#include <MembraneAbinitio.hh>

Inheritance diagram for protocols::abinitio::MembraneAbinitio:

[legend]

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

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
	MembraneAbinitio (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_small_top25, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int)
	This constructor does not work – Fix it before using it. More...

	MembraneAbinitio (core::fragment::FragSetCOP fragset_small, core::fragment::FragSetCOP fragset_small_top25, core::fragment::FragSetCOP fragset_large, core::kinematics::MoveMapCOP movemap)
	constructor: supply fragsets for large and small fragment moves More...

void	init (core::pose::Pose const &pose) override
	setup moves, mc-object, scores More...

moves::MoverOP	clone () const override
	MembraneAbinitio 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_top25 ()

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	add_spanning_region (core::pose::Pose &pose)

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

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

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	clear_checkpoints (void)
	for debugging, one wants to have access to the native pose. More...

virtual bool	recover_checkpoint (core::pose::Pose &pose, std::string const &id)

virtual void	checkpoint (core::pose::Pose &pose, std::string const &id)

virtual void	set_score_weight (core::scoring::ScoreType, core::Real setting, StageID stage=ALL_STAGES)
	for debugging, one wants to have access to the native pose. More...

bool	just_smooth_cycles () const

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

void	set_only_stage4 (bool value)

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 bool	supports_trRosetta_constraints () const
	Report whether this protocol supports trRosetta constraints. The base class returns false; derived classes can override this and return true. More...

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...

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	set_current_weight (core::scoring::ScoreType type, core::Real setting)

virtual int	do_stage1_cycles (core::pose::Pose &pose)

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

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

virtual int	do_stage3b_cycles (core::pose::Pose &pose)

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

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 void	set_trials ()

moves::TrialMoverOP	trial_large ()

moves::TrialMoverOP	trial_small ()

moves::TrialMoverOP	trial_small_top25 ()

moves::TrialMoverOP	trial_smooth ()

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

virtual void	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_

Private Types
typedef Protocol	Parent

Private Member Functions
core::Size	get_tmh_inserted (core::pose::Pose const &pose) const

core::scoring::MembraneEmbed const &	MembraneEmbed_from_pose (core::pose::Pose const &) const

core::scoring::MembraneEmbed &	nonconst_MembraneEmbed_from_pose (core::pose::Pose &) const

core::scoring::MembraneTopology const &	MembraneTopology_from_pose (core::pose::Pose const &) const

core::scoring::MembraneTopology &	nonconst_MembraneTopology_from_pose (core::pose::Pose &) const

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	only_stage4_

bool	bQuickTest_

core::Real	temperature_

core::kinematics::MoveMapCOP	movemap_

moves::MonteCarloOP	mc_

simple_moves::FragmentMoverOP	brute_move_small_

simple_moves::FragmentMoverOP	brute_move_small_top25_

simple_moves::FragmentMoverOP	brute_move_large_

simple_moves::FragmentMoverOP	smooth_move_small_

moves::TrialMoverOP	trial_large_

moves::TrialMoverOP	trial_small_

moves::TrialMoverOP	trial_small_top25_

moves::TrialMoverOP	smooth_trial_small_

std::vector< std::string >	checkpoint_ids_

core::Size	total_trials_

checkpoint::CheckPointer	checkpoint_

Detailed Description

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

call MembraneAbinitio::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::MembraneAbinitio::Parent

private

Member Enumeration Documentation

◆ StageID

enum protocols::abinitio::MembraneAbinitio::StageID

Enumerator
ALL_STAGES
STAGE_1
STAGE_2
STAGE_3a
STAGE_3b
STAGE_4

Constructor & Destructor Documentation

◆ MembraneAbinitio() [1/2]

protocols::abinitio::MembraneAbinitio::MembraneAbinitio	(	simple_moves::FragmentMoverOP	brute_move_small,
		simple_moves::FragmentMoverOP	brute_move_small_top25,
		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(), movemap_, and protocols::moves::Mover::type().

