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protocols::abinitio::KinematicAbinitio Class Reference

#include <KinematicAbinitio.hh>

Inheritance diagram for protocols::abinitio::KinematicAbinitio:
Inheritance graph
[legend]

Public Member Functions

 KinematicAbinitio (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy)
 
 KinematicAbinitio (core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap)
 
 ~KinematicAbinitio () override
 
moves::MoverOP clone () const override
 ... More...
 
void apply (core::pose::Pose &pose) override
 run the protocol More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_max_seq_sep (core::pose::Pose &pose, core::Size setting) override
 
bool prepare_stage1 (core::pose::Pose &pose) override
 
bool prepare_stage2 (core::pose::Pose &pose) override
 
bool prepare_stage3 (core::pose::Pose &pose) override
 
bool prepare_loop_in_stage3 (core::pose::Pose &, core::Size, core::Size) override
 
bool prepare_loop_in_stage4 (core::pose::Pose &, core::Size, core::Size) override
 
moves::TrialMoverOP stage1_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in) override
 
moves::TrialMoverOP stage2_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in) override
 
moves::TrialMoverOP stage3_mover (core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in) override
 
moves::TrialMoverOP stage4_mover (core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in) override
 
void closure_protocol (loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol)
 set the closure_protocol... if not set no closure... More...
 
- Public Member Functions inherited from protocols::abinitio::FoldConstraints
 FoldConstraints (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy)
 c'stor from Movers More...
 
 FoldConstraints (core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap)
 c'stor from FragSets — ClassicFragmentMover and SmoothFragmentMover will be created More...
 
 FoldConstraints (FoldConstraints const &src)
 Explicit copy constructor to handle OPs. More...
 
 ~FoldConstraints () override
 Explicit destructor to handle OPs. More...
 
void set_constraint_weight (core::Real setting)
 
void set_show_viol_level (core::Size setting)
 
- 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 () override
 Explicit destructor since this class contains OPs of other classes. More...
 
void init (core::pose::Pose const &pose) override
 setup moves, mc-object, scores More...
 
simple_moves::FragmentMoverOP smooth_move_small ()
 
simple_moves::FragmentMoverOP brute_move_small ()
 
simple_moves::FragmentMoverOP brute_move_large ()
 
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)
 
core::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
 
core::Size stage1_cycles () const
 
core::Size stage2_cycles () const
 
core::Size stage3_cycles () const
 
void set_stage4_cycles (core::Size stage4_cycles_new)
 
core::Size stage4_cycles () const
 
core::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 () override=default
 
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 apply (core::pose::Pose &) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
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 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...
 
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...
 

Static Public Member Functions

static void register_options ()
 
- Static Public Member Functions inherited from protocols::abinitio::FoldConstraints
static void register_options ()
 Why is this not being registered ? Probably not actually needed. More...
 
- Static Public Member Functions inherited from protocols::abinitio::ClassicAbinitio
static void register_options ()
 
- Static Public Member Functions inherited from protocols::abinitio::Protocol
static void register_options ()
 
- 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

void set_default_scores () override
 sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0 More...
 
void set_default_options () override
 
void replace_scorefxn (core::pose::Pose &pose, StageID, core::Real intra_stage_progress) override
 
- Protected Member Functions inherited from protocols::abinitio::FoldConstraints
bool prepare_stage4 (core::pose::Pose &pose) override
 
bool do_stage1_cycles (core::pose::Pose &pose) override
 
bool do_stage2_cycles (core::pose::Pose &pose) override
 
virtual void setup_default_min_move ()
 
void set_movemap (core::kinematics::MoveMapCOP mm) override
 
void set_min_move (protocols::minimization_packing::MinMoverOP mm)
 
protocols::minimization_packing::MinMovermin_move ()
 
void min_trial (core::pose::Pose &pose)
 
core::Real max_seq_sep_fudge () const
 
void max_seq_sep_fudge (core::Real setting)
 
constraints_additional::MaxSeqSepConstraintSet
const & 
constraints ()
 
void bIgnoreSequenceSeparation (bool setting)
 
bool bIgnoreSequenceSeparation ()
 
core::Size total_res (core::pose::Pose const &pose) const
 
void set_seq_sep_stage1 (core::Real setting)
 
void set_seq_sep_stage3 (core::Real setting)
 
- 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_mc (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn)
 
core::scoring::ScoreFunction
const & 
current_scorefxn () const
 
void current_scorefxn (core::scoring::ScoreFunction const &scorefxn)
 
void recover_low (core::pose::Pose &pose, StageID stage)
 
void set_current_weight (core::scoring::ScoreType type, core::Real setting)
 
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 stage4rot_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_stage5 (core::pose::Pose &pose)
 
void output_debug_structure (core::pose::Pose &pose, std::string prefix) override
 
moves::MonteCarloOP mc_ptr ()
 
- 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...
 

