A protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure a smooth fragment is chosen according to the FragmentCost Functor; a cutpoint is inserted just in front of or just after the fragment a loop is defined around the fragment and cutpoint to be closed with ccd: a cut_Cterm insertion: -—lfff bbb-— f: fragment_res b: buffer_res -: immovable residues a !cut_Cterm insertion: —bbb fffl— the number of b resiudes is controlled by buffer_length_ (default 3); the move is used by apply() (inherited from FragmentMover). the insertion and loop closure is implemented in the virtual method apply_fragment(). More...

#include <WobbleMover.hh>

Public Types
typedef protocols::simple_moves::SmoothFragmentMover	Parent

Public Types inherited from protocols::simple_moves::SmoothFragmentMover
typedef ClassicFragmentMover	Parent

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

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
	WobbleMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, protocols::simple_moves::FragmentCostOP cost)

	WobbleMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap)

	~WobbleMover ()

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

void	set_defaults ()
	set defaults More...

void	set_buffer_length (core::Size setting)

Public Member Functions inherited from protocols::simple_moves::SmoothFragmentMover
	SmoothFragmentMover (core::fragment::FragSetCOP fragset, FragmentCostOP cost)

	SmoothFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, FragmentCostOP cost)

	~SmoothFragmentMover ()

Public Member Functions inherited from protocols::simple_moves::ClassicFragmentMover
	ClassicFragmentMover ()
	Empty constructor. More...

	ClassicFragmentMover (core::fragment::FragSetCOP fragset)
	Constructor with supplied FragSet. More...

	ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap)
	Constructor with supplied FragSet and MoveMap. More...

	ClassicFragmentMover (core::fragment::ConstantLengthFragSet const &fragset, core::kinematics::MoveMap const &movemap)
	Constructor with supplied ConstantLengthFragSet and MoveMap. More...

	~ClassicFragmentMover ()

void	apply (core::pose::Pose &)
	Applies classic fragment insertion based on a FragSet. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

void	set_check_ss (bool setting)
	check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2) More...

bool	check_ss () const
	accessor More...

core::Real	end_bias () const

void	set_end_bias (core::Real setting)

bool	end_bias_check_enabled () const

void	enable_end_bias_check (bool setting=true)

void	set_min_overlap (Size setting)
	min_overlap controls the behaviour fragset->region() More...

void	set_min_frag_length (Size setting)
	min_frag_length controls the behaviour fragset->region() More...

void	define_start_window (Size window_start)
	apply fragment at predefined position More...

virtual bool	choose_window_start (core::pose::Pose const &, Size window_length, Size &window_start) const
	yields a start position (window_start) for fragment window to sample from ( return false, if nothing suitable is found ) More...

virtual bool	choose_window_length (core::pose::Pose const &, Size &window_length) const
	yields a length (window_length) of the fragment window to sample from ( return false, if no suitable length is found ) More...

void	on_new_fragments ()
	is called from set_fragments() More...

virtual bool	end_bias_check (core::pose::Pose const &, Size window_start) const

virtual bool	valid_ss (std::string const &new_ss) const
	returns true if the ss string is acceptable More...

Public Member Functions inherited from protocols::simple_moves::FragmentMover
	~FragmentMover ()

virtual bool	apply (core::pose::Pose &, Size pos) const
	apply a fragment at pos to movemable dofs More...

virtual Size	apply_at_all_positions (core::pose::Pose &) const
	apply at all movemable positions — honors movemap More...

core::fragment::FragSetCOP	fragments () const
	accessor to the fragment set More...

virtual void	set_fragments (core::fragment::FragSetCOP new_frags_)
	setter for the fragment set More...

virtual void	set_movemap (core::kinematics::MoveMapCOP movemap)
	setter for the movemap More...

core::kinematics::MoveMapCOP	movemap () const

core::fragment::InsertMap const &	insert_map () const

core::fragment::InsertSize const &	insert_size () const

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

virtual	~Mover ()

virtual MoverSP	create ()

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

virtual void	parse_state (SerializableState const &state)

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

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

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

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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

void	set_current_tag (std::string const &new_tag)

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

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

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

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

void	type (const std::string &type_in)

virtual void	parse_my_tag (TagCOP tag, basic::datacache::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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

Protected Member Functions
bool	apply_fragment (core::fragment::Frame const &frame, core::Size frag_num, core::kinematics::MoveMap const &movemap, core::pose::Pose &pose) const
	make a wobble move ( smooth move + ccd loop closure ) NEEDS MORE WORK IF MULTIPLE CHAINS OR JUMPS ARE USED: total_residue!=end of chain More...

bool	ccd_closure (core::pose::Pose &pose, protocols::loops::Loops const &loops, core::kinematics::MoveMap const &mm) const
	close loop and return if successful ( deviations smaller than thresholds ) More...

