#include <FragmentSampler.hh>

Inheritance diagram for protocols::abinitio::FragmentSampler:

Collaboration diagram for protocols::abinitio::FragmentSampler:

Public Member Functions
virtual	~FragmentSampler ()

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

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

virtual void	set_cycles (core::Real increase_cycles=1.0)

virtual 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

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::moves::Mover
static std::string	name ()

static void	register_options ()
	overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Protected Member Functions
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::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

Detailed Description

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

call FragmentSampler::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 125 of file FragmentSampler.hh.

Member Typedef Documentation

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

private

Definition at line 127 of file FragmentSampler.hh.

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

private

Definition at line 126 of file FragmentSampler.hh.

Constructor & Destructor Documentation

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

virtual

Definition at line 107 of file FragmentSampler.cc.

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)

Definition at line 98 of file FragmentSampler.cc.

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

Referenced by clone().

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

Reimplemented in protocols::abinitio::ConstraintFragmentSampler.

Definition at line 158 of file FragmentSampler.cc.

References protocols::topology_broker::TopologyBroker::apply_filter(), checkpointed_cycle_block(), protocols::moves::MonteCarlo::clear_poses(), protocols::abinitio::contains_stageid(), current_scorefxn(), do_stage1_cycles(), do_stage2_cycles(), do_stage3_cycles(), do_stage4_cycles(), protocols::abinitio::END_ABINITIO, protocols::checkpoint::CheckPointer::flush_checkpoints(), get_checkpoints(), protocols::moves::Mover::get_current_tag(), mc(), protocols::jd2::output_intermediate_pose(), prepare_stage1(), prepare_stage2(), prepare_stage3(), prepare_stage4(), protocols::moves::MonteCarlo::recover_low(), replace_scorefxn(), protocols::moves::MonteCarlo::reset(), 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

Definition at line 288 of file FragmentSampler.hh.

References bQuickTest_.

Referenced by set_default_options().

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

virtual

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

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::abinitio::ConstraintFragmentSampler.

Definition at line 111 of file FragmentSampler.cc.

References FragmentSampler().

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

Definition at line 318 of file FragmentSampler.cc.

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

Definition at line 323 of file FragmentSampler.cc.

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.

Definition at line 389 of file FragmentSampler.cc.

References protocols::moves::RepeatMover::apply(), current_scorefxn(), 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

Definition at line 395 of file FragmentSampler.cc.

References protocols::moves::RepeatMover::apply(), current_scorefxn(), mc_ptr(), mover(), 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() )

Definition at line 413 of file FragmentSampler.cc.

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(), 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

Definition at line 451 of file FragmentSampler.cc.

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(), 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

Definition at line 153 of file FragmentSampler.hh.

References checkpoints_.

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

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

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::abinitio::ConstraintFragmentSampler.

Definition at line 216 of file FragmentSampler.cc.

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

inlineprivate

Definition at line 358 of file FragmentSampler.hh.

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

Referenced by checkpointed_cycle_block().

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

inlineprivate

Definition at line 353 of file FragmentSampler.hh.

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

Referenced by checkpointed_cycle_block().

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

inline

Definition at line 253 of file FragmentSampler.hh.

References just_smooth_cycles_.

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

inlineprotected

Definition at line 170 of file FragmentSampler.hh.

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

Definition at line 175 of file FragmentSampler.hh.

References mc_.

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

inlineprotected

Definition at line 310 of file FragmentSampler.hh.

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

Definition at line 384 of file FragmentSampler.cc.

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.

Definition at line 520 of file FragmentSampler.cc.

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.

Definition at line 528 of file FragmentSampler.cc.

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.

Definition at line 502 of file FragmentSampler.cc.

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.

Definition at line 508 of file FragmentSampler.cc.

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

Definition at line 512 of file FragmentSampler.cc.

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

Referenced by apply().

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

protectedvirtual

Definition at line 516 of file FragmentSampler.cc.

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

Referenced by apply().

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

protected

Definition at line 471 of file FragmentSampler.cc.