Private Types

typedef FoldConstraints Parent
 

Private Member Functions

moves::MoverOP create_bb_moves (core::pose::Pose &pose, moves::MoverOP std_moves, bool bLargeWobble, core::Real crank_up_angle)
 
void dump_jump_log (core::pose::Pose &pose, std::string const &file_name)
 
moves::MoverOP create_jump_moves (moves::MoverOP stdmove)
 

Private Attributes

bool bRampChainbreaks_
 
bool bOverlapChainbreaks_
 
loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol_
 
core::scoring::constraints::ConstraintSetOP full_constraint_set_
 

Additional Inherited Members

- Public Types inherited from protocols::abinitio::FoldConstraints
typedef ClassicAbinitio Parent
 
- Public Types inherited from protocols::abinitio::ClassicAbinitio
enum  StageID {
  ALL_STAGES = 0, STAGE_1, STAGE_2, STAGE_3a,
  STAGE_3b, STAGE_4, STAGE_4rot, STAGE_5
}
 
- Public Types inherited from protocols::abinitio::Protocol
typedef Mover BaseClass
 
- 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
 
- Public Attributes inherited from protocols::abinitio::ClassicAbinitio
bool bSkipStage1_
 
bool bSkipStage2_
 
bool bSkipStage3_
 
bool bSkipStage4_
 
bool bSkipStage5_
 
utility::vector1< StageIDrecover_low_stages_
 
- Protected Attributes inherited from protocols::abinitio::ClassicAbinitio
core::Size stage1_cycles_
 
core::Size stage2_cycles_
 
core::Size stage3_cycles_
 
core::Size stage4_cycles_
 
core::Size stage5_cycles_
 
core::Real stage4_cycles_pack_rate_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::abinitio::KinematicAbinitio::KinematicAbinitio ( simple_moves::FragmentMoverOP  brute_move_small,
simple_moves::FragmentMoverOP  brute_move_large,
simple_moves::FragmentMoverOP  smooth_move_small,
int  dummy 
)
protocols::abinitio::KinematicAbinitio::KinematicAbinitio ( core::fragment::FragSetCOP  fragset3mer,
core::fragment::FragSetCOP  fragset9mer,
core::kinematics::MoveMapCOP  movemap 
)
protocols::abinitio::KinematicAbinitio::~KinematicAbinitio ( )
overridedefault

Member Function Documentation

void protocols::abinitio::KinematicAbinitio::apply ( core::pose::Pose pose)
overridevirtual

run the protocol

Reimplemented from protocols::abinitio::FoldConstraints.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper.

References protocols::abinitio::FoldConstraints::apply(), protocols::idealize::IdealizeMover::apply(), protocols::abinitio::ClassicAbinitio::brute_move_small(), clone(), protocols::jumping::close_chainbreaks(), closure_protocol_, core::pose::Pose::constraint_set(), protocols::abinitio::ClassicAbinitio::current_scorefxn(), core::pack::interaction_graph::debug, dump_jump_log(), protocols::abinitio::Protocol::evaluator(), protocols::moves::FAIL_RETRY, protocols::idealize::IdealizeMover::fast(), protocols::abinitio::filename(), core::io::silent::SilentStruct::fill_pose(), core::pose::Pose::fold_tree(), full_constraint_set_, protocols::abinitio::Protocol::get_checkpoints(), protocols::moves::Mover::get_current_job(), protocols::moves::Mover::get_current_tag(), protocols::moves::Mover::get_last_move_status(), core::io::silent::SilentFileData::get_structure(), core::io::silent::SilentFileData::has_tag(), protocols::abinitio::Protocol::kinematics(), protocols::abinitio::FoldConstraints::max_seq_sep_fudge(), protocols::mean_field::min(), protocols::abinitio::ClassicAbinitio::movemap(), protocols::moves::MS_SUCCESS, protocols::abinitio::ClassicAbinitio::output_debug_structure(), protocols::abinitio::KinematicControl::prepare_pose_for_sampling(), core::io::silent::SilentFileData::read_file(), core::scoring::rg, protocols::moves::Mover::set_current_tag(), protocols::abinitio::Protocol::set_kinematics(), protocols::moves::Mover::set_last_move_status(), protocols::abinitio::FoldConstraints::set_movemap(), protocols::abinitio::FoldConstraints::set_seq_sep_stage1(), protocols::abinitio::FoldConstraints::set_seq_sep_stage3(), protocols::abinitio::ClassicAbinitio::set_skip_stage1(), protocols::abinitio::ClassicAbinitio::set_skip_stage2(), protocols::loops::skip_rate, protocols::jumping::JumpSample::steal_orientation_and_pleating(), tr(), protocols::hybridization::val, and core::fragment::FragmentIO::write_data().

