#include <ClassicAbinitio.hh>

Inheritance diagram for protocols::abinitio::ClassicAbinitio:

Collaboration diagram for protocols::abinitio::ClassicAbinitio:

Public Types
enum	StageID { ALL_STAGES = 0, STAGE_1, STAGE_2, STAGE_3a, STAGE_3b, STAGE_4, STAGE_5 }

Public Types inherited from protocols::abinitio::Protocol
typedef Mover	BaseClass

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Public Member Functions
	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 void	apply (core::pose::Pose &pose)

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::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::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...

Public Attributes
bool	bSkipStage1_

bool	bSkipStage2_

bool	bSkipStage3_

bool	bSkipStage4_

bool	bSkipStage5_

utility::vector1< StageID >	recover_low_stages_

Protected Member Functions
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
Size	stage1_cycles_

Size	stage2_cycles_

Size	stage3_cycles_

Size	stage4_cycles_

Size	stage5_cycles_

Private Types
typedef Protocol	Parent

Private Member Functions
ClassicAbinitio const &	operator= (ClassicAbinitio const &src)
	Private, unimplemented assignment operator to prevent assignment of this class. Copy-constructor copying only. More...

Private Attributes
core::scoring::ScoreFunctionOP	score_stage1_

core::scoring::ScoreFunctionOP	score_stage2_

core::scoring::ScoreFunctionOP	score_stage3a_

core::scoring::ScoreFunctionOP	score_stage3b_

core::scoring::ScoreFunctionOP	score_stage4_

core::scoring::ScoreFunctionOP	score_stage5_

bool	apply_large_frags_

bool	short_insert_region_

bool	just_smooth_cycles_

bool	bQuickTest_

bool	close_chbrk_

core::Real	temperature_

core::kinematics::MoveMapCOP	movemap_

moves::MonteCarloOP	mc_

simple_moves::FragmentMoverOP	brute_move_small_

simple_moves::FragmentMoverOP	brute_move_large_

simple_moves::FragmentMoverOP	smooth_move_small_

moves::TrialMoverOP	trial_large_

moves::TrialMoverOP	trial_small_

moves::TrialMoverOP	smooth_trial_small_

Size	total_trials_

Detailed Description

@ detail general usage: ClassicAbinitio abinitio; abinitio.init( pose ); ... while(nstruct) { abinitio.apply( pose ); }

call ClassicAbinitio::register_options() before core::init to add relevant options to the applications help

, with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:

Stage 1: large (usually 9mer) randomly selected fragment insertions, only VDW term turned on. Uses score0.wts_patch and runs for either a maximum of 2000 cycles or until all moveable phi/psi values have been changed.
Stage 2: large randomly selected fragment insertions, more score terms turned on. Uses score1.wts_patch and runs for 2000 cycles.
Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch, running tunable numbers of 2000-cycle iterations between the two scoring functions.
Stage 4: uses small (usually 3mer) fragment insertions with the fragment selection based on the Gunn cost for finding local fragment moves. Runs for 4000-cycles and uses score3.wts_patch.

The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() ...

Behaviour can be changed in the following ways:

use non-classic FragmentMover –> eg. not uniformly sampled fragments, but using some weighting –> large and small moves doesn't have to be 3mers and 9mers... use other movers... —> or other fragets for the "convenience constructor" use custom trial classes –> overload update_moves()

change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves ...

change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()

Definition at line 119 of file ClassicAbinitio.hh.

Member Typedef Documentation

typedef Protocol protocols::abinitio::ClassicAbinitio::Parent

private

Definition at line 120 of file ClassicAbinitio.hh.

Member Enumeration Documentation

enum protocols::abinitio::ClassicAbinitio::StageID

Enumerator
ALL_STAGES
STAGE_1
STAGE_2
STAGE_3a
STAGE_3b
STAGE_4
STAGE_5

Definition at line 122 of file ClassicAbinitio.hh.

