#include <FragmentSampler.hh>

Inheritance diagram for protocols::abinitio::FragmentSampler:

Public Member Functions
	~FragmentSampler () override

	FragmentSampler (topology_broker::TopologyBrokerOP broker)
	This constructor does not work – Fix it before using it. More...

moves::MoverOP	clone () const override
	FragmentSampler 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...

void	set_cycles (core::Real increase_cycles=1.0)

void	set_score_weight (core::scoring::ScoreType, core::Real setting, StageID stage=ALL_STAGES)
	sets a score weight for all stages of abinitio More...

virtual checkpoint::CheckPointer &	get_checkpoints ()

void	topology_broker (topology_broker::TopologyBrokerOP set)

core::scoring::ScoreFunction const &	current_scorefxn () const

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

bool	bQuickTest () const

bool	check_loops (core::pose::Pose &pose)

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, 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...

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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions
topology_broker::TopologyBroker const &	topology_broker ()

void	set_mc (moves::MonteCarloOP)

moves::MonteCarlo &	mc ()

moves::MonteCarlo const &	mc () const

void	set_defaults ()

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 void	do_stage1_cycles (core::pose::Pose &pose)

virtual void	do_stage2_cycles (core::pose::Pose &pose)

virtual void	do_stage3_cycles (core::pose::Pose &pose)

virtual void	do_stage4_cycles (core::pose::Pose &pose)

virtual moves::MoverOP	mover (core::pose::Pose const &pose, StageID stage_id, core::scoring::ScoreFunction const &scorefxn, core::Real progress=1.0)

virtual void	prepare_stage1 (core::pose::Pose &pose)

virtual void	prepare_stage2 (core::pose::Pose &pose)

virtual void	prepare_stage3 (core::pose::Pose &pose)

virtual void	prepare_stage4 (core::pose::Pose &pose)

virtual void	prepare_loop_in_stage3 (core::pose::Pose &, Size, Size)

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

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
Size	stage1_cycles_

Size	stage2_cycles_

Size	stage3_cycles_

Size	stage4_cycles_

Private Types
typedef moves::Mover	Parent

typedef moves::Mover	BaseClass

Private Member Functions
void	set_default_options ()

void	set_default_scores ()

void	set_default_mc (core::scoring::ScoreFunction const &scorefxn)

void	checkpointed_cycle_block (core::pose::Pose &, StageID, void(FragmentSampler::*cycles)(core::pose::Pose &))

std::string const &	id2string (StageID id)

basic::ProfTag	id2proftag (StageID id)

Static Private Attributes
static std::string const	id2string_ [] = { "all_stages", "stage1", "stage2", "stage3", "stage3", "stage3", "stage4"}

static basic::ProfTag const	id2proftag_ [] = { basic::STAGE1, basic::STAGE1, basic::STAGE2, basic::STAGE3, basic::STAGE3, basic::STAGE3, basic::STAGE4 }

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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

Detailed Description

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

call FragmentSampler::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

typedef moves::Mover protocols::abinitio::FragmentSampler::BaseClass

private

typedef moves::Mover protocols::abinitio::FragmentSampler::Parent

private

Constructor & Destructor Documentation

protocols::abinitio::FragmentSampler::~FragmentSampler ( )

overridedefault

protocols::abinitio::FragmentSampler::FragmentSampler ( topology_broker::TopologyBrokerOP broker )

This constructor does not work – Fix it before using it.

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

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

Member Function Documentation

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::topology_broker::TopologyBroker::apply_filter(), check_loops(), checkpointed_cycle_block(), protocols::moves::MonteCarlo::clear_poses(), protocols::abinitio::contains_stageid(), current_scorefxn(), core::pack::interaction_graph::debug, do_stage1_cycles(), do_stage2_cycles(), do_stage3_cycles(), do_stage4_cycles(), protocols::abinitio::END_ABINITIO, protocols::moves::FAIL_RETRY, protocols::moves::Mover::get_current_tag(), mc(), protocols::jd2::output_intermediate_pose(), prepare_stage1(), prepare_stage2(), prepare_stage3(), prepare_stage4(), replace_scorefxn(), protocols::moves::MonteCarlo::reset(), protocols::moves::Mover::set_last_move_status(), skip_stages_, protocols::abinitio::STAGE_1, protocols::abinitio::STAGE_2, protocols::abinitio::STAGE_3, protocols::abinitio::STAGE_3b, protocols::abinitio::STAGE_4, topology_broker(), topology_broker_, total_trials_, and tr().

