#include <ClassicAbinitio.hh>

Inheritance diagram for protocols::abinitio::ClassicAbinitio:

[legend]

Public Types
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 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 () 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...

moves::MoverOP	clone () const override
	ClassicAbinitio has virtual functions... use this to obtain a new instance. More...

void	apply (core::pose::Pose &pose) override
	Main Method. More...

std::string	get_name () const override
	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)

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	supports_trRosetta_constraints () const override
	This overrides the default and indicates that the ClassicAbInitio protocol DOES support trRosetta constraints. 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)

void	set_use_trRosetta_constraints (bool const setting)
	Set whether we're using trRosetta constraints. More...

core::scoring::ScoreFunctionOP	fullatom_scorefxn ()

core::scoring::ScoreFunctionOP	centroid_scorefxn ()

virtual checkpoint::CheckPointer &	get_checkpoints ()

bool	use_trRosetta_constraints () const
	Get whether we're using trRosetta constraints. More...

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 Strings &	info ()
	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::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...

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	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_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 &, core::Size, core::Size)

virtual bool	prepare_loop_in_stage4 (core::pose::Pose &, core::Size, core::Size)

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...

Protected Attributes
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_

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_stage4rot_

core::scoring::ScoreFunctionOP	score_stage4rot_sc_

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_

moves::TrialMoverOP	trial_small_pack_

moves::TrialMoverOP	smooth_trial_small_pack_

minimization_packing::PackRotamersMoverOP	pack_rotamers_

core::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::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()

Member Typedef Documentation

◆ Parent

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

private

Member Enumeration Documentation

◆ StageID

enum protocols::abinitio::ClassicAbinitio::StageID

Enumerator
ALL_STAGES
STAGE_1
STAGE_2
STAGE_3a
STAGE_3b
STAGE_4
STAGE_4rot
STAGE_5

Constructor & Destructor Documentation

◆ ClassicAbinitio() [1/3]

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.

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

References brute_move_large(), bSkipStage1_, bSkipStage2_, close_chbrk_, protocols::abinitio::Protocol::get_checkpoints(), movemap_, protocols::checkpoint::CheckPointer::set_type(), stage4_cycles_pack_rate_, and protocols::moves::Mover::type().

◆ ClassicAbinitio() [2/3]

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

References brute_move_large_, brute_move_small_, bSkipStage1_, bSkipStage2_, close_chbrk_, core::pack::interaction_graph::debug, protocols::abinitio::Protocol::get_checkpoints(), movemap(), pack_rotamers_, protocols::checkpoint::CheckPointer::set_type(), smooth_move_small_, stage4_cycles_pack_rate_, and protocols::moves::Mover::type().

◆ ClassicAbinitio() [3/3]

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.

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_stage4rot_, 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_.

◆ ~ClassicAbinitio()

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

overridedefault

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.

Member Function Documentation

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

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

References core::pose::Pose::add_constraints(), 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(), core::pose::Pose::remove_constraints(), 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_, tr(), and protocols::abinitio::Protocol::use_trRosetta_constraints().

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

◆ bQuickTest()

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

inline

References bQuickTest_.

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

◆ brute_move_large()

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

References brute_move_large_.

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

◆ brute_move_small()

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

References brute_move_small_.

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

◆ clone()

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

overridevirtual

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

Reimplemented from protocols::moves::Mover.

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

Referenced by set_current_weight().

◆ current_scorefxn() [1/2]

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

protected

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

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

◆ current_scorefxn() [2/2]

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

protected

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::ScoreFunction::clone(), core::scoring::dihedral_constraint, mc(), protocols::moves::MonteCarlo::score_function(), and protocols::abinitio::Protocol::use_trRosetta_constraints().

◆ do_stage1_cycles()

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

protectedvirtual

Reimplemented in protocols::abinitio::FoldConstraints.

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().

◆ do_stage2_cycles()

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

protectedvirtual

Reimplemented in protocols::abinitio::FoldConstraints.