Constructor & Destructor Documentation

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.

large (stage1/stage2) small(stage2/stage3/stage4) smooth_small ( stage3/stage4)

Definition at line 137 of file ClassicAbinitio.cc.

References bSkipStage1_, bSkipStage2_, close_chbrk_, protocols::abinitio::Protocol::get_checkpoints(), movemap_, protocols::checkpoint::CheckPointer::set_type(), and protocols::moves::Mover::type().

Referenced by clone().

protocols::abinitio::ClassicAbinitio::ClassicAbinitio	(	core::fragment::FragSetCOP	fragset_small,
		core::fragment::FragSetCOP	fragset_large,
		core::kinematics::MoveMapCOP	movemap
	)

constructor: supply fragsets for large and small fragment moves

Definition at line 159 of file ClassicAbinitio.cc.

References brute_move_large_, brute_move_small_, bSkipStage1_, bSkipStage2_, close_chbrk_, core::pack::interaction_graph::debug, protocols::abinitio::Protocol::get_checkpoints(), protocols::checkpoint::CheckPointer::set_type(), smooth_move_small_, and protocols::moves::Mover::type().

protocols::abinitio::ClassicAbinitio::ClassicAbinitio ( ClassicAbinitio const & src)

Explicit copy constructor since this class contains OPs of other classes.

Call parent's copy constructor and perform a shallow copy of all the data. NOTE: Shallow copy is only to preserve behavior pre 9/7/2009 when the compiler-provided copy constructor was being invoked.

Definition at line 209 of file ClassicAbinitio.cc.

References apply_large_frags_, bQuickTest_, brute_move_large_, brute_move_small_, bSkipStage1_, bSkipStage2_, bSkipStage3_, bSkipStage4_, bSkipStage5_, close_chbrk_, just_smooth_cycles_, mc_, movemap_, recover_low_stages_, score_stage1_, score_stage2_, score_stage3a_, score_stage3b_, score_stage4_, score_stage5_, short_insert_region_, smooth_move_small_, smooth_trial_small_, stage1_cycles_, stage2_cycles_, stage3_cycles_, stage4_cycles_, stage5_cycles_, temperature_, total_trials_, trial_large_, and trial_small_.

protocols::abinitio::ClassicAbinitio::~ClassicAbinitio ( )

Explicit destructor since this class contains OPs of other classes.

Explicit destructor is needed to destroy all the OPs The compiler does all the work, but it requires that we place the destructor in the .cc file.

Definition at line 250 of file ClassicAbinitio.cc.

Member Function Documentation

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

virtual

Reimplemented from protocols::abinitio::Protocol.

Reimplemented in protocols::abinitio::Stage1Sampler, protocols::abinitio::JumpingFoldConstraintsWrapper, protocols::abinitio::FoldConstraints, protocols::abinitio::KinematicAbinitio, and protocols::abinitio::JumpingFoldConstraints.

Definition at line 270 of file ClassicAbinitio.cc.

References protocols::abinitio::Protocol::apply(), bSkipStage1_, bSkipStage2_, bSkipStage3_, bSkipStage4_, bSkipStage5_, protocols::checkpoint::CheckPointer::checkpoint(), close_chbrk_, core::pose::Pose::constraint_set(), current_scorefxn(), core::pack::interaction_graph::debug, protocols::checkpoint::CheckPointer::debug(), do_stage1_cycles(), do_stage2_cycles(), do_stage3_cycles(), do_stage4_cycles(), do_stage5_cycles(), protocols::moves::FAIL_RETRY, protocols::checkpoint::CheckPointer::flush_checkpoints(), protocols::abinitio::Protocol::get_checkpoints(), protocols::moves::Mover::get_current_tag(), core::scoring::linear_chainbreak, mc(), output_debug_structure(), prepare_stage1(), prepare_stage2(), prepare_stage3(), prepare_stage4(), prepare_stage5(), recover_low(), protocols::moves::MonteCarlo::reset_counters(), protocols::moves::Mover::set_last_move_status(), set_score_weight(), core::scoring::ScoreFunction::show(), protocols::moves::MonteCarlo::show_counters(), stage1_cycles(), stage2_cycles(), stage3_cycles(), stage4_cycles(), stage5_cycles(), STAGE_1, STAGE_2, STAGE_3b, STAGE_4, STAGE_5, protocols::moves::MonteCarlo::total_trials(), total_trials_, and tr().

