extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees ) This is achieved by replacing the pose's ConstraintSet with the special purpose class MaxSeqSepConstraintSet the latter class will only score constraints that are sufficiently close in FoldTree/Sequence ( as controlled by the threshold with set_max_seq_sep() ) the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages. to this extend it overloads methods prepare_stageX() do_stage1_cycles() More...

#include <FoldConstraints.hh>

Inheritance diagram for protocols::abinitio::FoldConstraints:

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Collaboration diagram for protocols::abinitio::FoldConstraints:

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Public Types
typedef ClassicAbinitio	Parent

Public Types inherited from protocols::abinitio::ClassicAbinitio
enum	StageID { ALL_STAGES = 0, STAGE_1, STAGE_2, STAGE_3a, STAGE_3b, STAGE_4, STAGE_5 }

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
	FoldConstraints (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy)
	c'stor from Movers More...

	FoldConstraints (core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap)
	c'stor from FragSets — ClassicFragmentMover and SmoothFragmentMover will be created More...

	FoldConstraints (FoldConstraints const &src)
	Explicit copy constructor to handle OPs. More...

	~FoldConstraints ()
	Explicit destructor to handle OPs. More...

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

virtual void	apply (core::pose::Pose &pose)
	run the protocol More...

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

void	set_default_scores ()
	sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0 More...

void	set_constraint_weight (core::Real setting)

virtual void	set_default_options ()

void	set_show_viol_level (core::Size setting)

Public Member Functions inherited from protocols::abinitio::ClassicAbinitio
	ClassicAbinitio (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int)
	This constructor does not work – Fix it before using it. More...

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

	ClassicAbinitio (ClassicAbinitio const &src)
	Explicit copy constructor since this class contains OPs of other classes. More...

	~ClassicAbinitio ()
	Explicit destructor since this class contains OPs of other classes. More...

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

simple_moves::FragmentMoverOP	smooth_move_small ()

simple_moves::FragmentMoverOP	brute_move_small ()

simple_moves::FragmentMoverOP	brute_move_large ()

core::kinematics::MoveMapCOP	movemap ()

void	set_moves (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small)

void	set_mc (moves::MonteCarloOP)

moves::MonteCarlo &	mc ()

moves::MonteCarlo const &	mc () const

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

Size	total_trials () const

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

bool	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

Size	stage5_cycles () const

bool	bQuickTest () const

void	set_skip_stage1 (bool setting)

void	set_skip_stage2 (bool setting)

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

	~Protocol ()

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 ()
	Why is this not being registered ? Probably not actually needed. More...

Static Public Member Functions inherited from protocols::abinitio::ClassicAbinitio
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
bool	prepare_stage1 (core::pose::Pose &pose)

bool	prepare_stage2 (core::pose::Pose &pose)

bool	prepare_stage4 (core::pose::Pose &pose)

bool	prepare_loop_in_stage3 (core::pose::Pose &pose, Size loop_iteration, Size total_iterations)

bool	prepare_loop_in_stage4 (core::pose::Pose &pose, Size loop_iteration, Size total_iterations)

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

bool	do_stage2_cycles (core::pose::Pose &pose)

virtual void	setup_default_min_move ()

virtual void	set_movemap (core::kinematics::MoveMapCOP mm)

void	set_min_move (protocols::simple_moves::MinMoverOP mm)

protocols::simple_moves::MinMover &	min_move ()

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

virtual void	set_max_seq_sep (core::pose::Pose &pose, Size setting)

core::Real	max_seq_sep_fudge () const

void	max_seq_sep_fudge (core::Real setting)

constraints_additional::MaxSeqSepConstraintSet const &	constraints ()

void	bIgnoreSequenceSeparation (bool setting)

bool	bIgnoreSequenceSeparation ()

Size	total_res (core::pose::Pose const &pose) const

void	set_seq_sep_stage1 (core::Real setting)

void	set_seq_sep_stage3 (core::Real setting)

