Rosetta Protocols  2014.35
Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
protocols::abinitio::JumpingFoldConstraints Class Reference

#include <JumpingFoldConstraints.hh>

Public Member Functions

 JumpingFoldConstraints (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, jumping::BaseJumpSetupOP jump_def, int dummy)
 JumpingFoldConstraints (core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap, jumping::BaseJumpSetupOP jump_def)
 ~JumpingFoldConstraints ()
virtual moves::MoverOP clone () const
 ... More...
virtual void apply (core::pose::Pose &pose)
 run the protocol More...
virtual void set_max_seq_sep (core::pose::Pose &pose, Size setting)
void set_native_pose (core::pose::Pose const &native_pose)
void set_defeat_purpose (bool setting)
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_loop_in_stage3 (core::pose::Pose &, Size, Size)
virtual bool prepare_loop_in_stage4 (core::pose::Pose &, Size, Size)
void jump_cycles (core::pose::Pose &pose, Size cycles)
moves::TrialMoverOP stage2_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)
moves::TrialMoverOP stage3_mover (core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in)
moves::TrialMoverOP stage4_mover (core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in)
- 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 ()
 Explicit destructor to handle OPs. More...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. 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 ()
 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...
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)
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
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)
virtual void parse_my_tag (TagCOP tag, basic::datacache::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
 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...
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...

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

virtual void setup_default_min_move ()
virtual void set_default_scores ()
 sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0 More...
virtual void set_default_options ()
- Protected Member Functions inherited from protocols::abinitio::FoldConstraints
bool prepare_stage4 (core::pose::Pose &pose)
bool do_stage1_cycles (core::pose::Pose &pose)
bool do_stage2_cycles (core::pose::Pose &pose)
virtual void set_movemap (core::kinematics::MoveMapCOP mm)
void set_min_move (protocols::simple_moves::MinMoverOP mm)
protocols::simple_moves::MinMovermin_move ()
void min_trial (core::pose::Pose &pose)
core::Real max_seq_sep_fudge () const
void max_seq_sep_fudge (core::Real setting)
const & 
constraints ()
void bIgnoreSequenceSeparation (bool setting)
bool bIgnoreSequenceSeparation ()
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)
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_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 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)
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)
moves::MoverOP create_jump_moves (moves::MoverOP stdmove)
void setup_foldtree (core::pose::Pose &)

Private Attributes

jumping::BaseJumpSetupOP jump_def_
bool bChainbreaksAlwaysActive_
bool bRampChainbreaks_
bool bOverlapChainbreaks_
bool bSampleJumps_
bool bStealJumps_
bool bJumpFragMoves_
jumping::JumpSample current_jumps_
core::pose::PoseOP native_pose_
core::pose::Pose starting_pose_
core::fragment::FragSetOP pure_large_frags_
core::fragment::FragSetOP jump_frags_
Size nr_jump_cycles_

Additional Inherited Members

- Public Types inherited from protocols::abinitio::FoldConstraints
typedef ClassicAbinitio Parent
- Public Types inherited from protocols::abinitio::ClassicAbinitio
enum  StageID {
  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::stringStrings
- 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
Size stage1_cycles_
Size stage2_cycles_
Size stage3_cycles_
Size stage4_cycles_
Size stage5_cycles_
core::Real stage4_cycles_pack_rate_

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::abinitio::JumpingFoldConstraints::JumpingFoldConstraints ( simple_moves::FragmentMoverOP  brute_move_small,
simple_moves::FragmentMoverOP  brute_move_large,
simple_moves::FragmentMoverOP  smooth_move_small,
jumping::BaseJumpSetupOP  jump_def,
int  dummy 

Referenced by clone().

protocols::abinitio::JumpingFoldConstraints::JumpingFoldConstraints ( core::fragment::FragSetCOP  fragset3mer,
core::fragment::FragSetCOP  fragset9mer,
core::kinematics::MoveMapCOP  movemap,
jumping::BaseJumpSetupOP  jump_def 
protocols::abinitio::JumpingFoldConstraints::~JumpingFoldConstraints ( )