Referenced by protocols::surface_docking::SurfaceDockingProtocol::abinitio(), protocols::abinitio::DomainAssembly::apply(), and protocols::abinitio::FoldConstraints::apply().

bool protocols::abinitio::ClassicAbinitio::bQuickTest ( ) const

inline

Definition at line 371 of file ClassicAbinitio.hh.

References bQuickTest_.

Referenced by protocols::abinitio::FoldConstraints::set_default_options(), and set_default_options().

simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::brute_move_large ( )

Definition at line 537 of file ClassicAbinitio.cc.

References brute_move_large_.

Referenced by protocols::abinitio::KinematicAbinitio::create_bb_moves(), do_stage1_cycles(), and set_moves().

simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::brute_move_small ( )

Definition at line 531 of file ClassicAbinitio.cc.

References brute_move_small_.

Referenced by protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::KinematicAbinitio::create_bb_moves(), and set_moves().

moves::MoverOP protocols::abinitio::ClassicAbinitio::clone ( ) const

virtual

ClassicAbinitio has virtual functions... use this to obtain a new instance.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper, protocols::abinitio::FoldConstraints, protocols::abinitio::KinematicAbinitio, and protocols::abinitio::JumpingFoldConstraints.

Definition at line 265 of file ClassicAbinitio.cc.

References ClassicAbinitio().

scoring::ScoreFunction const & protocols::abinitio::ClassicAbinitio::current_scorefxn ( ) const

protected

Definition at line 713 of file ClassicAbinitio.cc.

References mc(), and protocols::moves::MonteCarlo::score_function().

Referenced by protocols::abinitio::KinematicAbinitio::apply(), apply(), protocols::abinitio::FoldConstraints::do_stage2_cycles(), do_stage3_cycles(), do_stage4_cycles(), protocols::abinitio::FoldConstraints::min_trial(), protocols::abinitio::KinematicAbinitio::replace_scorefxn(), and replace_scorefxn().

void protocols::abinitio::ClassicAbinitio::current_scorefxn ( core::scoring::ScoreFunction const & scorefxn)

protected

Definition at line 718 of file ClassicAbinitio.cc.

References mc(), and protocols::moves::MonteCarlo::score_function().

bool protocols::abinitio::ClassicAbinitio::do_stage1_cycles ( core::pose::Pose & pose)

protectedvirtual

Reimplemented in protocols::abinitio::FoldConstraints.

Definition at line 837 of file ClassicAbinitio.cc.

References brute_move_large(), mc(), movemap(), protocols::moves::MonteCarlo::reset(), protocols::abinitio::AllResiduesChanged::show_unmoved(), stage1_cycles(), stage1_mover(), tr(), and trial_large().

Referenced by apply(), and protocols::abinitio::FoldConstraints::do_stage1_cycles().

bool protocols::abinitio::ClassicAbinitio::do_stage2_cycles ( core::pose::Pose & pose)

protectedvirtual

Reimplemented in protocols::abinitio::FoldConstraints.

Definition at line 859 of file ClassicAbinitio.cc.

References protocols::moves::RepeatMover::apply(), apply_large_frags_, mc_ptr(), short_insert_region_, stage2_cycles(), stage2_mover(), trial_large_, and trial_small_.