Protected Member Functions inherited from protocols::simple_moves::SmoothFragmentMover
	SmoothFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, FragmentCostOP cost, std::string move_type)

virtual bool	choose_fragment (core::fragment::FrameList const &, core::pose::Pose const &, Size &frame_num, Size &frag_num) const
	given FrameList and pose, this method yields a fragment ( frame_num/ frag_num); return false if nothing suitable is found More...

virtual bool	use_ss_length_screen () const

Protected Member Functions inherited from protocols::simple_moves::ClassicFragmentMover
	ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string type)
	alternative Constructor to be used by derived classes More...

	ClassicFragmentMover (core::fragment::FragSetCOP fragset, std::string type)
	alternative Constructor to be used by derived classes More...

virtual bool	apply_frames (core::pose::Pose &, core::fragment::FrameList const &) const

Protected Member Functions inherited from protocols::simple_moves::FragmentMover
	FragmentMover (std::string type)
	Empty constructor. More...

	FragmentMover (core::fragment::FragSetCOP fragset, std::string type)

	FragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string type)
	constructor More...

void	update_insert_map ()

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 Attributes
core::Size	buffer_length_
	how many variable residues on opposite side of fragment More...

core::Real	forward_threshold_
	cutoffs that ccd has to undercut to be accepted More...

core::Real	backward_threshold_

Additional Inherited Members
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 Attributes inherited from protocols::simple_moves::FragmentMover
core::fragment::FragSetCOP	fragset_

core::kinematics::MoveMapCOP	movemap_

core::fragment::InsertMap	insert_map_

core::fragment::InsertSize	insert_size_

Detailed Description

A protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure a smooth fragment is chosen according to the FragmentCost Functor; a cutpoint is inserted just in front of or just after the fragment a loop is defined around the fragment and cutpoint to be closed with ccd: a cut_Cterm insertion: -—lfff bbb-— f: fragment_res b: buffer_res -: immovable residues a !cut_Cterm insertion: —bbb fffl— the number of b resiudes is controlled by buffer_length_ (default 3); the move is used by apply() (inherited from FragmentMover). the insertion and loop closure is implemented in the virtual method apply_fragment().

Member Typedef Documentation

typedef protocols::simple_moves::SmoothFragmentMover protocols::simple_moves::WobbleMover::Parent

Constructor & Destructor Documentation

protocols::simple_moves::WobbleMover::WobbleMover	(	core::fragment::FragSetCOP	fragset,
		core::kinematics::MoveMapCOP	movemap,
		protocols::simple_moves::FragmentCostOP	cost
	)

References set_defaults().

protocols::simple_moves::WobbleMover::WobbleMover	(	core::fragment::FragSetCOP	fragset,
		core::kinematics::MoveMapCOP	movemap
	)

References set_defaults().

protocols::simple_moves::WobbleMover::~WobbleMover ( )

Copy constructor disabled until the virtual base class ClassicFragmentMover's construction is sorted out

Member Function Documentation

bool protocols::simple_moves::WobbleMover::apply_fragment	(	core::fragment::Frame const &	frame,
		core::Size	frag_num,
		core::kinematics::MoveMap const &	movemap,
		core::pose::Pose &	pose
	)		const

protectedvirtual

make a wobble move ( smooth move + ccd loop closure ) NEEDS MORE WORK IF MULTIPLE CHAINS OR JUMPS ARE USED: total_residue!=end of chain

Reimplemented from protocols::simple_moves::ClassicFragmentMover.

References protocols::loops::Loops::add_loop(), buffer_length_, ccd_closure(), fold_tree, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::simple_moves::RG, core::pose::Pose::total_residue(), protocols::simple_moves::TR, and numeric::random::RandomGenerator::uniform().

bool protocols::simple_moves::WobbleMover::ccd_closure	(	core::pose::Pose &	pose,
		protocols::loops::Loops const &	loops,
		core::kinematics::MoveMap const &	mm
	)		const