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

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

inline

References bQuickTest_.

Referenced by set_default_options().

bool protocols::abinitio::FragmentSampler::check_loops ( core::pose::Pose & pose )

References core::pose::Pose::data(), core::pose::Pose::fold_tree(), protocols::loophash::get_rt_over_leap_fast(), core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY, protocols::loophash::LoopHashMap::radial_count(), core::scoring::rg, core::kinematics::FoldTree::show(), core::pose::Pose::size(), protocols::loops::start, protocols::loops::stop, and tr().

Referenced by apply().

void protocols::abinitio::FragmentSampler::checkpointed_cycle_block	(	core::pose::Pose &	pose,
		StageID	stage_id,
		void(FragmentSampler::*)(core::pose::Pose &)	cycles
	)

private

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

overridevirtual

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

Reimplemented from protocols::moves::Mover.

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

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

Referenced by apply(), checkpointed_cycle_block(), protocols::abinitio::ConstraintFragmentSampler::do_stage1_cycles(), do_stage1_cycles(), do_stage2_cycles(), do_stage3_cycles(), do_stage4_cycles(), recover_low(), replace_scorefxn(), and protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep().

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

protected

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

void protocols::abinitio::FragmentSampler::do_stage1_cycles ( core::pose::Pose & pose )

protectedvirtual

Reimplemented in protocols::abinitio::ConstraintFragmentSampler.

References protocols::moves::RepeatMover::apply(), current_scorefxn(), core::pack::interaction_graph::debug, mc(), mc_ptr(), mover(), protocols::jd2::output_intermediate_pose(), protocols::moves::MonteCarlo::reset(), stage1_cycles(), and protocols::abinitio::STAGE_1.

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

void protocols::abinitio::FragmentSampler::do_stage2_cycles ( core::pose::Pose & pose )

protectedvirtual

References protocols::moves::RepeatMover::apply(), current_scorefxn(), mc_ptr(), mover(), protocols::jd2::output_intermediate_pose(), stage2_cycles(), and protocols::abinitio::STAGE_2.

Referenced by apply().

void protocols::abinitio::FragmentSampler::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() )

References protocols::moves::RepeatMover::apply(), protocols::checkpoint::CheckPointer::checkpoint(), current_scorefxn(), protocols::checkpoint::CheckPointer::debug(), get_checkpoints(), protocols::moves::Mover::get_current_tag(), mc_ptr(), mover(), protocols::jd2::output_intermediate_pose(), prepare_loop_in_stage3(), recover_low(), short_insert_region_, stage3_cycles(), protocols::abinitio::STAGE_3a, protocols::abinitio::STAGE_3b, and tr().

Referenced by apply().

void protocols::abinitio::FragmentSampler::do_stage4_cycles ( core::pose::Pose & pose )

protectedvirtual

References protocols::moves::RepeatMover::apply(), protocols::checkpoint::CheckPointer::checkpoint(), current_scorefxn(), protocols::checkpoint::CheckPointer::debug(), get_checkpoints(), protocols::moves::Mover::get_current_tag(), mc_ptr(), mover(), protocols::jd2::output_intermediate_pose(), prepare_loop_in_stage4(), recover_low(), stage4_cycles(), protocols::abinitio::STAGE_4, and tr().

Referenced by apply().

virtual checkpoint::CheckPointer& protocols::abinitio::FragmentSampler::get_checkpoints ( )

inlinevirtual

References checkpoints_.

Referenced by checkpointed_cycle_block(), do_stage3_cycles(), and do_stage4_cycles().

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

overridevirtual

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

Implements protocols::moves::Mover.

basic::ProfTag protocols::abinitio::FragmentSampler::id2proftag ( StageID id )

inlineprivate

References id2proftag_, and protocols::abinitio::LAST_STAGE.

Referenced by checkpointed_cycle_block().

std::string const& protocols::abinitio::FragmentSampler::id2string ( StageID id )

inlineprivate

References id2string_, and protocols::abinitio::LAST_STAGE.

Referenced by checkpointed_cycle_block().

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

inline

References just_smooth_cycles_.

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

inlineprotected

References mc_.

Referenced by protocols::abinitio::ConstraintFragmentSampler::apply(), apply(), checkpointed_cycle_block(), current_scorefxn(), protocols::abinitio::ConstraintFragmentSampler::do_stage1_cycles(), do_stage1_cycles(), set_current_weight(), and protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep().

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

inlineprotected

References mc_.