Referenced by apply(), and protocols::abinitio::FoldConstraints::do_stage2_cycles().

bool protocols::abinitio::ClassicAbinitio::do_stage3_cycles ( core::pose::Pose & pose)

protectedvirtual

stage3 cycles: nloop1 : outer iterations nloop2 : inner iterations stage3_cycle : trials per inner iteration every inner iteration we switch between score_stage3a ( default: score2 ) and score_stage3b ( default: score 5 )

prepare_loop_in_stage3() is called before the stage3_cycles() of trials are started.

first outer loop-iteration is done with TrialMover trial_large() all following iterations with trial_small()

start each iteration with the lowest_score_pose. ( mc->recover_low() – called in prepare_loop_in_stage3() )

Definition at line 888 of file ClassicAbinitio.cc.

References protocols::moves::WhileMover::apply(), protocols::moves::RepeatMover::apply(), protocols::checkpoint::CheckPointer::checkpoint(), current_scorefxn(), protocols::checkpoint::CheckPointer::debug(), protocols::abinitio::Protocol::get_checkpoints(), protocols::moves::Mover::get_current_tag(), prepare_loop_in_stage3(), recover_low(), short_insert_region_, stage3_cycles(), stage3_mover(), STAGE_3a, STAGE_3b, tr(), trial_large(), and trial_small().

Referenced by apply().

bool protocols::abinitio::ClassicAbinitio::do_stage4_cycles ( core::pose::Pose & pose)

protectedvirtual

stage4 cycles: nloop_stage4: iterations stage4_cycle : trials per iteration

first iteration: use trial_small() following iterations: use trial_smooth() only trial_smooth() if just_smooth_cycles==true

prepare_loop_in_stage4() is called each time before the stage4_cycles_ of trials are started.

start each iteration with the lowest_score_pose. ( mc->recover_low() in prepare_loop_in_stage4() )

Definition at line 957 of file ClassicAbinitio.cc.

References protocols::moves::RepeatMover::apply(), protocols::checkpoint::CheckPointer::checkpoint(), current_scorefxn(), protocols::checkpoint::CheckPointer::debug(), protocols::abinitio::Protocol::get_checkpoints(), protocols::moves::Mover::get_current_tag(), just_smooth_cycles_, prepare_loop_in_stage4(), recover_low(), stage4_cycles(), stage4_mover(), STAGE_4, tr(), trial_small(), and trial_smooth().

Referenced by apply().

bool protocols::abinitio::ClassicAbinitio::do_stage5_cycles ( core::pose::Pose & pose)

protectedvirtual

Definition at line 990 of file ClassicAbinitio.cc.

References protocols::moves::RepeatMover::apply(), mc(), mc_ptr(), movemap(), protocols::moves::MonteCarlo::reset(), stage5_cycles(), stage5_mover(), and temperature_.

Referenced by apply().

std::string protocols::abinitio::ClassicAbinitio::get_name ( ) const

virtual

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

Reimplemented from protocols::abinitio::Protocol.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper, protocols::abinitio::FoldConstraints, and protocols::abinitio::KinematicAbinitio.

Definition at line 519 of file ClassicAbinitio.cc.

void protocols::abinitio::ClassicAbinitio::init ( core::pose::Pose const & pose)

virtual

setup moves, mc-object, scores

can't call this from constructor; virtual functions don't operate until construction has completed.

Reimplemented from protocols::abinitio::Protocol.

Definition at line 257 of file ClassicAbinitio.cc.

References set_defaults().

Referenced by protocols::surface_docking::SurfaceDockingProtocol::abinitio(), and protocols::abinitio::DomainAssembly::apply().

bool protocols::abinitio::ClassicAbinitio::just_smooth_cycles ( ) const

inline

Definition at line 329 of file ClassicAbinitio.hh.

References just_smooth_cycles_.

moves::MonteCarlo& protocols::abinitio::ClassicAbinitio::mc ( )

inline

Definition at line 194 of file ClassicAbinitio.hh.

References mc_.

