protocols::abinitio::KinematicAbinitio Class Reference

#include <KinematicAbinitio.hh>

Inheritance diagram for protocols::abinitio::KinematicAbinitio:

Public Member Functions
	KinematicAbinitio (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy)
	KinematicAbinitio (core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap)
	~KinematicAbinitio () override
moves::MoverOP	clone () const override
	... More...
void	apply (core::pose::Pose &pose) override
	run the protocol More...
std::string	get_name () const override
	Each derived class must specify its name. The class name. More...
void	set_max_seq_sep (core::pose::Pose &pose, core::Size setting) override
bool	prepare_stage1 (core::pose::Pose &pose) override
bool	prepare_stage2 (core::pose::Pose &pose) override
bool	prepare_stage3 (core::pose::Pose &pose) override
bool	prepare_loop_in_stage3 (core::pose::Pose &, core::Size, core::Size) override
bool	prepare_loop_in_stage4 (core::pose::Pose &, core::Size, core::Size) override
moves::TrialMoverOP	stage1_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in) override
moves::TrialMoverOP	stage2_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in) override
moves::TrialMoverOP	stage3_mover (core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in) override
moves::TrialMoverOP	stage4_mover (core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in) override
void	closure_protocol (loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol)
	set the closure_protocol... if not set no closure... More...
Public Member Functions inherited from 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 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 () override
	Explicit destructor to handle OPs. More...
void	set_constraint_weight (core::Real setting)
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 () override
	Explicit destructor since this class contains OPs of other classes. More...
void	init (core::pose::Pose const &pose) override
	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)
core::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	supports_trRosetta_constraints () const override
	This overrides the default and indicates that the ClassicAbInitio protocol DOES support trRosetta constraints. 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
core::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 () 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 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::FoldConstraints
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. More...

Protected Member Functions
void	set_default_scores () override
	sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0 More...
void	set_default_options () override
void	replace_scorefxn (core::pose::Pose &pose, StageID, core::Real intra_stage_progress) override
Protected Member Functions inherited from protocols::abinitio::FoldConstraints
bool	prepare_stage4 (core::pose::Pose &pose) override
bool	do_stage1_cycles (core::pose::Pose &pose) override
bool	do_stage2_cycles (core::pose::Pose &pose) override
virtual void	setup_default_min_move ()
void	set_movemap (core::kinematics::MoveMapCOP mm) override
void	set_min_move (protocols::minimization_packing::MinMoverOP mm)
protocols::minimization_packing::MinMover &	min_move ()
void	min_trial (core::pose::Pose &pose)
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 ()
core::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)
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	stage4rot_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_stage5 (core::pose::Pose &pose)
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...

Private Types
typedef FoldConstraints	Parent

Private Member Functions
moves::MoverOP	create_bb_moves (core::pose::Pose &pose, moves::MoverOP std_moves, bool bLargeWobble, core::Real crank_up_angle)
void	dump_jump_log (core::pose::Pose &pose, std::string const &file_name)
moves::MoverOP	create_jump_moves (moves::MoverOP stdmove)

Private Attributes
bool	bRampChainbreaks_
bool	bOverlapChainbreaks_
loops::loop_closure::ccd::SlidingWindowLoopClosureOP	closure_protocol_
core::scoring::constraints::ConstraintSetOP	full_constraint_set_

Additional Inherited Members
Public Types inherited from protocols::abinitio::FoldConstraints
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_4rot , STAGE_5 }
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 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
core::Size	stage1_cycles_
core::Size	stage2_cycles_
core::Size	stage3_cycles_
core::Size	stage4_cycles_
core::Size	stage5_cycles_
core::Real	stage4_cycles_pack_rate_

Member Typedef Documentation

Parent

typedef FoldConstraints protocols::abinitio::KinematicAbinitio::Parent

private

Constructor & Destructor Documentation

KinematicAbinitio() [1/2]

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

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

KinematicAbinitio() [2/2]

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

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

~KinematicAbinitio()

protocols::abinitio::KinematicAbinitio::~KinematicAbinitio ( )

overridedefault

Member Function Documentation

apply()

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

overridevirtual

run the protocol

Reimplemented from protocols::abinitio::FoldConstraints.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper.

