#include <BiasedFragmentMover.hh>

Public Member Functions
	BiasedFragmentMover (const PolicyOP &policy, const Probabilities &probs)
	Creates a new BiasedFragmentMover that selects uniformly from the available fragments at the selected insertion position. More...

	~BiasedFragmentMover ()

void	apply (core::pose::Pose &pose)
	Inserts a single fragment into pose. More...

std::string	get_name () const
	Returns the name of this mover. More...

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

void	set_type (std::string const &setting)

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 MoverOP	clone () const
	Return a clone of the Mover object. More...

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...

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

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

jobdist::BasicJobCOP	get_current_job () const

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

Private Types
typedef boost::unordered_map < unsigned, core::fragment::Frame >	FrameMap

typedef core::fragment::FragSetCOP	FragSetCOP

typedef utility::vector1< double >	Probabilities

Private Member Functions
void	initialize_library ()
	Creates a position-indexable list of Frames. More...

void	initialize_probabilities ()
	Generates cdf from pdf. More...

void	verify_probabilities_or_die (const core::kinematics::FoldTree &tree) const
	Verifies that the probability of selecting invalid positions is 0. More...

unsigned	random_position () const
	Returns a randomly chosen position according to the input probabilities. More...

Private Attributes
core::kinematics::MoveMap	movable_
	Avoid creating a useless MoveMap for each call to Frame::apply(). More...

FragSetCOP	fragments_
	Fragment library. More...

FrameMap	frames_
	Position-indexable Frame lookup. More...

PolicyOP	policy_
	Guidance for selecting the fragment to be inserted at a given position. More...

Probabilities	pdf_
	PDF of residue sampling probabilities. Must remain in sync with cdf_. More...

Probabilities	cdf_
	CDF of residue sampling probabilities. Must remain in sync with pdf_. More...

Additional Inherited Members
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

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 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...

Member Typedef Documentation

typedef core::fragment::FragSetCOP protocols::nonlocal::BiasedFragmentMover::FragSetCOP

private

typedef boost::unordered_map<unsigned, core::fragment::Frame> protocols::nonlocal::BiasedFragmentMover::FrameMap

private

typedef utility::vector1<double> protocols::nonlocal::BiasedFragmentMover::Probabilities

private

Constructor & Destructor Documentation

protocols::nonlocal::BiasedFragmentMover::BiasedFragmentMover	(	const PolicyOP &	policy,
		const Probabilities &	probs
	)

Creates a new BiasedFragmentMover that selects uniformly from the available fragments at the selected insertion position.

References fragments_, initialize_library(), initialize_probabilities(), movable_, and core::kinematics::MoveMap::set_bb().

protocols::nonlocal::BiasedFragmentMover::~BiasedFragmentMover ( )

inline

Member Function Documentation

void protocols::nonlocal::BiasedFragmentMover::apply ( core::pose::Pose & pose )

virtual

Inserts a single fragment into pose.

Insertion position is chosen in a biased manner using the per-residue probabilities provided in the constructor. The decision on which fragment to insert from the fragment library is delegated to the policy specified in the constructor.

Respects the underlying kinematics of the system.

Implements protocols::moves::Mover.

References core::fragment::Frame::apply(), core::pose::Pose::fold_tree(), frame(), frames_, movable_, policy_, random_position(), and verify_probabilities_or_die().