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().

◆ do_stage3_cycles()

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

protectedvirtual

@detail 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() )

References protocols::moves::RepeatMover::apply(), protocols::moves::WhileMover::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().

◆ do_stage4_cycles()

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

protectedvirtual

@detail 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() )

References protocols::moves::RepeatMover::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::chemical::CENTROID_ROT, protocols::checkpoint::CheckPointer::checkpoint(), current_scorefxn(), protocols::checkpoint::CheckPointer::debug(), protocols::abinitio::Protocol::get_checkpoints(), protocols::moves::Mover::get_current_tag(), just_smooth_cycles_, mc_, pack_rotamers_, prepare_loop_in_stage4(), recover_low(), replace_scorefxn(), score_stage4rot_, score_stage4rot_sc_, stage4_cycles(), stage4_mover(), stage4rot_mover(), STAGE_4, STAGE_4rot, tr(), trial_small(), trial_smooth(), and core::scoring::vdw.

Referenced by apply().

◆ do_stage5_cycles()

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

protectedvirtual

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

Referenced by apply().

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

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

◆ init()

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

overridevirtual

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.

References set_defaults().

Referenced by protocols::abinitio::DomainAssembly::apply().

◆ just_smooth_cycles()

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

inline

References just_smooth_cycles_.

◆ mc() [1/2]

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

inline

References mc_.

Referenced by apply(), protocols::abinitio::FoldConstraints::apply(), protocols::abinitio::KinematicAbinitio::create_bb_moves(), current_scorefxn(), do_stage1_cycles(), protocols::abinitio::FoldConstraints::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::FoldConstraints::set_max_seq_sep(), and protocols::abinitio::KinematicAbinitio::set_max_seq_sep().

◆ mc() [2/2]

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

inline

References mc_.

◆ mc_ptr()

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

protected

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().

◆ movemap()

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

References movemap_.

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

◆ operator=()

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

private

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

◆ output_debug_structure()

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

overrideprotectedvirtual

Reimplemented from protocols::abinitio::Protocol.

References 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 apply(), and protocols::abinitio::KinematicAbinitio::apply().

◆ prepare_loop_in_stage3()

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

protectedvirtual

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

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

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

◆ prepare_loop_in_stage4()

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

protectedvirtual

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

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

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

◆ prepare_stage1()

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

protectedvirtual

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

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

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

◆ prepare_stage2()

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

protectedvirtual

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

References replace_scorefxn(), and STAGE_2.

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

◆ prepare_stage3()

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

protectedvirtual

Reimplemented in protocols::abinitio::KinematicAbinitio.

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

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

◆ prepare_stage4()

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

protectedvirtual

Reimplemented in protocols::abinitio::FoldConstraints.

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

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

◆ prepare_stage5()

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

protectedvirtual

References replace_scorefxn(), and STAGE_5.

Referenced by apply().

◆ recover_low()

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

protected

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

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

◆ register_options()

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

static

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

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

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

◆ replace_scorefxn()

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

protectedvirtual

◆ set_current_weight()

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

protected

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

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

◆ set_cycles()

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

virtual

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

Referenced by set_default_options().

◆ set_default_mc()

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

protectedvirtual

References set_mc(), and temperature_.

Referenced by set_defaults().

◆ set_default_options()

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

protectedvirtual

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

References apply_large_frags_, bQuickTest(), bQuickTest_, bSkipStage1_, bSkipStage2_, bSkipStage3_, bSkipStage4_, bSkipStage5_, close_chbrk_, 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().

◆ set_default_scores()

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

protectedvirtual

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

References ALL_STAGES, core::scoring::ScoreFunctionFactory::create_score_function(), score_stage1_, score_stage2_, score_stage3a_, score_stage3b_, score_stage4_, score_stage4rot_, score_stage4rot_sc_, score_stage5_, set_score_weight(), tr(), and core::scoring::vdw.

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

◆ set_defaults()

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

protectedvirtual

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

Referenced by init().

