#include <MembraneAbinitio.hh>

Inheritance diagram for protocols::abinitio::MembraneAbinitio:

Collaboration diagram for protocols::abinitio::MembraneAbinitio:

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::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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

Public Member Functions
	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...

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

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

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

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

simple_moves::FragmentMoverOP	smooth_move_small ()

simple_moves::FragmentMoverOP	brute_move_small_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)

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

Size	stage1_cycles () const

Size	stage2_cycles () const

Size	stage3_cycles () const

void	set_stage4_cycles (Size stage4_cycles_new)

Size	stage4_cycles () const

bool	bQuickTest () const

void	set_only_stage4 (bool value)

Public Member Functions inherited from protocols::abinitio::Protocol
	Protocol ()

	~Protocol ()

void	set_evaluation (evaluation::MetaPoseEvaluatorOP ev)

void	add_evaluation (evaluation::PoseEvaluatorOP ev)

void	evaluate_pose (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const

evaluation::MetaPoseEvaluatorOP	evaluator ()

void	set_kinematics (abinitio::KinematicControlOP kc)

abinitio::KinematicControl const &	kinematics ()

virtual bool	start_from_centroid () const

virtual bool	return_centroid () const

virtual void	return_centroid (bool setting)

void	set_fullatom_scorefxn (core::scoring::ScoreFunctionOP sfxn)

void	set_centroid_scorefxn (core::scoring::ScoreFunctionOP sfxn)

void	set_silentout_file_name (std::string str)

core::scoring::ScoreFunctionOP	fullatom_scorefxn ()

core::scoring::ScoreFunctionOP	centroid_scorefxn ()

virtual checkpoint::CheckPointer &	get_checkpoints ()

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::abinitio::Protocol
static void	register_options ()

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

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

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 &, Size, Size)

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

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

moves::MonteCarloOP	mc_ptr ()

Protected Attributes
Size	stage1_cycles_

Size	stage2_cycles_

Size	stage3_cycles_

Size	stage4_cycles_

Private Types
typedef Protocol	Parent

Private Member Functions
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_

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 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 111 of file MembraneAbinitio.hh.

Member Typedef Documentation

typedef Protocol protocols::abinitio::MembraneAbinitio::Parent

private

Definition at line 112 of file MembraneAbinitio.hh.

Member Enumeration Documentation

enum protocols::abinitio::MembraneAbinitio::StageID

Enumerator
ALL_STAGES
STAGE_1
STAGE_2
STAGE_3a
STAGE_3b
STAGE_4

Definition at line 114 of file MembraneAbinitio.hh.

Constructor & Destructor Documentation

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.

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

Definition at line 151 of file MembraneAbinitio.cc.

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

Referenced by clone().

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

Definition at line 173 of file MembraneAbinitio.cc.

References brute_move_large_, brute_move_small_, brute_move_small_top25_, smooth_move_small_, and protocols::moves::Mover::type().

Member Function Documentation

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

Definition at line 677 of file MembraneAbinitio.cc.

References core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::sequence::end, core::pose::Pose::fold_tree(), movemap(), nonconst_MembraneTopology_from_pose(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::num_jump(), set_movemap(), protocols::loops::start, core::pose::Pose::total_residue(), tr(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by apply().

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

virtual

Reimplemented from protocols::abinitio::Protocol.

Definition at line 233 of file MembraneAbinitio.cc.

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().

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

inline

Definition at line 376 of file MembraneAbinitio.hh.

References bQuickTest_.

Referenced by set_default_options().

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

Definition at line 501 of file MembraneAbinitio.cc.

References brute_move_large_.

Referenced by do_stage1_cycles(), and set_moves().

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

Definition at line 490 of file MembraneAbinitio.cc.

References brute_move_small_.

Referenced by set_moves().

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

Definition at line 495 of file MembraneAbinitio.cc.

References brute_move_small_top25_.

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

virtual

Definition at line 1631 of file MembraneAbinitio.cc.

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().

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

virtual

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

Definition at line 1659 of file MembraneAbinitio.cc.

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

Referenced by apply().

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

virtual

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

Reimplemented from protocols::moves::Mover.

Definition at line 228 of file MembraneAbinitio.cc.

References MembraneAbinitio().

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

protected

Definition at line 638 of file MembraneAbinitio.cc.

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

Referenced by apply(), and print_debug().

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

protected

Definition at line 643 of file MembraneAbinitio.cc.