Protected Member Functions inherited from protocols::abinitio::ClassicAbinitio
virtual void	update_moves ()

virtual void	set_defaults (core::pose::Pose const &pose)

virtual void	set_default_mc (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn)

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

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

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

virtual void	replace_scorefxn (core::pose::Pose &pose, StageID stage, core::Real intra_stage_progress)

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

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

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

virtual bool	do_stage5_cycles (core::pose::Pose &pose)

virtual moves::TrialMoverOP	stage1_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)

virtual moves::TrialMoverOP	stage2_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)

virtual moves::TrialMoverOP	stage3_mover (core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in)

virtual moves::TrialMoverOP	stage4_mover (core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in)

virtual moves::TrialMoverOP	stage5_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)

virtual void	set_trials ()

moves::TrialMoverOP	trial_large ()

moves::TrialMoverOP	trial_small ()

moves::TrialMoverOP	trial_smooth ()

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

virtual bool	prepare_stage5 (core::pose::Pose &pose)

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

moves::MonteCarloOP	mc_ptr ()

Private Member Functions
core::Real	evaluate_constraint_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &) const

Additional Inherited Members
Public Attributes inherited from protocols::abinitio::ClassicAbinitio
bool	bSkipStage1_

bool	bSkipStage2_

bool	bSkipStage3_

bool	bSkipStage4_

bool	bSkipStage5_

utility::vector1< StageID >	recover_low_stages_

Protected Attributes inherited from protocols::abinitio::ClassicAbinitio
Size	stage1_cycles_

Size	stage2_cycles_

Size	stage3_cycles_

Size	stage4_cycles_

Size	stage5_cycles_

Detailed Description

extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees ) This is achieved by replacing the pose's ConstraintSet with the special purpose class MaxSeqSepConstraintSet the latter class will only score constraints that are sufficiently close in FoldTree/Sequence ( as controlled by the threshold with set_max_seq_sep() ) the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages. to this extend it overloads methods prepare_stageX() do_stage1_cycles()

the other substantial difference to ClassicAbinitio is that minimizations are carried out. method min_trial() is called each time the max_seq_sep is changed. ( inhibit: -no_minimize )

Definition at line 83 of file FoldConstraints.hh.

Member Typedef Documentation

typedef ClassicAbinitio protocols::abinitio::FoldConstraints::Parent

Definition at line 85 of file FoldConstraints.hh.

Constructor & Destructor Documentation

protocols::abinitio::FoldConstraints::FoldConstraints	(	simple_moves::FragmentMoverOP	brute_move_small,
		simple_moves::FragmentMoverOP	brute_move_large,
		simple_moves::FragmentMoverOP	smooth_move_small,
		int	dummy
	)

c'stor from Movers

Definition at line 100 of file FoldConstraints.cc.

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

Referenced by clone().

protocols::abinitio::FoldConstraints::FoldConstraints	(	core::fragment::FragSetCOP	fragset3mer,
		core::fragment::FragSetCOP	fragset9mer,
		core::kinematics::MoveMapCOP	movemap
	)

c'stor from FragSets — ClassicFragmentMover and SmoothFragmentMover will be created

Definition at line 113 of file FoldConstraints.cc.

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

protocols::abinitio::FoldConstraints::FoldConstraints ( FoldConstraints const & src)

Explicit copy constructor to handle OPs.

SHALLOW copy.

Definition at line 125 of file FoldConstraints.cc.

References bIgnoreSequenceSeparation_, bMinTrial_, bSkipOnNoViolation_, constraint_threshold_, constraint_weight_, constraints_, max_seq_sep_fudge_, min_move_, ramp_cst_cycles_, ramp_iterations_, run_, seq_sep_stage1_, seq_sep_stage3_, seq_sep_stage4_, show_viol_level_, and start_ramp_cstweight_.

protocols::abinitio::FoldConstraints::~FoldConstraints ( )

Explicit destructor to handle OPs.

