles=1.0)
 
Size total_trials () const
 
virtual void set_score_weight (core::scoring::ScoreType, core::Real setting, StageID stage=ALL_STAGES)
 for debugging, one wants to have access to the native pose. More...
 
bool just_smooth_cycles () const
 
Size stage1_cycles () const
 
Size stage2_cycles () const
 
Size stage3_cycles () const
 
void set_stage4_cycles (Size stage4_cycles_new)
 
Size stage4_cycles () const
 
Size stage5_cycles () const
 
bool bQuickTest () const
 
void set_skip_stage1 (bool setting)
 
void set_skip_stage2 (bool setting)
 
- Public Member Functions inherited from protocols::abinitio::Protocol
 Protocol ()
 
 ~Protocol ()
 
void set_evaluation (evaluation::MetaPoseEvaluatorOP ev)
 
void add_evaluation (evaluation::PoseEvaluatorOP ev)
 
void evaluate_pose (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const
 
evaluation::MetaPoseEvaluatorOP evaluator ()
 
void set_kinematics (abinitio::KinematicControlOP kc)
 
abinitio::KinematicControl const & kinematics ()
 
virtual bool start_from_centroid () const
 
virtual bool return_centroid () const
 
virtual void return_centroid (bool setting)
 
void set_fullatom_scorefxn (core::scoring::ScoreFunctionOP sfxn)
 
void set_centroid_scorefxn (core::scoring::ScoreFunctionOP sfxn)
 
void set_silentout_file_name (std::string str)
 
core::scoring::ScoreFunctionOP fullatom_scorefxn ()
 
core::scoring::ScoreFunctionOP centroid_scorefxn ()
 
virtual checkpoint::CheckPointerget_checkpoints ()
 
- 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...
 
virtual MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Additional Inherited Members

- Public Types inherited from protocols::abinitio::ClassicAbinitio
enum  StageID {
  ALL_STAGES = 0, STAGE_1, STAGE_2, STAGE_3a,
  STAGE_3b, STAGE_4, STAGE_5
}
 
- Static Public Member Functions inherited from protocols::abinitio::ClassicAbinitio
static void register_options ()
 
- Public Attributes inherited from protocols::abinitio::ClassicAbinitio
bool bSkipStage1_
 
bool bSkipStage2_
 
bool bSkipStage3_
 
bool bSkipStage4_
 
bool bSkipStage5_
 
utility::vector1< StageIDrecover_low_stages_
 
- Protected Member Functions inherited from protocols::abinitio::ClassicAbinitio
virtual void update_moves ()
 
virtual void set_defaults (core::pose::Pose const &pose)
 
virtual void set_default_options ()
 
virtual void set_default_mc (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn)
 
virtual void set_default_scores ()
 
core::scoring::ScoreFunction
const & 
current_scorefxn () const
 
void current_scorefxn (core::scoring::ScoreFunction const &scorefxn)
 
void recover_low (core::pose::Pose &pose, StageID stage)
 
virtual void replace_scorefxn (core::pose::Pose &pose, StageID stage, core::Real intra_stage_progress)
 
void set_current_weight (core::scoring::ScoreType type, core::Real setting)
 
virtual bool do_stage1_cycles (core::pose::Pose &pose)
 
virtual bool do_stage2_cycles (core::pose::Pose &pose)
 
virtual bool do_stage3_cycles (core::pose::Pose &pose)
 
virtual bool do_stage4_cycles (core::pose::Pose &pose)
 
virtual bool do_stage5_cycles (core::pose::Pose &pose)
 
virtual moves::TrialMoverOP stage1_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)
 
virtual moves::TrialMoverOP stage2_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)
 
virtual moves::TrialMoverOP stage3_mover (core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in)
 
virtual moves::TrialMoverOP stage4_mover (core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in)
 
virtual moves::TrialMoverOP stage5_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)
 
virtual void set_trials ()
 
moves::TrialMoverOP trial_large ()
 
moves::TrialMoverOP trial_small ()
 
moves::TrialMoverOP trial_smooth ()
 
virtual bool prepare_stage1 (core::pose::Pose &pose)
 
virtual bool prepare_stage2 (core::pose::Pose &pose)
 
virtual bool prepare_stage3 (core::pose::Pose &pose)
 
virtual bool prepare_stage4 (core::pose::Pose &pose)
 
virtual bool prepare_stage5 (core::pose::Pose &pose)
 
virtual bool prepare_loop_in_stage3 (core::pose::Pose &, Size, Size)
 
virtual bool prepare_loop_in_stage4 (core::pose::Pose &, Size, Size)
 
void output_debug_structure (core::pose::Pose &pose, std::string prefix)
 
moves::MonteCarloOP mc_ptr ()
 
- Protected Attributes inherited from protocols::abinitio::ClassicAbinitio
Size stage1_cycles_
 
Size stage2_cycles_
 
Size stage3_cycles_
 
Size stage4_cycles_
 
Size stage5_cycles_
 

Constructor & Destructor Documentation

protocols::abinitio::Stage1Sampler::Stage1Sampler ( core::fragment::FragSetCOP  fragset_large,
core::kinematics::MoveMapCOP  movemap 
)
inline
protocols::abinitio::Stage1Sampler::Stage1Sampler ( protocols::simple_moves::FragmentMoverOP  brute_move_large)
inline

Member Function Documentation

void protocols::abinitio::Stage1Sampler::apply ( core::pose::Pose pose)
virtual

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