Referenced by protocols::abinitio::FoldConstraints::apply(), apply(), protocols::abinitio::KinematicAbinitio::create_bb_moves(), current_scorefxn(), protocols::abinitio::FoldConstraints::do_stage1_cycles(), do_stage1_cycles(), protocols::abinitio::FoldConstraints::do_stage2_cycles(), do_stage5_cycles(), protocols::abinitio::FoldConstraints::min_trial(), output_debug_structure(), set_current_weight(), protocols::abinitio::KinematicAbinitio::set_max_seq_sep(), and protocols::abinitio::FoldConstraints::set_max_seq_sep().

moves::MonteCarlo const& protocols::abinitio::ClassicAbinitio::mc ( ) const

inline

Definition at line 199 of file ClassicAbinitio.hh.

References mc_.

moves::MonteCarloOP protocols::abinitio::ClassicAbinitio::mc_ptr ( )

protected

Definition at line 1181 of file ClassicAbinitio.cc.

References mc_.

Referenced by do_stage2_cycles(), do_stage5_cycles(), protocols::abinitio::KinematicAbinitio::stage1_mover(), protocols::abinitio::KinematicAbinitio::stage2_mover(), protocols::abinitio::KinematicAbinitio::stage3_mover(), and protocols::abinitio::KinematicAbinitio::stage4_mover().

core::kinematics::MoveMapCOP protocols::abinitio::ClassicAbinitio::movemap ( )

Definition at line 568 of file ClassicAbinitio.cc.

References movemap_.

Referenced by protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::JumpingFoldConstraintsWrapper::apply(), protocols::abinitio::KinematicAbinitio::create_bb_moves(), do_stage1_cycles(), do_stage5_cycles(), prepare_stage3(), prepare_stage4(), and protocols::abinitio::FoldConstraints::setup_default_min_move().

ClassicAbinitio const& protocols::abinitio::ClassicAbinitio::operator= ( ClassicAbinitio const & src)

private

Private, unimplemented assignment operator to prevent assignment of this class. Copy-constructor copying only.

void protocols::abinitio::ClassicAbinitio::output_debug_structure	(	core::pose::Pose &	pose,
		std::string	prefix
	)

protectedvirtual

Reimplemented from protocols::abinitio::Protocol.

Definition at line 1186 of file ClassicAbinitio.cc.

References protocols::simple_moves::LoggedFragmentMover::clear(), core::pose::Pose::dump_pdb(), protocols::abinitio::filename(), protocols::moves::Mover::get_current_tag(), mc(), protocols::abinitio::Protocol::output_debug_structure(), protocols::moves::MonteCarlo::score_function(), and protocols::simple_moves::LoggedFragmentMover::show().

Referenced by protocols::abinitio::KinematicAbinitio::apply(), and apply().

bool protocols::abinitio::ClassicAbinitio::prepare_loop_in_stage3	(	core::pose::Pose &	pose,
		Size	iteration,
		Size	total
	)

protectedvirtual

Reimplemented in protocols::abinitio::FoldConstraints, protocols::abinitio::KinematicAbinitio, and protocols::abinitio::JumpingFoldConstraints.

Definition at line 1137 of file ClassicAbinitio.cc.

References close_chbrk_, core::scoring::linear_chainbreak, recover_low(), replace_scorefxn(), set_score_weight(), STAGE_3a, STAGE_3b, and tr().

Referenced by do_stage3_cycles(), and protocols::abinitio::FoldConstraints::prepare_loop_in_stage3().

bool protocols::abinitio::ClassicAbinitio::prepare_loop_in_stage4	(	core::pose::Pose &	pose,
		Size	iteration,
		Size	total
	)

protectedvirtual

Reimplemented in protocols::abinitio::FoldConstraints, protocols::abinitio::KinematicAbinitio, and protocols::abinitio::JumpingFoldConstraints.

Definition at line 1168 of file ClassicAbinitio.cc.

References close_chbrk_, core::scoring::linear_chainbreak, replace_scorefxn(), set_current_weight(), and STAGE_4.