Definition at line 147 of file FoldConstraints.cc.

Member Function Documentation

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

virtual

run the protocol

Reimplemented from protocols::abinitio::ClassicAbinitio.

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

Definition at line 359 of file FoldConstraints.cc.

References protocols::abinitio::ClassicAbinitio::apply(), bIgnoreSequenceSeparation(), core::pose::Pose::constraint_set(), constraints_, core::pose::Pose::fold_tree(), protocols::abinitio::ClassicAbinitio::mc(), protocols::moves::MonteCarlo::reset(), run_, core::pose::Pose::total_residue(), and tr().

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

void protocols::abinitio::FoldConstraints::bIgnoreSequenceSeparation ( bool setting)

inlineprotected

Definition at line 170 of file FoldConstraints.hh.

References bIgnoreSequenceSeparation_.

bool protocols::abinitio::FoldConstraints::bIgnoreSequenceSeparation ( )

inlineprotected

Definition at line 175 of file FoldConstraints.hh.

References bIgnoreSequenceSeparation_.

Referenced by apply(), and set_max_seq_sep().

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

virtual

...

Reimplemented from protocols::abinitio::ClassicAbinitio.

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

Definition at line 152 of file FoldConstraints.cc.

References FoldConstraints().

constraints_additional::MaxSeqSepConstraintSet const& protocols::abinitio::FoldConstraints::constraints ( )

inlineprotected

Definition at line 165 of file FoldConstraints.hh.

References constraints_.

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

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

protectedvirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

Definition at line 222 of file FoldConstraints.cc.

References bSkipOnNoViolation_, core::pose::Pose::constraint_set(), protocols::abinitio::ClassicAbinitio::do_stage1_cycles(), evaluate_constraint_energy(), protocols::abinitio::ClassicAbinitio::mc(), protocols::abinitio::noe_stage(), seq_sep_stage1_, set_max_seq_sep(), show_viol_level_, protocols::abinitio::ClassicAbinitio::stage1_cycles(), protocols::abinitio::ClassicAbinitio::stage1_mover(), total_res(), tr(), and protocols::abinitio::ClassicAbinitio::trial_large().

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

protectedvirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

Definition at line 265 of file FoldConstraints.cc.

References core::scoring::atom_pair_constraint, protocols::abinitio::ClassicAbinitio::current_scorefxn(), protocols::abinitio::ClassicAbinitio::do_stage2_cycles(), protocols::abinitio::ClassicAbinitio::mc(), protocols::abinitio::noe_stage(), ramp_cst_cycles_, ramp_iterations_, protocols::moves::MonteCarlo::recover_low(), seq_sep_stage1_, protocols::abinitio::ClassicAbinitio::set_current_weight(), set_max_seq_sep(), protocols::abinitio::ClassicAbinitio::stage2_mover(), start_ramp_cstweight_, total_res(), and protocols::abinitio::ClassicAbinitio::trial_large().

core::Real protocols::abinitio::FoldConstraints::evaluate_constraint_energy	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	scfxn
	)		const

inlineprivate

Definition at line 423 of file FoldConstraints.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::pose::Pose::energies(), and core::scoring::Energies::total_energies().

Referenced by do_stage1_cycles().

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

virtual

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

Reimplemented from protocols::abinitio::ClassicAbinitio.

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

Definition at line 382 of file FoldConstraints.cc.

core::Real protocols::abinitio::FoldConstraints::max_seq_sep_fudge ( ) const

inlineprotected

Definition at line 157 of file FoldConstraints.hh.

References max_seq_sep_fudge_.

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

void protocols::abinitio::FoldConstraints::max_seq_sep_fudge ( core::Real setting)

inlineprotected

Definition at line 161 of file FoldConstraints.hh.

References max_seq_sep_fudge_.

protocols::simple_moves::MinMover& protocols::abinitio::FoldConstraints::min_move ( )

inlineprotected

Definition at line 149 of file FoldConstraints.hh.