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()

Definition at line 70 of file FragmentSampler.cc.

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

Definition at line 328 of file FragmentSampler.cc.

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)

virtual

Definition at line 243 of file FragmentSampler.cc.

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

Definition at line 230 of file FragmentSampler.cc.

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

Definition at line 335 of file FragmentSampler.cc.

References apply_large_frags_, bQuickTest(), bQuickTest_, core::sequence::end, 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

Definition at line 261 of file FragmentSampler.cc.

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

Definition at line 221 of file FragmentSampler.cc.

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

Definition at line 238 of file FragmentSampler.cc.

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`
	)

virtual

sets a score weight for all stages of abinitio

Definition at line 305 of file FragmentSampler.cc.

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

Definition at line 277 of file FragmentSampler.hh.

References stage4_cycles_.

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

inline

Definition at line 259 of file FragmentSampler.hh.

References stage1_cycles_.

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

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

inline

Definition at line 265 of file FragmentSampler.hh.

References stage2_cycles_.

Referenced by do_stage2_cycles().

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

inline

Definition at line 271 of file FragmentSampler.hh.

References stage3_cycles_.

Referenced by do_stage3_cycles().

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

inline

Definition at line 283 of file FragmentSampler.hh.

References stage4_cycles_.

Referenced by do_stage4_cycles().

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

Definition at line 252 of file FragmentSampler.cc.

References topology_broker_.

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

protected

Definition at line 256 of file FragmentSampler.cc.

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

Definition at line 329 of file FragmentSampler.hh.

Referenced by set_default_options().

bool protocols::abinitio::FragmentSampler::bQuickTest_

private

Definition at line 332 of file FragmentSampler.hh.

Referenced by bQuickTest(), and set_default_options().

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

private

Definition at line 344 of file FragmentSampler.hh.

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

Definition at line 351 of file FragmentSampler.hh.

Referenced by id2proftag().

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

staticprivate

Definition at line 350 of file FragmentSampler.hh.

Referenced by id2string().

bool protocols::abinitio::FragmentSampler::just_smooth_cycles_

private

Definition at line 331 of file FragmentSampler.hh.

Referenced by just_smooth_cycles(), and set_default_options().

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

private

Definition at line 338 of file FragmentSampler.hh.

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

Definition at line 346 of file FragmentSampler.hh.

Referenced by recover_low(), and set_default_options().

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

private

Definition at line 322 of file FragmentSampler.hh.

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

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

private

Definition at line 323 of file FragmentSampler.hh.

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

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

private

Definition at line 324 of file FragmentSampler.hh.

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

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

private

Definition at line 325 of file FragmentSampler.hh.

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

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

private

Definition at line 326 of file FragmentSampler.hh.

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

bool protocols::abinitio::FragmentSampler::short_insert_region_

private

Definition at line 330 of file FragmentSampler.hh.

Referenced by do_stage3_cycles(), and set_default_options().

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

private

Definition at line 347 of file FragmentSampler.hh.

Referenced by apply(), and set_default_options().

Size protocols::abinitio::FragmentSampler::stage1_cycles_

protected

Definition at line 315 of file FragmentSampler.hh.

Referenced by set_cycles(), and stage1_cycles().

Size protocols::abinitio::FragmentSampler::stage2_cycles_

protected

Definition at line 316 of file FragmentSampler.hh.

Referenced by set_cycles(), and stage2_cycles().

Size protocols::abinitio::FragmentSampler::stage3_cycles_

protected

Definition at line 317 of file FragmentSampler.hh.

Referenced by set_cycles(), and stage3_cycles().

Size protocols::abinitio::FragmentSampler::stage4_cycles_

protected

Definition at line 318 of file FragmentSampler.hh.

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

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

private

Definition at line 335 of file FragmentSampler.hh.

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

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

private

Definition at line 342 of file FragmentSampler.hh.

Referenced by apply(), and topology_broker().

Size protocols::abinitio::FragmentSampler::total_trials_

private

Definition at line 340 of file FragmentSampler.hh.

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_

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

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Detailed Description

Member Typedef Documentation

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