#include <KinematicAbinitio.hh>

Inheritance diagram for protocols::abinitio::KinematicAbinitio:

Collaboration diagram for protocols::abinitio::KinematicAbinitio:

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 ()

virtual moves::MoverOP	clone () const
	... More...

virtual void	apply (core::pose::Pose &pose)
	run the protocol More...

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

virtual void	set_max_seq_sep (core::pose::Pose &pose, Size 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)

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)

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 ()
	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 ()
	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::MonteCarlo &	mc ()

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::CheckPointer &	get_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)

Mover &	operator= (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 Strings &	info ()
	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

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. 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
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 ()

virtual void	replace_scorefxn (core::pose::Pose &pose, StageID, core::Real intra_stage_progress)

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	setup_default_min_move ()

virtual void	set_movemap (core::kinematics::MoveMapCOP mm)

void	set_min_move (protocols::simple_moves::MinMoverOP mm)

protocols::simple_moves::MinMover &	min_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 ()

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	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 ()

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 Attributes inherited from protocols::abinitio::ClassicAbinitio
bool	bSkipStage1_

bool	bSkipStage2_

bool	bSkipStage3_

bool	bSkipStage4_

bool	bSkipStage5_

utility::vector1< StageID >	recover_low_stages_

Protected Attributes inherited from protocols::abinitio::ClassicAbinitio
Size	stage1_cycles_

Size	stage2_cycles_

Size	stage3_cycles_

Size	stage4_cycles_

Size	stage5_cycles_

Detailed Description

Definition at line 67 of file KinematicAbinitio.hh.

Member Typedef Documentation

typedef FoldConstraints protocols::abinitio::KinematicAbinitio::Parent

private

Definition at line 68 of file KinematicAbinitio.hh.

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
	)

Definition at line 151 of file KinematicAbinitio.cc.

References full_constraint_set_, and protocols::moves::Mover::type().

Referenced by clone().

protocols::abinitio::KinematicAbinitio::KinematicAbinitio	(	core::fragment::FragSetCOP	fragset3mer,
		core::fragment::FragSetCOP	fragset9mer,
		core::kinematics::MoveMapCOP	movemap
	)

Definition at line 165 of file KinematicAbinitio.cc.

References full_constraint_set_, and protocols::moves::Mover::type().

protocols::abinitio::KinematicAbinitio::~KinematicAbinitio ( )

Definition at line 148 of file KinematicAbinitio.cc.

Member Function Documentation

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

virtual

run the protocol

Reimplemented from protocols::abinitio::FoldConstraints.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper.

Definition at line 306 of file KinematicAbinitio.cc.

Referenced by dump_jump_log().

virtual moves::MoverOP protocols::abinitio::KinematicAbinitio::clone ( ) const

inlinevirtual

...

Reimplemented from protocols::abinitio::FoldConstraints.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper.

Definition at line 85 of file KinematicAbinitio.hh.

References KinematicAbinitio().

void protocols::abinitio::KinematicAbinitio::closure_protocol ( loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol)

inline

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

Definition at line 137 of file KinematicAbinitio.hh.

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
	)