References min_move_.

void protocols::abinitio::FoldConstraints::min_trial ( core::pose::Pose & pose)

protected

Definition at line 406 of file FoldConstraints.cc.

References core::pose::Pose::constraint_set(), protocols::abinitio::ClassicAbinitio::current_scorefxn(), protocols::abinitio::ClassicAbinitio::mc(), min_move_, protocols::moves::MonteCarlo::reset(), setup_default_min_move(), core::scoring::ScoreFunction::show(), show_viol_level_, and tr().

Referenced by set_max_seq_sep().

bool protocols::abinitio::FoldConstraints::prepare_loop_in_stage3	(	core::pose::Pose &	pose,
		Size	loop_iteration,
		Size	total_iterations
	)

protectedvirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

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

Definition at line 290 of file FoldConstraints.cc.

References core::scoring::atom_pair_constraint, core::pose::Pose::constraint_set(), constraint_threshold_, constraints_, protocols::abinitio::noe_stage(), protocols::abinitio::ClassicAbinitio::prepare_loop_in_stage3(), seq_sep_stage1_, seq_sep_stage3_, set_max_seq_sep(), core::scoring::ScoreFunction::set_weight(), show_viol_level_, total_res(), core::pose::Pose::total_residue(), and tr().

Referenced by protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage3().

bool protocols::abinitio::FoldConstraints::prepare_loop_in_stage4	(	core::pose::Pose &	pose,
		Size	loop_iteration,
		Size	total_iterations
	)

protectedvirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

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

Definition at line 321 of file FoldConstraints.cc.

References core::pose::Pose::constraint_set(), constraints_, protocols::abinitio::noe_stage(), protocols::abinitio::ClassicAbinitio::prepare_loop_in_stage4(), seq_sep_stage3_, seq_sep_stage4_, set_max_seq_sep(), show_viol_level_, total_res(), and tr().

Referenced by protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage4().

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

protectedvirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

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

Definition at line 195 of file FoldConstraints.cc.

References protocols::abinitio::ClassicAbinitio::prepare_stage1(), and tr().

Referenced by protocols::abinitio::KinematicAbinitio::prepare_stage1().

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

protectedvirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

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

Definition at line 256 of file FoldConstraints.cc.

References core::pose::Pose::constraint_set(), protocols::abinitio::noe_stage(), protocols::abinitio::ClassicAbinitio::prepare_stage2(), seq_sep_stage1_, set_max_seq_sep(), show_viol_level_, total_res(), and tr().

Referenced by protocols::abinitio::KinematicAbinitio::prepare_stage2().

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

protectedvirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

Definition at line 338 of file FoldConstraints.cc.

References core::pose::Pose::constraint_set(), protocols::abinitio::ClassicAbinitio::prepare_stage4(), show_viol_level_, and tr().

void protocols::abinitio::FoldConstraints::register_options ( )

static

Why is this not being registered ? Probably not actually needed.

Definition at line 76 of file FoldConstraints.cc.

References protocols::abinitio::ClassicAbinitio::register_options().

void protocols::abinitio::FoldConstraints::set_constraint_weight ( core::Real setting)

inline

Definition at line 120 of file FoldConstraints.hh.

References core::scoring::atom_pair_constraint, constraint_weight_, and protocols::abinitio::ClassicAbinitio::set_score_weight().

Referenced by set_default_options().

void protocols::abinitio::FoldConstraints::set_default_options ( )

virtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

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

Definition at line 157 of file FoldConstraints.cc.

References bIgnoreSequenceSeparation_, bMinTrial_, protocols::abinitio::ClassicAbinitio::bQuickTest(), bSkipOnNoViolation_, constraint_threshold_, max_seq_sep_fudge_, ramp_cst_cycles_, seq_sep_stage1_, seq_sep_stage3_, seq_sep_stage4_, set_constraint_weight(), protocols::abinitio::ClassicAbinitio::set_default_options(), core::io::serialization::size(), and start_ramp_cstweight_.