◆ set_mc()

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

References mc_, smooth_trial_small_, trial_large_, and trial_small_.

Referenced by set_default_mc().

◆ set_movemap()

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

virtual

Reimplemented in protocols::abinitio::FoldConstraints.

References brute_move_large_, brute_move_small_, movemap_, and smooth_move_small_.

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

◆ set_moves()

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

References brute_move_large(), brute_move_large_, brute_move_small(), brute_move_small_, smooth_move_small(), smooth_move_small_, and update_moves().

◆ set_score_weight()

void protocols::abinitio::ClassicAbinitio::set_score_weight	(	core::scoring::ScoreType	type,
		core::Real	setting,
		StageID	stage = `ALL_STAGES`
	)

virtual

for debugging, one wants to have access to the native pose.

sets a score weight for all stages of abinitio

References ALL_STAGES, core::scoring::name_from_score_type(), score_stage1_, score_stage2_, score_stage3a_, score_stage3b_, score_stage4_, score_stage4rot_, score_stage5_, STAGE_1, STAGE_2, STAGE_3a, STAGE_3b, STAGE_4, STAGE_5, tr(), and protocols::moves::Mover::type().

Referenced by apply(), prepare_loop_in_stage3(), protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage3(), protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage4(), protocols::abinitio::KinematicAbinitio::prepare_stage1(), protocols::abinitio::FoldConstraints::set_constraint_weight(), set_default_scores(), protocols::abinitio::FoldConstraints::set_default_scores(), and protocols::abinitio::KinematicAbinitio::set_default_scores().

◆ set_skip_stage1()

void protocols::abinitio::ClassicAbinitio::set_skip_stage1 ( bool setting )

inline

References bSkipStage1_.

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

◆ set_skip_stage2()

void protocols::abinitio::ClassicAbinitio::set_skip_stage2 ( bool setting )

inline

References bSkipStage2_.

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

◆ set_stage4_cycles()

void protocols::abinitio::ClassicAbinitio::set_stage4_cycles ( core::Size stage4_cycles_new )

inline

References stage4_cycles_.

◆ set_trials()

void protocols::abinitio::ClassicAbinitio::set_trials ( )

protectedvirtual

References protocols::moves::accept_reject, brute_move_large_, brute_move_small_, mc_, pack_rotamers_, smooth_move_small_, smooth_trial_small_, smooth_trial_small_pack_, trial_large_, trial_small_, and trial_small_pack_.

Referenced by update_moves().

◆ smooth_move_small()

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

References smooth_move_small_.

Referenced by set_moves().

◆ stage1_cycles()

core::Size protocols::abinitio::ClassicAbinitio::stage1_cycles ( ) const

inline

References stage1_cycles_.

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

◆ stage1_mover()

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage1_mover	(	core::pose::Pose &	pose,
		moves::TrialMoverOP	trials_in
	)

protectedvirtual

Reimplemented in protocols::abinitio::KinematicAbinitio.

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

◆ stage2_cycles()

core::Size protocols::abinitio::ClassicAbinitio::stage2_cycles ( ) const

inline

References stage2_cycles_.

Referenced by apply(), and do_stage2_cycles().

◆ stage2_mover()

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage2_mover	(	core::pose::Pose &	pose,
		moves::TrialMoverOP	trials_in
	)

protectedvirtual

Reimplemented in protocols::abinitio::KinematicAbinitio.

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

◆ stage3_cycles()

core::Size protocols::abinitio::ClassicAbinitio::stage3_cycles ( ) const

inline

References stage3_cycles_.

Referenced by apply(), and do_stage3_cycles().

◆ stage3_mover()

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage3_mover	(	core::pose::Pose &	pose,
		int	lct1,
		int	lct2,
		moves::TrialMoverOP	trials_in
	)

protectedvirtual

Reimplemented in protocols::abinitio::KinematicAbinitio.

Referenced by do_stage3_cycles().