◆ MembraneAbinitio() [2/2]

protocols::abinitio::MembraneAbinitio::MembraneAbinitio	(	core::fragment::FragSetCOP	fragset_small,
		core::fragment::FragSetCOP	fragset_small_top25,
		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_, brute_move_small_top25_, movemap(), smooth_move_small_, and protocols::moves::Mover::type().

Member Function Documentation

◆ add_spanning_region()

void protocols::abinitio::MembraneAbinitio::add_spanning_region ( core::pose::Pose & pose )

References core::scoring::MembraneTopology::allow_tmh_scoring(), core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::sequence::end, core::pose::Pose::fold_tree(), core::chemical::element::I, movemap(), nonconst_MembraneTopology_from_pose(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::num_jump(), core::scoring::MembraneTopology::set_allow_scoring(), core::scoring::MembraneTopology::set_allow_tmh_scoring(), set_movemap(), core::scoring::MembraneTopology::set_tmh_inserted(), core::pose::Pose::size(), core::scoring::MembraneTopology::span_begin(), core::scoring::MembraneTopology::span_end(), protocols::loops::start, core::scoring::MembraneTopology::tmh_inserted(), core::scoring::MembraneTopology::tmhelix(), tr(), protocols::hybridization::u, and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by apply().

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), add_spanning_region(), protocols::abinitio::Protocol::apply(), checkpoint(), clear_checkpoints(), core::pose::Pose::conformation(), current_scorefxn(), core::pack::interaction_graph::debug, do_stage1_cycles(), do_stage2_cycles(), do_stage3_cycles(), do_stage3b_cycles(), do_stage4_cycles(), get_tmh_inserted(), mc(), MembraneTopology_from_pose(), move_all_inserted(), nonconst_MembraneTopology_from_pose(), only_stage4_, output_debug_structure(), prepare_stage1(), prepare_stage2(), prepare_stage3(), prepare_stage4(), print_debug(), recover_checkpoint(), protocols::moves::MonteCarlo::recover_low(), core::scoring::MembraneTopology::reset_allowed_scoring(), protocols::moves::MonteCarlo::reset_counters(), core::scoring::ScoreFunction::show(), protocols::moves::MonteCarlo::show_counters(), stage1_cycles(), stage2_cycles(), stage3_cycles(), stage4_cycles(), core::scoring::MembraneTopology::tmhelix(), protocols::moves::MonteCarlo::total_trials(), total_trials_, and tr().

◆ bQuickTest()

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

inline

References bQuickTest_.

Referenced by set_default_options().

◆ brute_move_large()

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

References brute_move_large_.

Referenced by do_stage1_cycles(), MembraneAbinitio(), and set_moves().

◆ brute_move_small()

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

References brute_move_small_.

Referenced by set_moves().

◆ brute_move_small_top25()

simple_moves::FragmentMoverOP protocols::abinitio::MembraneAbinitio::brute_move_small_top25 ( )

References brute_move_small_top25_.

◆ checkpoint()

void protocols::abinitio::MembraneAbinitio::checkpoint	(	core::pose::Pose &	pose,
		std::string const &	id
	)

virtual

References protocols::checkpoint::CheckPointer::checkpoint(), checkpoint_, and protocols::moves::Mover::get_current_tag().

Referenced by apply(), do_stage3_cycles(), do_stage3b_cycles(), and do_stage4_cycles().

◆ clear_checkpoints()

void protocols::abinitio::MembraneAbinitio::clear_checkpoints ( void )

virtual

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

References checkpoint_, and protocols::checkpoint::CheckPointer::clear_checkpoints().

Referenced by apply().

◆ clone()

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

overridevirtual

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

Reimplemented from protocols::moves::Mover.

Referenced by set_current_weight().

◆ current_scorefxn() [1/2]

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

protected

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

Referenced by apply(), and print_debug().

◆ current_scorefxn() [2/2]

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

protected

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

◆ do_stage1_cycles()

int protocols::abinitio::MembraneAbinitio::do_stage1_cycles ( core::pose::Pose & pose )

protectedvirtual

References brute_move_large(), mc(), protocols::moves::MonteCarlo::reset(), stage1_cycles(), tr(), and trial_large().

