#include <SingleFragmentMover.hh>

Inheritance diagram for protocols::nonlocal::SingleFragmentMover:

Public Types
typedef protocols::moves::Mover	Mover

typedef protocols::moves::MoverOP	MoverOP

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 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 () override=default

void	apply (Pose &pose) override
	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...

MoverOP	clone () const override
	Returns the name of this mover. More...

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Mover-specific parsing required by RosettaScripts. More...

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

void	movemap_factory (core::select::movemap::MoveMapFactoryCOP new_movemap_factory)

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

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

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 std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

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 boost::unordered_map < core::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, MoveMapOP const &movable)
	Creates a set of chunks by examining the stored MoveMap and FragSet in conjunction with <tree> More...

MoveMapOP	movemap (core::pose::Pose const &pose)
	Get the movemap for this pose. 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...

core::select::movemap::MoveMapFactoryCOP	movemap_factory_
	Defines restrictions on which degrees of freedom in the system can be modified. More...

MoveMapOP	movable_

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

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

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

private

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

private

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

private

Constructor & Destructor Documentation

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

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

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.

References initialize().

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

overridedefault

Member Function Documentation

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

overridevirtual

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.

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

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

overridevirtual

Returns the name of this mover.

Creates a new instance using the copy constructor

Reimplemented from protocols::moves::Mover.

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

overridevirtual

Creates a new instance using the default constructor.

Reimplemented from protocols::moves::Mover.

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

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

private

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

Referenced by parse_my_tag(), and SingleFragmentMover().

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

private

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

References chunks_, fragments_, core::kinematics::FoldTree::is_cutpoint(), protocols::nonlocal::Chunk::is_movable(), core::chemical::element::N, probs_, core::chemical::rings::q, and core::simple_metrics::metrics::sum.

Referenced by apply().

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

private

Creates a position-indexable list of Frames.

References fragments_, and library_.

Referenced by initialize().

core::kinematics::MoveMapOP protocols::nonlocal::SingleFragmentMover::movemap ( core::pose::Pose const & pose )

private

Get the movemap for this pose.

References movable_, and movemap_factory_.

Referenced by apply().

void protocols::nonlocal::SingleFragmentMover::movemap_factory ( core::select::movemap::MoveMapFactoryCOP new_movemap_factory )

inline

References movemap_factory_.

Referenced by parse_my_tag().

std::string protocols::nonlocal::SingleFragmentMover::mover_name ( )

static

Referenced by get_name(), protocols::nonlocal::SingleFragmentMoverCreator::keyname(), and provide_xml_schema().

void protocols::nonlocal::SingleFragmentMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Mover-specific parsing required by RosettaScripts.

Reimplemented from protocols::moves::Mover.

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

void protocols::nonlocal::SingleFragmentMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), mover_name(), protocols::moves::Mover::name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::nonlocal::SingleFragmentMoverCreator::provide_xml_schema().

const Chunk * protocols::nonlocal::SingleFragmentMover::random_chunk ( ) const

private

Returns a randomly chosen chunk with uniform probability.

References chunks_, and probs_.

Referenced by apply().

bool protocols::nonlocal::SingleFragmentMover::to_centroid ( Pose * pose ) const

private

If <pose> is fullatom, converts it to centroid and returns true. Otherwise, takes no action and returns false.

References core::chemical::CENTROID_t, core::pose::Pose::is_fullatom(), and core::util::switch_to_residue_type_set().

Referenced by apply().

bool protocols::nonlocal::SingleFragmentMover::valid ( ) const

Returns true if this instance is in a usable state, false otherwise.

References fragments_, movable_, movemap_factory_, and policy_.

Referenced by apply().

Member Data Documentation

Chunks protocols::nonlocal::SingleFragmentMover::chunks_

private

Regions of sequence on which to perform fragment insertion.

Referenced by apply(), initialize_chunks(), and random_chunk().

FragSetOP protocols::nonlocal::SingleFragmentMover::fragments_

private

The set of fragments to apply to the pose.

Referenced by initialize(), initialize_chunks(), initialize_library(), and valid().

FrameMap protocols::nonlocal::SingleFragmentMover::library_

private

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

Referenced by apply(), and initialize_library().

MoveMapOP protocols::nonlocal::SingleFragmentMover::movable_

private

Referenced by initialize(), movemap(), and valid().

core::select::movemap::MoveMapFactoryCOP protocols::nonlocal::SingleFragmentMover::movemap_factory_

private

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

Referenced by movemap(), movemap_factory(), and valid().

PolicyOP protocols::nonlocal::SingleFragmentMover::policy_

private

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

Referenced by apply(), initialize(), and valid().

FoldTreeOP protocols::nonlocal::SingleFragmentMover::previous_tree_

private

FoldTree used to initialize <chunks_> in a previous call to apply()

Referenced by apply().

utility::vector1<Real> protocols::nonlocal::SingleFragmentMover::probs_

private

Probability of selecting chunk c_i. Proportional to chunk length.

Referenced by apply(), initialize_chunks(), and random_chunk().

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

src/protocols/nonlocal/SingleFragmentMover.hh
src/protocols/nonlocal/SingleFragmentMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation