This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. For more fancy things see protocols/comparative_modeling. More...

#include <SimpleThreadingMover.hh>

Inheritance diagram for protocols::simple_moves::SimpleThreadingMover:

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Public Member Functions
	SimpleThreadingMover ()

	SimpleThreadingMover (std::string thread_sequence, core::Size start_position)

	SimpleThreadingMover (SimpleThreadingMover const &src)

	~SimpleThreadingMover () override

void	set_sequence (std::string thread_sequence, core::Size start_position)
	Set the sequence to thread onto the structure used in apply and where to start. More...

void	set_pack_neighbors (bool pack_neighbors)
	Pack the neighbor residues? More...

void	set_neighbor_distance (core::Real neighbor_dis)
	Set the packing distance for neighbor pack. More...

bool	get_pack_neighbors () const

core::Real	get_neighbor_distance () const

void	set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
	Set the scorefunction used for packing. More...

void	set_pack_rounds (core::Size pack_rounds)
	Set the number of pack rounds. More...

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

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

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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...

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 Member Functions
void	set_defaults ()

Private Attributes
core::Size	start_position_

std::string	thread_sequence_

bool	pack_neighbors_

core::Real	neighbor_dis_

core::scoring::ScoreFunctionCOP	scorefxn_

std::string	parsed_position_

bool	skip_unknown_mutant_

core::Size	pack_rounds_

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 std::list< std::string >	Strings

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

This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. For more fancy things see protocols/comparative_modeling.

It does the threading by allowing the task to only enable these residues and then does a repacking. Optionally repack neighbors so we save one more step. A sequence is just a string, additional '-' charactors denote to skip this position in the thread. Default is 5 rounds of packing.

Constructor & Destructor Documentation

protocols::simple_moves::SimpleThreadingMover::SimpleThreadingMover ( )

References set_defaults().

protocols::simple_moves::SimpleThreadingMover::SimpleThreadingMover	(	std::string	thread_sequence,
		core::Size	start_position
	)

References set_defaults(), and thread_sequence_.

protocols::simple_moves::SimpleThreadingMover::SimpleThreadingMover ( SimpleThreadingMover const & src )

default

protocols::simple_moves::SimpleThreadingMover::~SimpleThreadingMover ( )

overridedefault

Member Function Documentation

void protocols::simple_moves::SimpleThreadingMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::chemical::aa_from_oneletter_code(), core::select::fill_neighbor_residues(), core::pack::task::operation::RestrictResidueToRepacking::include_residue(), protocols::mean_field::min(), neighbor_dis_, core::chemical::oneletter_code_specifies_aa(), pack_neighbors_, pack_rounds_, core::pose::parse_resnum(), parsed_position_, scorefxn_, core::pose::Pose::size(), skip_unknown_mutant_, start_position_, thread_sequence_, core::id::to_string(), and protocols::simple_moves::TR().

protocols::moves::MoverOP protocols::simple_moves::SimpleThreadingMover::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

moves::MoverOP protocols::simple_moves::SimpleThreadingMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::simple_moves::SimpleThreadingMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Real protocols::simple_moves::SimpleThreadingMover::get_neighbor_distance ( ) const

References neighbor_dis_.

bool protocols::simple_moves::SimpleThreadingMover::get_pack_neighbors ( ) const

References pack_neighbors_.

std::string protocols::simple_moves::SimpleThreadingMover::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::SimpleThreadingMoverCreator::keyname(), provide_citation_info(), and provide_xml_schema().

void protocols::simple_moves::SimpleThreadingMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References neighbor_dis_, pack_neighbors_, pack_rounds_, core::scoring::parse_score_function(), parsed_position_, scorefxn_, skip_unknown_mutant_, and thread_sequence_.