Referenced by apply().

◆ do_stage2_cycles()

int protocols::abinitio::MembraneAbinitio::do_stage2_cycles ( core::pose::Pose & pose )

protectedvirtual

References protocols::moves::RepeatMover::apply(), mc_ptr(), stage2_cycles(), trial_large_, and trial_small_top25_.

Referenced by apply().

◆ do_stage3_cycles()

int protocols::abinitio::MembraneAbinitio::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(), checkpoint(), core::scoring::linear_chainbreak, mc_, prepare_loop_in_stage3(), recover_checkpoint(), score_stage3a_, score_stage3b_, stage3_cycles(), stage3_mover(), tr(), trial_large(), and trial_small_top25().

Referenced by apply().

◆ do_stage3b_cycles()

int protocols::abinitio::MembraneAbinitio::do_stage3b_cycles ( core::pose::Pose & pose )

protectedvirtual

References protocols::moves::RepeatMover::apply(), checkpoint(), core::scoring::linear_chainbreak, mc_, prepare_loop_in_stage3(), recover_checkpoint(), score_stage3a_, score_stage3b_, stage3_cycles(), stage3_mover(), tr(), and trial_small_top25().

Referenced by apply().

◆ do_stage4_cycles()

int protocols::abinitio::MembraneAbinitio::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(), checkpoint(), just_smooth_cycles_, core::scoring::linear_chainbreak, mc_, prepare_loop_in_stage4(), recover_checkpoint(), score_stage4_, stage4_cycles(), stage4_mover(), tr(), trial_small(), trial_small_top25(), and trial_smooth().

Referenced by apply().

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_tmh_inserted()

Size protocols::abinitio::MembraneAbinitio::get_tmh_inserted ( core::pose::Pose const & pose ) const

private

References MembraneTopology_from_pose(), and core::scoring::MembraneTopology::tmh_inserted().

Referenced by apply().

◆ init()

void protocols::abinitio::MembraneAbinitio::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().

◆ just_smooth_cycles()

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

inline

References just_smooth_cycles_.

◆ mc() [1/2]

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

inline

References mc_.

Referenced by apply(), current_scorefxn(), do_stage1_cycles(), output_debug_structure(), and set_current_weight().

◆ mc() [2/2]

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

inline

References mc_.

◆ mc_ptr()

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

inlineprotected

References mc_.

Referenced by do_stage2_cycles().

◆ MembraneEmbed_from_pose()

core::scoring::MembraneEmbed const & protocols::abinitio::MembraneAbinitio::MembraneEmbed_from_pose ( core::pose::Pose const & pose ) const

private

Pose must already contain a cenlist object or this method will fail.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_EMBED.

◆ MembraneTopology_from_pose()

core::scoring::MembraneTopology const & protocols::abinitio::MembraneAbinitio::MembraneTopology_from_pose ( core::pose::Pose const & pose ) const

private

Pose must already contain a cenlist object or this method will fail.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

Referenced by apply(), get_tmh_inserted(), and print_debug().

◆ move_all_inserted()

void protocols::abinitio::MembraneAbinitio::move_all_inserted ( core::pose::Pose & pose )

References core::scoring::MembraneTopology::allow_scoring(), movemap(), nonconst_MembraneTopology_from_pose(), set_movemap(), and core::pose::Pose::size().

Referenced by apply().

◆ movemap()

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

References movemap_.

Referenced by add_spanning_region(), MembraneAbinitio(), move_all_inserted(), and prepare_stage1().

◆ nonconst_MembraneEmbed_from_pose()

core::scoring::MembraneEmbed & protocols::abinitio::MembraneAbinitio::nonconst_MembraneEmbed_from_pose ( core::pose::Pose & pose ) const

private

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_EMBED.

◆ nonconst_MembraneTopology_from_pose()

core::scoring::MembraneTopology & protocols::abinitio::MembraneAbinitio::nonconst_MembraneTopology_from_pose ( core::pose::Pose & pose ) const

private

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

Referenced by add_spanning_region(), apply(), and move_all_inserted().