Referenced by dump_jump_log().

moves::MoverOP protocols::abinitio::KinematicAbinitio::clone ( ) const
inlineoverridevirtual
void protocols::abinitio::KinematicAbinitio::closure_protocol ( loops::loop_closure::ccd::SlidingWindowLoopClosureOP  closure_protocol)
inline

set the closure_protocol... if not set no closure...

References closure_protocol_.

moves::MoverOP protocols::abinitio::KinematicAbinitio::create_bb_moves ( core::pose::Pose pose,
moves::MoverOP  std_moves,
bool  bLargeWobble,
core::Real  crank_up_angle 
)
private
moves::MoverOP protocols::abinitio::KinematicAbinitio::create_jump_moves ( moves::MoverOP  stdmove)
private
void protocols::abinitio::KinematicAbinitio::dump_jump_log ( core::pose::Pose pose,
std::string const &  filename 
)
private
std::string protocols::abinitio::KinematicAbinitio::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::abinitio::FoldConstraints.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper.

bool protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage3 ( core::pose::Pose pose,
core::Size  iteration,
core::Size  total 
)
overridevirtual
bool protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage4 ( core::pose::Pose pose,
core::Size  iteration,
core::Size  total 
)
overridevirtual
bool protocols::abinitio::KinematicAbinitio::prepare_stage1 ( core::pose::Pose pose)
overridevirtual
bool protocols::abinitio::KinematicAbinitio::prepare_stage2 ( core::pose::Pose pose)
overridevirtual
bool protocols::abinitio::KinematicAbinitio::prepare_stage3 ( core::pose::Pose pose)
overridevirtual
void protocols::abinitio::KinematicAbinitio::register_options ( )
static
void protocols::abinitio::KinematicAbinitio::replace_scorefxn ( core::pose::Pose pose,
StageID  stage,
core::Real  intra_stage_progress 
)
overrideprotectedvirtual
void protocols::abinitio::KinematicAbinitio::set_default_options ( )
overrideprotectedvirtual
void protocols::abinitio::KinematicAbinitio::set_default_scores ( )
overrideprotectedvirtual
void protocols::abinitio::KinematicAbinitio::set_max_seq_sep ( core::pose::Pose pose,
core::Size  setting 
)
overridevirtual
moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage1_mover ( core::pose::Pose pose,
moves::TrialMoverOP  trials_in 
)
overridevirtual
moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage2_mover ( core::pose::Pose pose,
moves::TrialMoverOP  trials_in 
)
overridevirtual
moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage3_mover ( core::pose::Pose pose,
int  lct1,
int  lct2,
moves::TrialMoverOP  trials_in 
)
overridevirtual
moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage4_mover ( core::pose::Pose pose,
int  kk,
moves::TrialMoverOP  trials_in 
)
overridevirtual

Member Data Documentation

bool protocols::abinitio::KinematicAbinitio::bOverlapChainbreaks_
private
bool protocols::abinitio::KinematicAbinitio::bRampChainbreaks_
private
loops::loop_closure::ccd::SlidingWindowLoopClosureOP protocols::abinitio::KinematicAbinitio::closure_protocol_
private

Referenced by apply(), and closure_protocol().

core::scoring::constraints::ConstraintSetOP protocols::abinitio::KinematicAbinitio::full_constraint_set_
private

Referenced by apply(), and KinematicAbinitio().


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