References protocols::abinitio::FoldConstraints::apply(), protocols::idealize::IdealizeMover::apply(), protocols::abinitio::ClassicAbinitio::brute_move_small(), clone(), protocols::jumping::close_chainbreaks(), closure_protocol_, core::pose::Pose::constraint_set(), protocols::abinitio::ClassicAbinitio::current_scorefxn(), core::pack::interaction_graph::debug, dump_jump_log(), protocols::abinitio::Protocol::evaluator(), protocols::moves::FAIL_RETRY, protocols::idealize::IdealizeMover::fast(), protocols::abinitio::filename(), core::io::silent::SilentStruct::fill_pose(), core::pose::Pose::fold_tree(), full_constraint_set_, protocols::jumping::JumpSample::generate_jump_frames(), protocols::abinitio::Protocol::get_checkpoints(), protocols::moves::Mover::get_current_job(), protocols::moves::Mover::get_current_tag(), protocols::moves::Mover::get_last_move_status(), protocols::jumping::JumpSample::get_pairing(), core::io::silent::SilentFileData::get_structure(), core::io::silent::SilentFileData::has_tag(), protocols::abinitio::Protocol::kinematics(), protocols::abinitio::FoldConstraints::max_seq_sep_fudge(), protocols::mean_field::min(), protocols::abinitio::ClassicAbinitio::movemap(), protocols::moves::MS_SUCCESS, protocols::abinitio::ClassicAbinitio::output_debug_structure(), protocols::abinitio::KinematicControl::prepare_pose_for_sampling(), core::io::silent::SilentFileData::read_file(), core::scoring::rg, protocols::moves::Mover::set_current_tag(), protocols::abinitio::Protocol::set_kinematics(), protocols::moves::Mover::set_last_move_status(), protocols::abinitio::FoldConstraints::set_movemap(), protocols::abinitio::FoldConstraints::set_seq_sep_stage1(), protocols::abinitio::FoldConstraints::set_seq_sep_stage3(), protocols::abinitio::ClassicAbinitio::set_skip_stage1(), protocols::abinitio::ClassicAbinitio::set_skip_stage2(), protocols::loops::skip_rate, protocols::jumping::JumpSample::steal_orientation_and_pleating(), tr(), protocols::hybridization::val, and core::fragment::FragmentIO::write_data().

Referenced by dump_jump_log().

clone()

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

inlineoverridevirtual

...

Reimplemented from protocols::abinitio::FoldConstraints.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper.

Referenced by apply(), and replace_scorefxn().

closure_protocol()

void protocols::abinitio::KinematicAbinitio::closure_protocol ( loops::loop_closure::ccd::SlidingWindowLoopClosureOP  closure_protocol )

inline

set the closure_protocol... if not set no closure...

References closure_protocol_.

create_bb_moves()

moves::MoverOP protocols::abinitio::KinematicAbinitio::create_bb_moves ( core::pose::Pose &  pose, moves::MoverOP  std_moves, bool  bLargeWobble, core::Real  crank_up_angle  )

private

References protocols::abinitio::ClassicAbinitio::brute_move_large(), protocols::abinitio::ClassicAbinitio::brute_move_small(), protocols::abinitio::ClassicAbinitio::mc(), protocols::abinitio::ClassicAbinitio::movemap(), and protocols::moves::MonteCarlo::temperature().

Referenced by stage3_mover(), and stage4_mover().

create_jump_moves()

moves::MoverOP protocols::abinitio::KinematicAbinitio::create_jump_moves ( moves::MoverOP  stdmove )

private

References protocols::abinitio::KinematicControl::jump_mover(), and protocols::abinitio::Protocol::kinematics().

Referenced by stage1_mover(), stage2_mover(), stage3_mover(), and stage4_mover().

dump_jump_log()

void protocols::abinitio::KinematicAbinitio::dump_jump_log ( core::pose::Pose &  pose, std::string const &  filename  )

private

the native_pose_ is used to determine orientation and pleating of jumps

References apply(), protocols::abinitio::Protocol::evaluate_pose(), protocols::abinitio::filename(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::pose::Pose::fold_tree(), protocols::moves::Mover::get_current_tag(), core::io::silent::SilentStruct::get_energy(), protocols::moves::Mover::get_native_pose(), protocols::abinitio::Protocol::kinematics(), core::kinematics::FoldTree::num_jump(), core::conformation::membrane::out, and protocols::abinitio::KinematicControl::sampling_fold_tree().

Referenced by apply().

get_name()

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

overridevirtual

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

Reimplemented from protocols::abinitio::FoldConstraints.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper.

prepare_loop_in_stage3()

bool protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage3 ( core::pose::Pose &  pose, core::Size  iteration, core::Size  total  )

overridevirtual

Reimplemented from protocols::abinitio::FoldConstraints.

References bRampChainbreaks_, core::scoring::linear_chainbreak, protocols::abinitio::FoldConstraints::prepare_loop_in_stage3(), protocols::abinitio::ClassicAbinitio::set_score_weight(), protocols::abinitio::ClassicAbinitio::STAGE_3a, protocols::abinitio::ClassicAbinitio::STAGE_3b, and protocols::analysis::total.

prepare_loop_in_stage4()

bool protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage4 ( core::pose::Pose &  pose, core::Size  iteration, core::Size  total  )

overridevirtual

Reimplemented from protocols::abinitio::FoldConstraints.

References bOverlapChainbreaks_, bRampChainbreaks_, core::scoring::linear_chainbreak, core::scoring::overlap_chainbreak, protocols::abinitio::FoldConstraints::prepare_loop_in_stage4(), protocols::abinitio::ClassicAbinitio::set_current_weight(), protocols::abinitio::ClassicAbinitio::set_score_weight(), protocols::abinitio::ClassicAbinitio::STAGE_4, and protocols::analysis::total.

prepare_stage1()

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

overridevirtual

Reimplemented from protocols::abinitio::FoldConstraints.