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

void protocols::abinitio::FoldConstraints::set_default_scores ( )

virtual

sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0

Reimplemented from protocols::abinitio::ClassicAbinitio.

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

Definition at line 349 of file FoldConstraints.cc.

References core::scoring::atom_pair_constraint, constraint_weight_, protocols::abinitio::ClassicAbinitio::set_default_scores(), protocols::abinitio::ClassicAbinitio::set_score_weight(), and tr().

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

void protocols::abinitio::FoldConstraints::set_max_seq_sep	(	core::pose::Pose &	pose,
		Size	setting
	)

protectedvirtual

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

Definition at line 202 of file FoldConstraints.cc.

References bIgnoreSequenceSeparation(), bMinTrial_, core::pose::Pose::constraint_set(), constraints_, protocols::abinitio::ClassicAbinitio::mc(), min_trial(), protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::reset(), and tr().

Referenced by do_stage1_cycles(), do_stage2_cycles(), prepare_loop_in_stage3(), prepare_loop_in_stage4(), prepare_stage2(), and protocols::abinitio::KinematicAbinitio::set_max_seq_sep().

void protocols::abinitio::FoldConstraints::set_min_move ( protocols::simple_moves::MinMoverOP mm)

protected

Definition at line 401 of file FoldConstraints.cc.

References min_move_.

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

protectedvirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

Definition at line 395 of file FoldConstraints.cc.

References min_move_, and protocols::abinitio::ClassicAbinitio::set_movemap().

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

void protocols::abinitio::FoldConstraints::set_seq_sep_stage1 ( core::Real setting)

inlineprotected

Definition at line 181 of file FoldConstraints.hh.

References seq_sep_stage1_.

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

void protocols::abinitio::FoldConstraints::set_seq_sep_stage3 ( core::Real setting)

inlineprotected

Definition at line 185 of file FoldConstraints.hh.

References seq_sep_stage3_.

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

void protocols::abinitio::FoldConstraints::set_show_viol_level ( core::Size setting)

inline

Definition at line 128 of file FoldConstraints.hh.

References show_viol_level_.

void protocols::abinitio::FoldConstraints::setup_default_min_move ( )

protectedvirtual

Reimplemented in protocols::abinitio::JumpingFoldConstraints.

Definition at line 387 of file FoldConstraints.cc.

References min_move_, protocols::abinitio::ClassicAbinitio::movemap(), and tr().

Referenced by min_trial().

Size protocols::abinitio::FoldConstraints::total_res ( core::pose::Pose const & pose) const

protected

Definition at line 185 of file FoldConstraints.cc.

References constraints_, max_seq_sep_fudge_, and core::pose::Pose::total_residue().

Referenced by do_stage1_cycles(), do_stage2_cycles(), protocols::abinitio::noe_stage(), prepare_loop_in_stage3(), prepare_loop_in_stage4(), and prepare_stage2().

Member Data Documentation

bool protocols::abinitio::FoldConstraints::bIgnoreSequenceSeparation_

private

Definition at line 199 of file FoldConstraints.hh.

Referenced by bIgnoreSequenceSeparation(), FoldConstraints(), and set_default_options().

bool protocols::abinitio::FoldConstraints::bMinTrial_

private

Definition at line 198 of file FoldConstraints.hh.

Referenced by FoldConstraints(), set_default_options(), and set_max_seq_sep().

bool protocols::abinitio::FoldConstraints::bSkipOnNoViolation_

private

Definition at line 210 of file FoldConstraints.hh.

Referenced by do_stage1_cycles(), FoldConstraints(), and set_default_options().

Size protocols::abinitio::FoldConstraints::constraint_threshold_

private

Definition at line 216 of file FoldConstraints.hh.