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

inlineprotected

References mc_.

Referenced by protocols::abinitio::ConstraintFragmentSampler::do_stage1_cycles(), do_stage1_cycles(), do_stage2_cycles(), do_stage3_cycles(), and do_stage4_cycles().

moves::MoverOP protocols::abinitio::FragmentSampler::mover	(	core::pose::Pose const &	pose,
		StageID	stage_id,
		core::scoring::ScoreFunction const &	scorefxn,
		core::Real	progress = `1.0`
	)

protectedvirtual

References protocols::topology_broker::TopologyBroker::apply_filter(), protocols::topology_broker::TopologyBroker::mover(), and topology_broker().

Referenced by protocols::abinitio::ConstraintFragmentSampler::do_stage1_cycles(), do_stage1_cycles(), do_stage2_cycles(), do_stage3_cycles(), and do_stage4_cycles().

void protocols::abinitio::FragmentSampler::prepare_loop_in_stage3	(	core::pose::Pose &	pose,
		Size	iteration,
		Size	total
	)

protectedvirtual

Reimplemented in protocols::abinitio::ConstraintFragmentSampler.

References replace_scorefxn(), protocols::abinitio::STAGE_3a, and protocols::abinitio::STAGE_3b.

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

void protocols::abinitio::FragmentSampler::prepare_loop_in_stage4	(	core::pose::Pose &	pose,
		Size	iteration,
		Size	total
	)

protectedvirtual

Reimplemented in protocols::abinitio::ConstraintFragmentSampler.

References replace_scorefxn(), and protocols::abinitio::STAGE_4.

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

void protocols::abinitio::FragmentSampler::prepare_stage1 ( core::pose::Pose & pose )

protectedvirtual

Reimplemented in protocols::abinitio::ConstraintFragmentSampler.

References mc_, replace_scorefxn(), protocols::abinitio::STAGE_1, and temperature_.

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

void protocols::abinitio::FragmentSampler::prepare_stage2 ( core::pose::Pose & pose )

protectedvirtual

Reimplemented in protocols::abinitio::ConstraintFragmentSampler.

References replace_scorefxn(), and protocols::abinitio::STAGE_2.

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

void protocols::abinitio::FragmentSampler::prepare_stage3 ( core::pose::Pose & pose )

protectedvirtual

References replace_scorefxn(), and protocols::abinitio::STAGE_3a.

Referenced by apply().

void protocols::abinitio::FragmentSampler::prepare_stage4 ( core::pose::Pose & pose )

protectedvirtual

References replace_scorefxn(), and protocols::abinitio::STAGE_4.

Referenced by apply().

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

protected

References protocols::abinitio::contains_stageid(), current_scorefxn(), mc_, recover_low_stages_, core::scoring::ScoreFunction::show(), and tr().

Referenced by checkpointed_cycle_block(), do_stage3_cycles(), and do_stage4_cycles().

void protocols::abinitio::FragmentSampler::register_options ( )

static

call this: FragmentSampler::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().

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

protectedvirtual

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

protected

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

Referenced by protocols::abinitio::ConstraintFragmentSampler::replace_scorefxn().

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

References stage1_cycles_, stage2_cycles_, stage3_cycles_, and stage4_cycles_.

Referenced by set_default_options().

void protocols::abinitio::FragmentSampler::set_default_mc ( core::scoring::ScoreFunction const & scorefxn )

private

References mc_, set_mc(), protocols::canonical_sampling::mc_convergence_checks::setup_convergence_checks_from_cmdline(), and temperature_.

Referenced by set_defaults().

void protocols::abinitio::FragmentSampler::set_default_options ( )

private

References apply_large_frags_, bQuickTest(), bQuickTest_, just_smooth_cycles_, recover_low_stages_, set_cycles(), short_insert_region_, skip_stages_, protocols::abinitio::STAGE_1, protocols::abinitio::STAGE_2, protocols::abinitio::STAGE_3, protocols::abinitio::STAGE_3a, protocols::abinitio::STAGE_3b, and protocols::abinitio::STAGE_4.

Referenced by set_defaults().

void protocols::abinitio::FragmentSampler::set_default_scores ( )

private

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

Referenced by set_defaults().

void protocols::abinitio::FragmentSampler::set_defaults ( )

protected

References score_stage4_, set_default_mc(), set_default_options(), set_default_scores(), and temperature_.

Referenced by FragmentSampler(), and protocols::abinitio::ConstraintFragmentSampler::set_defaults().

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

protected

References mc_.