◆ stage4_cycles()

core::Size protocols::abinitio::ClassicAbinitio::stage4_cycles ( ) const

inline

References stage4_cycles_.

Referenced by apply(), and do_stage4_cycles().

◆ stage4_mover()

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage4_mover	(	core::pose::Pose &	pose,
		int	kk,
		moves::TrialMoverOP	trials_in
	)

protectedvirtual

Reimplemented in protocols::abinitio::KinematicAbinitio.

Referenced by do_stage4_cycles().

◆ stage4rot_mover()

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage4rot_mover	(	core::pose::Pose &	pose,
		int	kk,
		moves::TrialMoverOP	trials_in
	)

protectedvirtual

References smooth_trial_small_pack_, trial_small_, and trial_small_pack_.

Referenced by do_stage4_cycles().

◆ stage5_cycles()

core::Size protocols::abinitio::ClassicAbinitio::stage5_cycles ( ) const

inline

References stage5_cycles_.

Referenced by apply(), and do_stage5_cycles().

◆ stage5_mover()

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage5_mover	(	core::pose::Pose &	pose,
		moves::TrialMoverOP	trials_in
	)

protectedvirtual

Referenced by do_stage5_cycles().

◆ supports_trRosetta_constraints()

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

overridevirtual

This overrides the default and indicates that the ClassicAbInitio protocol DOES support trRosetta constraints.

Reimplemented from protocols::abinitio::Protocol.

◆ total_trials()

core::Size protocols::abinitio::ClassicAbinitio::total_trials ( ) const

inline

References total_trials_.

◆ trial_large()

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_large ( )

protected

References apply_large_frags_, trial_large_, and trial_small_.

Referenced by do_stage1_cycles(), protocols::abinitio::FoldConstraints::do_stage1_cycles(), protocols::abinitio::FoldConstraints::do_stage2_cycles(), and do_stage3_cycles().

◆ trial_small()

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_small ( )

protected

References trial_small_.

Referenced by do_stage3_cycles(), and do_stage4_cycles().

◆ trial_smooth()

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_smooth ( )

protected

References smooth_trial_small_.

Referenced by do_stage4_cycles().

◆ update_moves()

void protocols::abinitio::ClassicAbinitio::update_moves ( )

protectedvirtual

References set_trials().

Referenced by set_defaults(), and set_moves().

Member Data Documentation

◆ apply_large_frags_

bool protocols::abinitio::ClassicAbinitio::apply_large_frags_

private

Referenced by ClassicAbinitio(), do_stage2_cycles(), set_default_options(), and trial_large().

◆ bQuickTest_

bool protocols::abinitio::ClassicAbinitio::bQuickTest_

private

Referenced by bQuickTest(), ClassicAbinitio(), and set_default_options().

◆ brute_move_large_

simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::brute_move_large_

private

Referenced by brute_move_large(), ClassicAbinitio(), set_movemap(), set_moves(), and set_trials().

◆ brute_move_small_

simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::brute_move_small_

private

Referenced by brute_move_small(), ClassicAbinitio(), set_movemap(), set_moves(), and set_trials().

◆ bSkipStage1_

bool protocols::abinitio::ClassicAbinitio::bSkipStage1_

Referenced by apply(), ClassicAbinitio(), set_default_options(), set_defaults(), and set_skip_stage1().

◆ bSkipStage2_

bool protocols::abinitio::ClassicAbinitio::bSkipStage2_

Referenced by apply(), ClassicAbinitio(), set_cycles(), set_default_options(), set_defaults(), and set_skip_stage2().

◆ bSkipStage3_

bool protocols::abinitio::ClassicAbinitio::bSkipStage3_

Referenced by apply(), ClassicAbinitio(), set_cycles(), set_default_options(), and set_defaults().

◆ bSkipStage4_

bool protocols::abinitio::ClassicAbinitio::bSkipStage4_

Referenced by apply(), ClassicAbinitio(), set_default_options(), and set_defaults().

