#include <SingleFragmentMover.hh>

Inheritance diagram for protocols::nonlocal::SingleFragmentMover:

Collaboration diagram for protocols::nonlocal::SingleFragmentMover:

Public Member Functions
	SingleFragmentMover ()
	No-argument constructor required by RosettaScripts. The caller is responsible for initializing the instance. More...

	SingleFragmentMover (const FragSetOP &fragments, const MoveMapOP &movable)
	Creates a new SingleFragmentMover that selects uniformly from the available fragments at the selected insertion position. More...

	SingleFragmentMover (const FragSetOP &fragments, const MoveMapOP &movable, const PolicyOP &policy)
	Creates a new SingleFragmentMover that selects fragments at the selected insertion position using the given policy. More...

	~SingleFragmentMover ()

void	apply (Pose &pose)
	Performs a single fragment insertion on <pose>, drawn from the set of fragments specified in the constructor. Respects the underlying kinematics of the system, as determined by the Pose's FoldTree and the user-specified MoveMap. Fragment insertions will only occur in allowable regions of the pose. No moves will span jumps in the FoldTree. More...

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

virtual MoverOP	clone () const
	Creates a new instance using the copy constructor. More...

virtual MoverOP	fresh_instance () const
	Creates a new instance using the default constructor. More...

void	parse_my_tag (const utility::tag::TagPtr tag, protocols::moves::DataMap &data, const protocols::filters::Filters_map &filters, const protocols::moves::Movers_map &movers, const Pose &pose)
	Mover-specific parsing required by RosettaScripts. More...

void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache)
	Mover-specific parsing required by ElScripts. More...

bool	valid () const
	Returns true if this instance is in a usable state, false otherwise. 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	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)

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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Types
typedef core::Real	Real

typedef core::Size	Size

typedef core::fragment::FragSetOP	FragSetOP

typedef core::fragment::Frame	Frame

typedef core::kinematics::FoldTree	FoldTree

typedef core::kinematics::FoldTreeOP	FoldTreeOP

typedef core::kinematics::MoveMapOP	MoveMapOP

typedef core::pose::Pose	Pose

typedef protocols::moves::Mover	Mover

typedef protocols::moves::MoverOP	MoverOP

typedef boost::unordered_map < Size, Frame >	FrameMap

typedef utility::vector1< Chunk >	Chunks

Private Member Functions
void	initialize (const FragSetOP &fragments, const MoveMapOP &movable, const PolicyOP &policy)

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

void	initialize_chunks (const FoldTree &tree)
	Creates a set of chunks by examining the stored MoveMap and FragSet in conjunction with <tree> More...

const Chunk *	random_chunk () const
	Returns a randomly chosen chunk with uniform probability. More...

bool	to_centroid (Pose *pose) const
	If <pose> is fullatom, converts it to centroid and returns true. Otherwise, takes no action and returns false. More...

Private Attributes
FragSetOP	fragments_
	The set of fragments to apply to the pose. More...

MoveMapOP	movable_
	Defines restrictions on which degrees of freedom in the system can be modified. More...

PolicyOP	policy_
	Selects the fragment to be inserted at <insertion_pos> given knowledge of the fragment library and the current state of the pose. More...

FoldTreeOP	previous_tree_
	FoldTree used to initialize <chunks_> in a previous call to apply() More...

FrameMap	library_
	Provides index-based access to the data contained in the FragSet. More...

Chunks	chunks_
	Regions of sequence on which to perform fragment insertion. More...

utility::vector1< Real >	probs_
	Probability of selecting chunk c_i. Proportional to chunk length. More...

Additional Inherited Members
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

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 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...

Detailed Description

Definition at line 46 of file SingleFragmentMover.hh.

Member Typedef Documentation

typedef utility::vector1<Chunk> protocols::nonlocal::SingleFragmentMover::Chunks

private

Definition at line 59 of file SingleFragmentMover.hh.

typedef core::kinematics::FoldTree protocols::nonlocal::SingleFragmentMover::FoldTree

private

Definition at line 51 of file SingleFragmentMover.hh.

typedef core::kinematics::FoldTreeOP protocols::nonlocal::SingleFragmentMover::FoldTreeOP

private

Definition at line 52 of file SingleFragmentMover.hh.

typedef core::fragment::FragSetOP protocols::nonlocal::SingleFragmentMover::FragSetOP

private

Definition at line 49 of file SingleFragmentMover.hh.

typedef core::fragment::Frame protocols::nonlocal::SingleFragmentMover::Frame

private

Definition at line 50 of file SingleFragmentMover.hh.

typedef boost::unordered_map<Size, Frame> protocols::nonlocal::SingleFragmentMover::FrameMap

private

Definition at line 58 of file SingleFragmentMover.hh.

typedef core::kinematics::MoveMapOP protocols::nonlocal::SingleFragmentMover::MoveMapOP

private

Definition at line 53 of file SingleFragmentMover.hh.

typedef protocols::moves::Mover protocols::nonlocal::SingleFragmentMover::Mover

private

Definition at line 55 of file SingleFragmentMover.hh.

typedef protocols::moves::MoverOP protocols::nonlocal::SingleFragmentMover::MoverOP

private

Definition at line 56 of file SingleFragmentMover.hh.

typedef core::pose::Pose protocols::nonlocal::SingleFragmentMover::Pose

private

Definition at line 54 of file SingleFragmentMover.hh.

typedef core::Real protocols::nonlocal::SingleFragmentMover::Real

private

Definition at line 47 of file SingleFragmentMover.hh.

typedef core::Size protocols::nonlocal::SingleFragmentMover::Size

private

Definition at line 48 of file SingleFragmentMover.hh.