Member Function Documentation

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

run the protocol

Reimplemented from protocols::abinitio::FoldConstraints.

virtual moves::MoverOP protocols::abinitio::JumpingFoldConstraints::clone ( ) const
moves::MoverOP protocols::abinitio::JumpingFoldConstraints::create_bb_moves ( core::pose::Pose pose,
moves::MoverOP  std_moves,
bool  bLargeWobble,
core::Real  crank_up_angle 
moves::MoverOP protocols::abinitio::JumpingFoldConstraints::create_jump_moves ( moves::MoverOP  stdmove)
void protocols::abinitio::JumpingFoldConstraints::jump_cycles ( core::pose::Pose pose,
Size  cycles 
virtual bool protocols::abinitio::JumpingFoldConstraints::prepare_loop_in_stage3 ( core::pose::Pose ,
Size  ,
virtual bool protocols::abinitio::JumpingFoldConstraints::prepare_loop_in_stage4 ( core::pose::Pose ,
Size  ,
virtual bool protocols::abinitio::JumpingFoldConstraints::prepare_stage1 ( core::pose::Pose pose)
virtual bool protocols::abinitio::JumpingFoldConstraints::prepare_stage2 ( core::pose::Pose pose)
virtual bool protocols::abinitio::JumpingFoldConstraints::prepare_stage3 ( core::pose::Pose pose)
static void protocols::abinitio::JumpingFoldConstraints::register_options ( )
virtual void protocols::abinitio::JumpingFoldConstraints::set_default_options ( )
virtual void protocols::abinitio::JumpingFoldConstraints::set_default_scores ( )

sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0

Reimplemented from protocols::abinitio::FoldConstraints.

void protocols::abinitio::JumpingFoldConstraints::set_defeat_purpose ( bool  setting)
virtual void protocols::abinitio::JumpingFoldConstraints::set_max_seq_sep ( core::pose::Pose pose,
Size  setting 
void protocols::abinitio::JumpingFoldConstraints::set_native_pose ( core::pose::Pose const &  native_pose)
virtual void protocols::abinitio::JumpingFoldConstraints::setup_default_min_move ( )
void protocols::abinitio::JumpingFoldConstraints::setup_foldtree ( core::pose::Pose )
moves::TrialMoverOP protocols::abinitio::JumpingFoldConstraints::stage2_mover ( core::pose::Pose pose,
moves::TrialMoverOP  trials_in 
moves::TrialMoverOP protocols::abinitio::JumpingFoldConstraints::stage3_mover ( core::pose::Pose pose,
int  lct1,
int  lct2,
moves::TrialMoverOP  trials_in 
moves::TrialMoverOP protocols::abinitio::JumpingFoldConstraints::stage4_mover ( core::pose::Pose pose,
int  kk,
moves::TrialMoverOP  trials_in 

Member Data Documentation

bool protocols::abinitio::JumpingFoldConstraints::bChainbreaksAlwaysActive_

Referenced by set_defeat_purpose().

bool protocols::abinitio::JumpingFoldConstraints::bJumpFragMoves_
bool protocols::abinitio::JumpingFoldConstraints::bOverlapChainbreaks_
bool protocols::abinitio::JumpingFoldConstraints::bRampChainbreaks_
bool protocols::abinitio::JumpingFoldConstraints::bSampleJumps_
bool protocols::abinitio::JumpingFoldConstraints::bStealJumps_
jumping::JumpSample protocols::abinitio::JumpingFoldConstraints::current_jumps_
jumping::BaseJumpSetupOP protocols::abinitio::JumpingFoldConstraints::jump_def_
core::fragment::FragSetOP protocols::abinitio::JumpingFoldConstraints::jump_frags_
core::pose::PoseOP protocols::abinitio::JumpingFoldConstraints::native_pose_
Size protocols::abinitio::JumpingFoldConstraints::nr_jump_cycles_
core::fragment::FragSetOP protocols::abinitio::JumpingFoldConstraints::pure_large_frags_
core::pose::Pose protocols::abinitio::JumpingFoldConstraints::starting_pose_

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