◆ bSkipStage5_

bool protocols::abinitio::ClassicAbinitio::bSkipStage5_

Referenced by apply(), ClassicAbinitio(), set_default_options(), and set_defaults().

◆ close_chbrk_

bool protocols::abinitio::ClassicAbinitio::close_chbrk_

private

Referenced by apply(), ClassicAbinitio(), prepare_loop_in_stage3(), prepare_loop_in_stage4(), and set_default_options().

◆ just_smooth_cycles_

bool protocols::abinitio::ClassicAbinitio::just_smooth_cycles_

private

Referenced by ClassicAbinitio(), do_stage4_cycles(), just_smooth_cycles(), and set_default_options().

◆ mc_

moves::MonteCarloOP protocols::abinitio::ClassicAbinitio::mc_

private

Referenced by ClassicAbinitio(), do_stage4_cycles(), mc(), mc_ptr(), prepare_stage1(), recover_low(), replace_scorefxn(), set_mc(), and set_trials().

◆ movemap_

core::kinematics::MoveMapCOP protocols::abinitio::ClassicAbinitio::movemap_

private

Referenced by ClassicAbinitio(), movemap(), and set_movemap().

◆ pack_rotamers_

minimization_packing::PackRotamersMoverOP protocols::abinitio::ClassicAbinitio::pack_rotamers_

private

Referenced by ClassicAbinitio(), do_stage4_cycles(), and set_trials().

◆ recover_low_stages_

utility::vector1< StageID > protocols::abinitio::ClassicAbinitio::recover_low_stages_

Referenced by ClassicAbinitio(), recover_low(), and set_default_options().

◆ score_stage1_

core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage1_

private

Referenced by ClassicAbinitio(), replace_scorefxn(), set_default_scores(), set_defaults(), and set_score_weight().

◆ score_stage2_

core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage2_

private

Referenced by ClassicAbinitio(), replace_scorefxn(), set_default_scores(), and set_score_weight().

◆ score_stage3a_

core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage3a_

private

Referenced by ClassicAbinitio(), replace_scorefxn(), set_default_scores(), and set_score_weight().

◆ score_stage3b_

core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage3b_

private

Referenced by ClassicAbinitio(), replace_scorefxn(), set_default_scores(), and set_score_weight().

◆ score_stage4_

core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage4_

private

Referenced by ClassicAbinitio(), replace_scorefxn(), set_default_scores(), and set_score_weight().

◆ score_stage4rot_

core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage4rot_

private

Referenced by ClassicAbinitio(), do_stage4_cycles(), replace_scorefxn(), set_default_scores(), and set_score_weight().

◆ score_stage4rot_sc_

core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage4rot_sc_

private

Referenced by do_stage4_cycles(), and set_default_scores().

◆ score_stage5_

core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage5_

private

Referenced by ClassicAbinitio(), replace_scorefxn(), set_default_scores(), and set_score_weight().

◆ short_insert_region_

bool protocols::abinitio::ClassicAbinitio::short_insert_region_

private

Referenced by ClassicAbinitio(), do_stage2_cycles(), do_stage3_cycles(), and set_default_options().

◆ smooth_move_small_

simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::smooth_move_small_

private

Referenced by ClassicAbinitio(), set_movemap(), set_moves(), set_trials(), and smooth_move_small().

◆ smooth_trial_small_

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::smooth_trial_small_

private

Referenced by ClassicAbinitio(), set_mc(), set_trials(), and trial_smooth().

◆ smooth_trial_small_pack_

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::smooth_trial_small_pack_

private

Referenced by set_trials(), and stage4rot_mover().

◆ stage1_cycles_

core::Size protocols::abinitio::ClassicAbinitio::stage1_cycles_

protected

Referenced by ClassicAbinitio(), set_cycles(), and stage1_cycles().

◆ stage2_cycles_

core::Size protocols::abinitio::ClassicAbinitio::stage2_cycles_

protected

Referenced by ClassicAbinitio(), set_cycles(), and stage2_cycles().