Referenced by do_stage4_cycles(), and protocols::abinitio::FoldConstraints::prepare_loop_in_stage4().

bool protocols::abinitio::ClassicAbinitio::prepare_stage1 ( core::pose::Pose & pose)

protectedvirtual

Reimplemented in protocols::abinitio::FoldConstraints, protocols::abinitio::KinematicAbinitio, and protocols::abinitio::JumpingFoldConstraints.

Definition at line 1082 of file ClassicAbinitio.cc.

References mc_, replace_scorefxn(), STAGE_1, and temperature_.

Referenced by apply(), and protocols::abinitio::FoldConstraints::prepare_stage1().

bool protocols::abinitio::ClassicAbinitio::prepare_stage2 ( core::pose::Pose & pose)

protectedvirtual

Reimplemented in protocols::abinitio::FoldConstraints, protocols::abinitio::KinematicAbinitio, and protocols::abinitio::JumpingFoldConstraints.

Definition at line 1092 of file ClassicAbinitio.cc.

References replace_scorefxn(), and STAGE_2.

Referenced by apply(), and protocols::abinitio::FoldConstraints::prepare_stage2().

bool protocols::abinitio::ClassicAbinitio::prepare_stage3 ( core::pose::Pose & pose)

protectedvirtual

Reimplemented in protocols::abinitio::KinematicAbinitio, and protocols::abinitio::JumpingFoldConstraints.

Definition at line 1101 of file ClassicAbinitio.cc.

References movemap(), replace_scorefxn(), set_movemap(), and STAGE_3a.

Referenced by apply(), and protocols::abinitio::KinematicAbinitio::prepare_stage3().

bool protocols::abinitio::ClassicAbinitio::prepare_stage4 ( core::pose::Pose & pose)

protectedvirtual

Reimplemented in protocols::abinitio::FoldConstraints.

Definition at line 1113 of file ClassicAbinitio.cc.

References movemap(), replace_scorefxn(), set_movemap(), STAGE_4, and tr().

Referenced by apply(), and protocols::abinitio::FoldConstraints::prepare_stage4().

bool protocols::abinitio::ClassicAbinitio::prepare_stage5 ( core::pose::Pose & pose)

protectedvirtual

Definition at line 1128 of file ClassicAbinitio.cc.

References replace_scorefxn(), and STAGE_5.

Referenced by apply().

void protocols::abinitio::ClassicAbinitio::recover_low	(	core::pose::Pose &	pose,
		StageID	stage
	)

protected

Definition at line 1042 of file ClassicAbinitio.cc.

References protocols::abinitio::contains_stageid(), mc_, and recover_low_stages_.

Referenced by apply(), do_stage3_cycles(), do_stage4_cycles(), and prepare_loop_in_stage3().

void protocols::abinitio::ClassicAbinitio::register_options ( )

static

call this: ClassicAbinitio::register_options() before devel::init(). Derived classes that overload this function should also call Parent::register_options()

Definition at line 107 of file ClassicAbinitio.cc.

References core::pack::interaction_graph::debug, and protocols::moves::Mover::register_options().

Referenced by protocols::surface_docking::SurfaceDockingProtocol::abinitio(), and protocols::abinitio::FoldConstraints::register_options().

void protocols::abinitio::ClassicAbinitio::replace_scorefxn	(	core::pose::Pose &	pose,
		StageID	stage,
		core::Real	intra_stage_progress
	)

protectedvirtual

Reimplemented in protocols::abinitio::KinematicAbinitio.

Definition at line 1049 of file ClassicAbinitio.cc.

References current_scorefxn(), mc_, score_stage1_, score_stage2_, score_stage3a_, score_stage3b_, score_stage4_, score_stage5_, STAGE_1, STAGE_2, STAGE_3a, STAGE_3b, STAGE_4, STAGE_5, and temperature_.

Referenced by prepare_loop_in_stage3(), prepare_loop_in_stage4(), prepare_stage1(), prepare_stage2(), prepare_stage3(), prepare_stage4(), prepare_stage5(), and protocols::abinitio::KinematicAbinitio::replace_scorefxn().

void protocols::abinitio::ClassicAbinitio::set_current_weight	(	core::scoring::ScoreType	type,
		core::Real	setting
	)

protected

Definition at line 723 of file ClassicAbinitio.cc.