Referenced by set_default_mc().

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

sets a score weight for all stages of abinitio

References protocols::abinitio::ALL_STAGES, core::scoring::name_from_score_type(), score_stage1_, score_stage2_, score_stage3a_, score_stage3b_, score_stage4_, protocols::abinitio::STAGE_1, protocols::abinitio::STAGE_2, protocols::abinitio::STAGE_3a, protocols::abinitio::STAGE_3b, protocols::abinitio::STAGE_4, and tr().

Referenced by protocols::abinitio::ConstraintFragmentSampler::replace_scorefxn(), protocols::abinitio::ConstraintFragmentSampler::set_constraint_weight(), set_default_scores(), and protocols::abinitio::ConstraintFragmentSampler::set_defaults().

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

inline

References stage4_cycles_.

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

inline

References stage1_cycles_.

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

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

inline

References stage2_cycles_.

Referenced by do_stage2_cycles().

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

inline

References stage3_cycles_.

Referenced by do_stage3_cycles().

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

inline

References stage4_cycles_.

Referenced by do_stage4_cycles().

void protocols::abinitio::FragmentSampler::topology_broker ( topology_broker::TopologyBrokerOP set )

References topology_broker_.

topology_broker::TopologyBroker const & protocols::abinitio::FragmentSampler::topology_broker ( )

protected

References topology_broker_.

Referenced by apply(), mover(), and protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep().

Member Data Documentation

bool protocols::abinitio::FragmentSampler::apply_large_frags_

private

Referenced by set_default_options().

bool protocols::abinitio::FragmentSampler::bQuickTest_

private

Referenced by bQuickTest(), and set_default_options().

checkpoint::CheckPointer protocols::abinitio::FragmentSampler::checkpoints_

private

Referenced by get_checkpoints().

basic::ProfTag const protocols::abinitio::FragmentSampler::id2proftag_ = { basic::STAGE1, basic::STAGE1, basic::STAGE2, basic::STAGE3, basic::STAGE3, basic::STAGE3, basic::STAGE4 }

staticprivate

Referenced by id2proftag().

std::string const protocols::abinitio::FragmentSampler::id2string_ = { "all_stages", "stage1", "stage2", "stage3", "stage3", "stage3", "stage4"}

staticprivate

Referenced by id2string().

bool protocols::abinitio::FragmentSampler::just_smooth_cycles_

private

Referenced by just_smooth_cycles(), and set_default_options().

moves::MonteCarloOP protocols::abinitio::FragmentSampler::mc_

private

Referenced by mc(), mc_ptr(), prepare_stage1(), recover_low(), replace_scorefxn(), set_default_mc(), and set_mc().

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

private

Referenced by recover_low(), and set_default_options().

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage1_

private

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

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage2_

private

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

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage3a_

private

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

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage3b_

private

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

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage4_

private

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

bool protocols::abinitio::FragmentSampler::short_insert_region_

private

Referenced by do_stage3_cycles(), and set_default_options().

utility::vector1< StageID > protocols::abinitio::FragmentSampler::skip_stages_

private

Referenced by apply(), and set_default_options().

Size protocols::abinitio::FragmentSampler::stage1_cycles_

protected

Referenced by set_cycles(), and stage1_cycles().

Size protocols::abinitio::FragmentSampler::stage2_cycles_

protected

Referenced by set_cycles(), and stage2_cycles().

Size protocols::abinitio::FragmentSampler::stage3_cycles_

protected

Referenced by set_cycles(), and stage3_cycles().

Size protocols::abinitio::FragmentSampler::stage4_cycles_

protected

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

core::Real protocols::abinitio::FragmentSampler::temperature_

private

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

topology_broker::TopologyBrokerOP protocols::abinitio::FragmentSampler::topology_broker_

private

Referenced by apply(), and topology_broker().

Size protocols::abinitio::FragmentSampler::total_trials_

private

Referenced by apply(), and checkpointed_cycle_block().

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

src/protocols/abinitio/FragmentSampler.hh
src/protocols/abinitio/FragmentSampler.cc

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_

bool	apply_large_frags_

bool	short_insert_region_

bool	just_smooth_cycles_

bool	bQuickTest_

core::Real	temperature_

moves::MonteCarloOP	mc_

Size	total_trials_

topology_broker::TopologyBrokerOP	topology_broker_

checkpoint::CheckPointer	checkpoints_

utility::vector1< StageID >	recover_low_stages_

utility::vector1< StageID >	skip_stages_

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