◆ stage3_cycles_

core::Size protocols::abinitio::ClassicAbinitio::stage3_cycles_

protected

Referenced by ClassicAbinitio(), set_cycles(), and stage3_cycles().

◆ stage4_cycles_

core::Size protocols::abinitio::ClassicAbinitio::stage4_cycles_

protected

Referenced by ClassicAbinitio(), set_cycles(), set_stage4_cycles(), and stage4_cycles().

◆ stage4_cycles_pack_rate_

core::Real protocols::abinitio::ClassicAbinitio::stage4_cycles_pack_rate_

protected

Referenced by ClassicAbinitio().

◆ stage5_cycles_

core::Size protocols::abinitio::ClassicAbinitio::stage5_cycles_

protected

Referenced by ClassicAbinitio(), set_cycles(), and stage5_cycles().

◆ temperature_

core::Real protocols::abinitio::ClassicAbinitio::temperature_

private

Referenced by ClassicAbinitio(), do_stage5_cycles(), prepare_stage1(), replace_scorefxn(), set_default_mc(), and set_defaults().

◆ total_trials_

core::Size protocols::abinitio::ClassicAbinitio::total_trials_

private

Referenced by apply(), ClassicAbinitio(), and total_trials().

◆ trial_large_

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_large_

private

Referenced by ClassicAbinitio(), do_stage2_cycles(), set_mc(), set_trials(), and trial_large().

◆ trial_small_

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_small_

private

Referenced by ClassicAbinitio(), do_stage2_cycles(), set_mc(), set_trials(), stage4rot_mover(), trial_large(), and trial_small().

◆ trial_small_pack_

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_small_pack_

private

Referenced by set_trials(), and stage4rot_mover().

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

src/protocols/abinitio/ClassicAbinitio.hh
src/protocols/abinitio/ClassicAbinitio.cc

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Parent

Member Enumeration Documentation

◆ StageID

Constructor & Destructor Documentation

◆ ClassicAbinitio() [1/3]

◆ ClassicAbinitio() [2/3]

◆ ClassicAbinitio() [3/3]

◆ ~ClassicAbinitio()

Member Function Documentation

◆ apply()

◆ bQuickTest()

◆ brute_move_large()

◆ brute_move_small()

◆ clone()

◆ current_scorefxn() [1/2]

◆ current_scorefxn() [2/2]

◆ do_stage1_cycles()

◆ do_stage2_cycles()

◆ do_stage3_cycles()

◆ do_stage4_cycles()

◆ do_stage5_cycles()

◆ get_name()

◆ init()

◆ just_smooth_cycles()

◆ mc() [1/2]

◆ mc() [2/2]

◆ mc_ptr()

◆ movemap()

◆ operator=()

◆ output_debug_structure()

◆ prepare_loop_in_stage3()

◆ prepare_loop_in_stage4()

◆ prepare_stage1()

◆ prepare_stage2()

◆ prepare_stage3()

◆ prepare_stage4()

◆ prepare_stage5()

◆ recover_low()

◆ register_options()

◆ replace_scorefxn()

◆ set_current_weight()

◆ set_cycles()

◆ set_default_mc()

◆ set_default_options()

◆ set_default_scores()

◆ set_defaults()

◆ set_mc()

◆ set_movemap()

◆ set_moves()

◆ set_score_weight()

◆ set_skip_stage1()

◆ set_skip_stage2()

◆ set_stage4_cycles()

◆ set_trials()

◆ smooth_move_small()

◆ stage1_cycles()

◆ stage1_mover()

◆ stage2_cycles()

◆ stage2_mover()

◆ stage3_cycles()

◆ stage3_mover()

◆ stage4_cycles()

◆ stage4_mover()

◆ stage4rot_mover()

◆ stage5_cycles()

◆ stage5_mover()

◆ supports_trRosetta_constraints()

◆ total_trials()

◆ trial_large()