Constructor & Destructor Documentation

protocols::nonlocal::SingleFragmentMover::SingleFragmentMover ( )

No-argument constructor required by RosettaScripts. The caller is responsible for initializing the instance.

Definition at line 54 of file SingleFragmentMover.cc.

Referenced by clone(), and fresh_instance().

protocols::nonlocal::SingleFragmentMover::SingleFragmentMover	(	const FragSetOP &	fragments,
		const MoveMapOP &	movable
	)

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

Definition at line 56 of file SingleFragmentMover.cc.

References protocols::nonlocal::PolicyFactory::get_policy(), and initialize().

protocols::nonlocal::SingleFragmentMover::SingleFragmentMover	(	const FragSetOP &	fragments,
		const MoveMapOP &	movable,
		const PolicyOP &	policy
	)

Creates a new SingleFragmentMover that selects fragments at the selected insertion position using the given policy.

Definition at line 62 of file SingleFragmentMover.cc.

References initialize().

protocols::nonlocal::SingleFragmentMover::~SingleFragmentMover ( )

inline

Definition at line 77 of file SingleFragmentMover.hh.

Member Function Documentation

void protocols::nonlocal::SingleFragmentMover::apply ( Pose & pose)

virtual

Performs a single fragment insertion on <pose>, drawn from the set of fragments specified in the constructor. Respects the underlying kinematics of the system, as determined by the Pose's FoldTree and the user-specified MoveMap. Fragment insertions will only occur in allowable regions of the pose. No moves will span jumps in the FoldTree.

Assumptions:

<pose> has been instantiated (i.e. constructed from sequence or an alternate source) elsewhere
<pose>'s FoldTree is valid
<pose> is centroid-level (warning if full-atom)
The combination of FoldTree and MoveMap provide an unambiguous definition of what's movable and what's not

Implements protocols::moves::Mover.

Definition at line 85 of file SingleFragmentMover.cc.

References core::fragment::Frame::apply(), core::kinematics::FoldTree::check_fold_tree(), protocols::nonlocal::Chunk::choose(), chunks_, core::pose::Pose::fold_tree(), initialize_chunks(), library_, movable_, policy_, previous_tree_, probs_, random_chunk(), to_centroid(), core::pose::Pose::total_residue(), and valid().

protocols::moves::MoverOP protocols::nonlocal::SingleFragmentMover::clone ( ) const

virtual

Creates a new instance using the copy constructor.

Reimplemented from protocols::moves::Mover.

Definition at line 133 of file SingleFragmentMover.cc.

References SingleFragmentMover().

protocols::moves::MoverOP protocols::nonlocal::SingleFragmentMover::fresh_instance ( ) const

virtual

Creates a new instance using the default constructor.

Reimplemented from protocols::moves::Mover.

Definition at line 137 of file SingleFragmentMover.cc.

References SingleFragmentMover().

std::string protocols::nonlocal::SingleFragmentMover::get_name ( ) const

virtual

Returns the name of this mover.

Implements protocols::moves::Mover.

Definition at line 129 of file SingleFragmentMover.cc.

void protocols::nonlocal::SingleFragmentMover::initialize	(	const FragSetOP &	fragments,
		const MoveMapOP &	movable,
		const PolicyOP &	policy
	)

private

Definition at line 69 of file SingleFragmentMover.cc.

References fragments_, initialize_library(), movable_, and policy_.

Referenced by parse_def(), parse_my_tag(), and SingleFragmentMover().

void protocols::nonlocal::SingleFragmentMover::initialize_chunks ( const FoldTree & tree)

private

Creates a set of chunks by examining the stored MoveMap and FragSet in conjunction with <tree>

Definition at line 212 of file SingleFragmentMover.cc.

References chunks_, fragments_, core::kinematics::FoldTree::is_cutpoint(), protocols::nonlocal::Chunk::is_movable(), movable_, protocols::forge::build::SegmentInsertConnectionScheme::N, and probs_.

Referenced by apply().

void protocols::nonlocal::SingleFragmentMover::initialize_library ( )

private

Creates a position-indexable list of Frames.

Definition at line 204 of file SingleFragmentMover.cc.

References fragments_, and library_.

Referenced by initialize().

void protocols::nonlocal::SingleFragmentMover::parse_def	(	utility::lua::LuaObject const &	def,
		utility::lua::LuaObject const &	score_fxns,
		utility::lua::LuaObject const &	tasks,
		protocols::moves::MoverCacheSP	cache
	)

virtual

Mover-specific parsing required by ElScripts.

Reimplemented from protocols::moves::Mover.

Definition at line 169 of file SingleFragmentMover.cc.

References protocols::nonlocal::PolicyFactory::get_policy(), initialize(), and protocols::elscripts::parse_movemapdef().

void protocols::nonlocal::SingleFragmentMover::parse_my_tag	(	const utility::tag::TagPtr	tag,
		protocols::moves::DataMap &	data,
		const protocols::filters::Filters_map &	filters,
		const protocols::moves::Movers_map &	movers,
		const Pose &	pose
	)