References mc(), protocols::moves::MonteCarlo::score_function(), and core::scoring::ScoreFunction::set_weight().

Referenced by protocols::abinitio::FoldConstraints::do_stage2_cycles(), protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage4(), and prepare_loop_in_stage4().

void protocols::abinitio::ClassicAbinitio::set_cycles ( core::Real increase_cycles = 1.0)

virtual

Definition at line 632 of file ClassicAbinitio.cc.

References bSkipStage2_, bSkipStage3_, stage1_cycles_, stage2_cycles_, stage3_cycles_, stage4_cycles_, and stage5_cycles_.

Referenced by set_default_options().

void protocols::abinitio::ClassicAbinitio::set_default_mc	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	scorefxn
	)

protectedvirtual

Definition at line 616 of file ClassicAbinitio.cc.

References set_mc(), and temperature_.

Referenced by set_defaults().

void protocols::abinitio::ClassicAbinitio::set_default_options ( )

protectedvirtual

Reimplemented in protocols::abinitio::KinematicAbinitio, protocols::abinitio::JumpingFoldConstraints, and protocols::abinitio::FoldConstraints.

Definition at line 729 of file ClassicAbinitio.cc.

References apply_large_frags_, bQuickTest(), bQuickTest_, bSkipStage1_, bSkipStage2_, bSkipStage3_, bSkipStage4_, bSkipStage5_, close_chbrk_, core::sequence::end, just_smooth_cycles_, recover_low_stages_, set_cycles(), short_insert_region_, STAGE_1, STAGE_2, STAGE_3a, STAGE_3b, STAGE_4, and STAGE_5.

Referenced by protocols::abinitio::FoldConstraints::set_default_options(), and set_defaults().

void protocols::abinitio::ClassicAbinitio::set_default_scores ( )

protectedvirtual

Reimplemented in protocols::abinitio::KinematicAbinitio, protocols::abinitio::JumpingFoldConstraints, and protocols::abinitio::FoldConstraints.

Definition at line 648 of file ClassicAbinitio.cc.

References ALL_STAGES, core::scoring::ScoreFunctionFactory::create_score_function(), score_stage1_, score_stage2_, score_stage3a_, score_stage3b_, score_stage4_, score_stage5_, set_score_weight(), tr(), and core::scoring::vdw.

Referenced by protocols::abinitio::FoldConstraints::set_default_scores(), and set_defaults().

void protocols::abinitio::ClassicAbinitio::set_defaults ( core::pose::Pose const & pose)

protectedvirtual

Definition at line 573 of file ClassicAbinitio.cc.

References bSkipStage1_, bSkipStage2_, bSkipStage3_, bSkipStage4_, bSkipStage5_, score_stage1_, set_default_mc(), set_default_options(), set_default_scores(), temperature_, and update_moves().

Referenced by init().

void protocols::abinitio::ClassicAbinitio::set_mc ( moves::MonteCarloOP mc_in)

Definition at line 624 of file ClassicAbinitio.cc.

References mc_, smooth_trial_small_, trial_large_, and trial_small_.

Referenced by set_default_mc().

void protocols::abinitio::ClassicAbinitio::set_movemap ( core::kinematics::MoveMapCOP mm)

virtual

Reimplemented in protocols::abinitio::FoldConstraints.

Definition at line 544 of file ClassicAbinitio.cc.

References brute_move_large_, brute_move_small_, movemap_, and smooth_move_small_.

Referenced by prepare_stage3(), prepare_stage4(), and protocols::abinitio::FoldConstraints::set_movemap().

void protocols::abinitio::ClassicAbinitio::set_moves	(	simple_moves::FragmentMoverOP	brute_move_small,
		simple_moves::FragmentMoverOP	brute_move_large,
		simple_moves::FragmentMoverOP	smooth_move_small
	)