◆ output_debug_structure()

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

overrideprotectedvirtual

Reimplemented from protocols::abinitio::Protocol.

References core::pose::Pose::dump_pdb(), protocols::abinitio::Protocol::evaluate_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::moves::Mover::get_current_tag(), mc(), protocols::moves::MonteCarlo::score_function(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by apply().

◆ prepare_loop_in_stage3()

void protocols::abinitio::MembraneAbinitio::prepare_loop_in_stage3	(	core::pose::Pose &	,
		core::Size	,
		core::Size
	)

protectedvirtual

References mc_, and temperature_.

Referenced by do_stage3_cycles(), and do_stage3b_cycles().

◆ prepare_loop_in_stage4()

void protocols::abinitio::MembraneAbinitio::prepare_loop_in_stage4	(	core::pose::Pose &	,
		core::Size	,
		core::Size
	)

protectedvirtual

References mc_, and temperature_.

Referenced by do_stage4_cycles().

◆ prepare_stage1()

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

protectedvirtual

References mc_, movemap(), score_stage1_, set_movemap(), and temperature_.

Referenced by apply().

◆ prepare_stage2()

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

protectedvirtual

References mc_, score_stage2_, and temperature_.

Referenced by apply().

◆ prepare_stage3()

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

protectedvirtual

References mc_, score_stage3a_, and temperature_.

Referenced by apply().

◆ prepare_stage4()

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

protectedvirtual

References mc_, score_stage4_, and temperature_.

Referenced by apply().

◆ print_debug()

void protocols::abinitio::MembraneAbinitio::print_debug ( core::pose::Pose & pose )

References core::scoring::MembraneTopology::allow_scoring(), current_scorefxn(), mc_, MembraneTopology_from_pose(), movemap_, core::scoring::ScoreFunction::show(), core::pose::Pose::size(), core::scoring::MembraneTopology::span_begin(), core::scoring::MembraneTopology::span_end(), and core::scoring::MembraneTopology::tmhelix().

Referenced by apply().

◆ recover_checkpoint()

bool protocols::abinitio::MembraneAbinitio::recover_checkpoint	(	core::pose::Pose &	pose,
		std::string const &	id
	)

virtual

References checkpoint_, protocols::moves::Mover::get_current_tag(), and protocols::checkpoint::CheckPointer::recover_checkpoint().

Referenced by apply(), do_stage3_cycles(), do_stage3b_cycles(), and do_stage4_cycles().

◆ register_options()

void protocols::abinitio::MembraneAbinitio::register_options ( )

static

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

References core::pack::interaction_graph::debug.

◆ set_current_weight()

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

protected

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

◆ set_cycles()

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

virtual

References stage1_cycles_, stage2_cycles_, stage3_cycles_, and stage4_cycles_.

Referenced by set_default_options().

◆ set_default_mc()

void protocols::abinitio::MembraneAbinitio::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::MembraneAbinitio::set_default_options ( )

protectedvirtual

References apply_large_frags_, bQuickTest(), bQuickTest_, just_smooth_cycles_, only_stage4_, set_cycles(), and short_insert_region_.

Referenced by set_defaults().

◆ set_default_scores()

void protocols::abinitio::MembraneAbinitio::set_default_scores ( )

protectedvirtual

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

Referenced by set_defaults().

◆ set_defaults()

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

protectedvirtual

References score_stage1_, set_default_mc(), set_default_options(), set_default_scores(), temperature_, and update_moves().

Referenced by init().

◆ set_mc()

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

References mc_, smooth_trial_small_, trial_large_, trial_small_, and trial_small_top25_.

Referenced by set_default_mc().

◆ set_movemap()

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

virtual

References brute_move_large_, brute_move_small_, brute_move_small_top25_, movemap_, and smooth_move_small_.

Referenced by add_spanning_region(), move_all_inserted(), and prepare_stage1().

◆ set_moves()

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