References protocols::abinitio::ClassicAbinitio::ALL_STAGES, bRampChainbreaks_, core::scoring::linear_chainbreak, protocols::abinitio::FoldConstraints::prepare_stage1(), protocols::abinitio::ClassicAbinitio::set_score_weight(), and protocols::abinitio::ClassicAbinitio::STAGE_2.

prepare_stage2()

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

overridevirtual

Reimplemented from protocols::abinitio::FoldConstraints.

References protocols::abinitio::FoldConstraints::prepare_stage2().

prepare_stage3()

bool protocols::abinitio::KinematicAbinitio::prepare_stage3 ( core::pose::Pose &  pose )

overridevirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

References protocols::abinitio::ClassicAbinitio::prepare_stage3().

register_options()

void protocols::abinitio::KinematicAbinitio::register_options ( )

static

References core::scoring::overlap_chainbreak, and protocols::moves::Mover::register_options().

replace_scorefxn()

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

overrideprotectedvirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

References protocols::abinitio::KinematicControl::add_score_weights(), clone(), protocols::abinitio::ClassicAbinitio::current_scorefxn(), protocols::abinitio::Protocol::kinematics(), and protocols::abinitio::ClassicAbinitio::replace_scorefxn().

set_default_options()

void protocols::abinitio::KinematicAbinitio::set_default_options ( )

overrideprotectedvirtual

Reimplemented from protocols::abinitio::FoldConstraints.

References bOverlapChainbreaks_, bRampChainbreaks_, core::scoring::overlap_chainbreak, and protocols::abinitio::FoldConstraints::set_default_options().

set_default_scores()

void protocols::abinitio::KinematicAbinitio::set_default_scores ( )

overrideprotectedvirtual

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

Reimplemented from protocols::abinitio::FoldConstraints.

References bRampChainbreaks_, core::scoring::linear_chainbreak, protocols::abinitio::FoldConstraints::set_default_scores(), protocols::abinitio::ClassicAbinitio::set_score_weight(), protocols::abinitio::ClassicAbinitio::STAGE_1, protocols::abinitio::ClassicAbinitio::STAGE_2, protocols::abinitio::ClassicAbinitio::STAGE_3a, protocols::abinitio::ClassicAbinitio::STAGE_3b, and protocols::abinitio::ClassicAbinitio::STAGE_4.

set_max_seq_sep()

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

overridevirtual

Reimplemented from protocols::abinitio::FoldConstraints.

References protocols::abinitio::KinematicControl::add_chainbreak_variants(), protocols::abinitio::FoldConstraints::constraints(), protocols::abinitio::Protocol::kinematics(), protocols::abinitio::ClassicAbinitio::mc(), protocols::moves::MonteCarlo::reset(), protocols::abinitio::FoldConstraints::set_max_seq_sep(), and core::chemical::shortest_path().

stage1_mover()

moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage1_mover ( core::pose::Pose &  pose, moves::TrialMoverOP  trials_in  )

overridevirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

References create_jump_moves(), protocols::abinitio::Protocol::kinematics(), and protocols::abinitio::ClassicAbinitio::mc_ptr().

stage2_mover()

moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage2_mover ( core::pose::Pose &  pose, moves::TrialMoverOP  trials_in  )

overridevirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

References create_jump_moves(), protocols::abinitio::Protocol::kinematics(), and protocols::abinitio::ClassicAbinitio::mc_ptr().

stage3_mover()

moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage3_mover ( core::pose::Pose &  pose, int  lct1, int  lct2, moves::TrialMoverOP  trials_in  )

overridevirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

References protocols::moves::accept_reject, create_bb_moves(), create_jump_moves(), protocols::abinitio::Protocol::kinematics(), and protocols::abinitio::ClassicAbinitio::mc_ptr().

stage4_mover()

moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage4_mover ( core::pose::Pose &  pose, int  kk, moves::TrialMoverOP  trials_in  )

overridevirtual

Reimplemented from protocols::abinitio::ClassicAbinitio.

References create_bb_moves(), create_jump_moves(), protocols::abinitio::Protocol::kinematics(), and protocols::abinitio::ClassicAbinitio::mc_ptr().

Member Data Documentation

bOverlapChainbreaks_

bool protocols::abinitio::KinematicAbinitio::bOverlapChainbreaks_

private

Referenced by prepare_loop_in_stage4(), and set_default_options().

bRampChainbreaks_

bool protocols::abinitio::KinematicAbinitio::bRampChainbreaks_

private

Referenced by prepare_loop_in_stage3(), prepare_loop_in_stage4(), prepare_stage1(), set_default_options(), and set_default_scores().

closure_protocol_

loops::loop_closure::ccd::SlidingWindowLoopClosureOP protocols::abinitio::KinematicAbinitio::closure_protocol_

private

Referenced by apply(), and closure_protocol().

full_constraint_set_

core::scoring::constraints::ConstraintSetOP protocols::abinitio::KinematicAbinitio::full_constraint_set_

private

Referenced by apply(), and KinematicAbinitio().

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

• src/protocols/abinitio/KinematicAbinitio.hh
• src/protocols/abinitio/KinematicAbinitio.cc