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

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

protectedvirtual

Definition at line 1188 of file MembraneAbinitio.cc.

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

Referenced by apply().

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

protectedvirtual

Definition at line 1216 of file MembraneAbinitio.cc.

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

Referenced by apply().

int protocols::abinitio::MembraneAbinitio::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 1306 of file MembraneAbinitio.cc.

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().

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

protectedvirtual

Definition at line 1386 of file MembraneAbinitio.cc.

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().

int protocols::abinitio::MembraneAbinitio::do_stage4_cycles ( core::pose::Pose & pose)

protectedvirtual

stage4 cycles: nloop_stage4: iterations stage4_cycle : trials per iteration

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

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

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

Definition at line 1494 of file MembraneAbinitio.cc.

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().

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

virtual

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

Reimplemented from protocols::abinitio::Protocol.

Definition at line 484 of file MembraneAbinitio.cc.

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

private

Definition at line 1704 of file MembraneAbinitio.cc.

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

Referenced by apply().

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

virtual

setup moves, mc-object, scores

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

Reimplemented from protocols::abinitio::Protocol.

Definition at line 219 of file MembraneAbinitio.cc.

References set_defaults().

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

inline

Definition at line 340 of file MembraneAbinitio.hh.

References just_smooth_cycles_.

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

inline

Definition at line 190 of file MembraneAbinitio.hh.

References mc_.

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

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

inline

Definition at line 195 of file MembraneAbinitio.hh.

References mc_.

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

inlineprotected

Definition at line 384 of file MembraneAbinitio.hh.

References mc_.

Referenced by do_stage2_cycles().

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.

Definition at line 1735 of file MembraneAbinitio.cc.

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

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.

Definition at line 1710 of file MembraneAbinitio.cc.

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

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

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

Definition at line 1011 of file MembraneAbinitio.cc.

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

Referenced by apply().

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

Definition at line 533 of file MembraneAbinitio.cc.

References movemap_.

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

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.

Definition at line 1746 of file MembraneAbinitio.cc.

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

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.

Definition at line 1721 of file MembraneAbinitio.cc.

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

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

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

protectedvirtual

Reimplemented from protocols::abinitio::Protocol.

Definition at line 1672 of file MembraneAbinitio.cc.

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().

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

protectedvirtual

Definition at line 1590 of file MembraneAbinitio.cc.

References mc_, and temperature_.

Referenced by do_stage3_cycles(), and do_stage3b_cycles().

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

protectedvirtual

Definition at line 1595 of file MembraneAbinitio.cc.

References mc_, and temperature_.

Referenced by do_stage4_cycles().

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

protectedvirtual

Definition at line 1529 of file MembraneAbinitio.cc.

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

Referenced by apply().

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

protectedvirtual

Definition at line 1547 of file MembraneAbinitio.cc.

References mc_, score_stage2_, and temperature_.

Referenced by apply().

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

protectedvirtual

Definition at line 1558 of file MembraneAbinitio.cc.

References mc_, score_stage3a_, and temperature_.

Referenced by apply().

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

protectedvirtual

Definition at line 1573 of file MembraneAbinitio.cc.

References mc_, score_stage4_, and temperature_.

Referenced by apply().

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

Definition at line 1024 of file MembraneAbinitio.cc.

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

Referenced by apply().

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

virtual

Definition at line 1600 of file MembraneAbinitio.cc.

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().

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

static

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

Definition at line 127 of file MembraneAbinitio.cc.

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

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

protected

Definition at line 648 of file MembraneAbinitio.cc.

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

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

virtual

Definition at line 598 of file MembraneAbinitio.cc.

References stage1_cycles_, stage2_cycles_, stage3_cycles_, and stage4_cycles_.

Referenced by set_default_options().

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

protectedvirtual

Definition at line 584 of file MembraneAbinitio.cc.

References set_mc(), and temperature_.

Referenced by set_defaults().

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

protectedvirtual

Definition at line 654 of file MembraneAbinitio.cc.

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

Referenced by set_defaults().

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

protectedvirtual

Definition at line 612 of file MembraneAbinitio.cc.

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

Referenced by set_defaults().

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

protectedvirtual

Definition at line 538 of file MembraneAbinitio.cc.

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

Referenced by init().

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

Definition at line 589 of file MembraneAbinitio.cc.

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

Referenced by set_default_mc().

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

virtual

Definition at line 508 of file MembraneAbinitio.cc.

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().

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