Referenced by FoldConstraints(), prepare_loop_in_stage3(), and set_default_options().

core::Real protocols::abinitio::FoldConstraints::constraint_weight_

private

Definition at line 196 of file FoldConstraints.hh.

Referenced by FoldConstraints(), set_constraint_weight(), and set_default_scores().

constraints_additional::MaxSeqSepConstraintSetOP protocols::abinitio::FoldConstraints::constraints_

private

Definition at line 195 of file FoldConstraints.hh.

Referenced by apply(), constraints(), FoldConstraints(), prepare_loop_in_stage3(), prepare_loop_in_stage4(), set_max_seq_sep(), and total_res().

core::Real protocols::abinitio::FoldConstraints::max_seq_sep_fudge_

private

Definition at line 202 of file FoldConstraints.hh.

Referenced by FoldConstraints(), max_seq_sep_fudge(), set_default_options(), and total_res().

protocols::simple_moves::MinMoverOP protocols::abinitio::FoldConstraints::min_move_

private

Definition at line 193 of file FoldConstraints.hh.

Referenced by FoldConstraints(), min_move(), min_trial(), set_min_move(), set_movemap(), and setup_default_min_move().

core::Size protocols::abinitio::FoldConstraints::ramp_cst_cycles_

private

Definition at line 208 of file FoldConstraints.hh.

Referenced by do_stage2_cycles(), FoldConstraints(), and set_default_options().

core::Size protocols::abinitio::FoldConstraints::ramp_iterations_

private

Definition at line 209 of file FoldConstraints.hh.

Referenced by do_stage2_cycles(), and FoldConstraints().

Size protocols::abinitio::FoldConstraints::run_

private

Definition at line 200 of file FoldConstraints.hh.

Referenced by apply(), and FoldConstraints().

core::Real protocols::abinitio::FoldConstraints::seq_sep_stage1_

private

Definition at line 203 of file FoldConstraints.hh.

Referenced by do_stage1_cycles(), do_stage2_cycles(), FoldConstraints(), prepare_loop_in_stage3(), prepare_stage2(), set_default_options(), and set_seq_sep_stage1().

core::Real protocols::abinitio::FoldConstraints::seq_sep_stage3_

private

Definition at line 204 of file FoldConstraints.hh.

Referenced by FoldConstraints(), prepare_loop_in_stage3(), prepare_loop_in_stage4(), set_default_options(), and set_seq_sep_stage3().

core::Real protocols::abinitio::FoldConstraints::seq_sep_stage4_

private

Definition at line 205 of file FoldConstraints.hh.

Referenced by FoldConstraints(), prepare_loop_in_stage4(), and set_default_options().

Size protocols::abinitio::FoldConstraints::show_viol_level_

private

Definition at line 213 of file FoldConstraints.hh.

Referenced by do_stage1_cycles(), FoldConstraints(), min_trial(), prepare_loop_in_stage3(), prepare_loop_in_stage4(), prepare_stage2(), prepare_stage4(), and set_show_viol_level().

core::Real protocols::abinitio::FoldConstraints::start_ramp_cstweight_

private

Definition at line 207 of file FoldConstraints.hh.

Referenced by do_stage2_cycles(), FoldConstraints(), and set_default_options().

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

src/protocols/abinitio/FoldConstraints.hh
src/protocols/abinitio/FoldConstraints.cc

Private Attributes
protocols::simple_moves::MinMoverOP	min_move_

constraints_additional::MaxSeqSepConstraintSetOP	constraints_

core::Real	constraint_weight_

bool	bMinTrial_

bool	bIgnoreSequenceSeparation_

Size	run_

core::Real	max_seq_sep_fudge_

core::Real	seq_sep_stage1_

core::Real	seq_sep_stage3_

core::Real	seq_sep_stage4_

core::Real	start_ramp_cstweight_

core::Size	ramp_cst_cycles_

core::Size	ramp_iterations_

bool	bSkipOnNoViolation_

Size	show_viol_level_

Size	constraint_threshold_

Public Types

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Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

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