a mover that packs the side-chains around a given set of target residues in a greedy fashion, and then packs the rest using the sim annealer. More...

#include <PackRotamersMoverPartGreedy.hh>

Inheritance diagram for protocols::enzdes::PackRotamersMoverPartGreedy:

[legend]

Public Member Functions
	PackRotamersMoverPartGreedy (ScoreFunctionOP scorefxn, PackerTaskOP task, core::select::residue_selector::ResidueSelectorCOP target_residues)
	default constructors More...

	PackRotamersMoverPartGreedy ()

	~PackRotamersMoverPartGreedy () override

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

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

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

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

void	greedy_around (core::pose::Pose &pose, utility::vector1< core::Size > const &target_res, core::pack::task::PackerTaskOP task, core::scoring::ScoreFunctionCOP scorefxn)

utility::vector1< core::Size >	compute_designable_neighbors (core::Size const &position, core::pack::task::PackerTaskCOP task, core::pose::Pose const &pose)

void	update_task_and_neighbors (core::Size const &best_neigh, core::pack::task::PackerTaskOP task, utility::vector1< core::Size > &current_neighbors)

void	task_factory (core::pack::task::TaskFactoryOP p)

void	task (core::pack::task::PackerTaskOP task)

void	target_residues (core::select::residue_selector::ResidueSelectorCOP trg_res)

utility::vector1< core::Size >	choose_n_best (core::pose::Pose const &pose, core::Size const &n_best)

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::pack::task::PackerTaskOP	PackerTaskOP

typedef core::pack::task::TaskFactoryOP	TaskFactoryOP

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

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

a mover that packs the side-chains around a given set of target residues in a greedy fashion, and then packs the rest using the sim annealer.

Member Typedef Documentation

◆ PackerTaskOP

typedef core::pack::task::PackerTaskOP protocols::enzdes::PackRotamersMoverPartGreedy::PackerTaskOP

private

◆ ScoreFunctionOP

typedef core::scoring::ScoreFunctionOP protocols::enzdes::PackRotamersMoverPartGreedy::ScoreFunctionOP

private

◆ TaskFactoryOP

typedef core::pack::task::TaskFactoryOP protocols::enzdes::PackRotamersMoverPartGreedy::TaskFactoryOP

private

Constructor & Destructor Documentation

◆ PackRotamersMoverPartGreedy() [1/2]

protocols::enzdes::PackRotamersMoverPartGreedy::PackRotamersMoverPartGreedy	(	ScoreFunctionOP	scorefxn,
		PackerTaskOP	task,
		core::select::residue_selector::ResidueSelectorCOP	target_residues
	)

default constructors

◆ PackRotamersMoverPartGreedy() [2/2]

protocols::enzdes::PackRotamersMoverPartGreedy::PackRotamersMoverPartGreedy ( )

◆ ~PackRotamersMoverPartGreedy()

protocols::enzdes::PackRotamersMoverPartGreedy::~PackRotamersMoverPartGreedy ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::enzdes::PackRotamersMoverPartGreedy::apply ( core::pose::Pose & )

overridevirtual

◆ choose_n_best()

utility::vector1< core::Size > protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best	(	core::pose::Pose const &	pose,
		core::Size const &	n_best
	)

References core::scoring::EnergyEdge::dot(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::conformation::Residue::is_ligand(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::enzdes::TR(), and core::scoring::Energies::weights().

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::enzdes::PackRotamersMoverPartGreedy::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.

◆ compute_designable_neighbors()

utility::vector1< core::Size > protocols::enzdes::PackRotamersMoverPartGreedy::compute_designable_neighbors	(	core::Size const &	position,
		core::pack::task::PackerTaskCOP	task,
		core::pose::Pose const &	pose
	)

References core::kinematics::distance(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), core::pose::Pose::size(), task(), threshold_, protocols::enzdes::TR(), and core::conformation::Residue::xyz().

Referenced by greedy_around().

◆ fresh_instance()

protocols::moves::MoverOP protocols::enzdes::PackRotamersMoverPartGreedy::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.

◆ get_name()

std::string protocols::enzdes::PackRotamersMoverPartGreedy::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ greedy_around()

void protocols::enzdes::PackRotamersMoverPartGreedy::greedy_around	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	target_res,
		core::pack::task::PackerTaskOP	task,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

References compute_designable_neighbors(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), core::pose::Pose::energies(), core::conformation::Residue::name3(), core::chemical::num_canonical_aas, core::pose::Pose::residue(), scorefxn_minimize_, core::pose::Pose::size(), target_residues(), task(), core::scoring::Energies::total_energies(), core::scoring::total_score, protocols::enzdes::TR(), and update_task_and_neighbors().

Referenced by apply().

◆ mover_name()

std::string protocols::enzdes::PackRotamersMoverPartGreedy::mover_name ( )

static

Referenced by get_name(), protocols::enzdes::PackRotamersMoverPartGreedyCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::enzdes::PackRotamersMoverPartGreedy::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 cstid_list_, core::pose::get_resnum_selector(), n_best_, core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), scorefxn_minimize_, scorefxn_repack_, scorefxn_repack_greedy_, target_residues_, task_factory(), task_factory_, threshold_, and use_cstids_.

◆ provide_xml_schema()

void protocols::enzdes::PackRotamersMoverPartGreedy::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations_w_factory(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::enzdes::PackRotamersMoverPartGreedyCreator::provide_xml_schema().

◆ target_residues()

void protocols::enzdes::PackRotamersMoverPartGreedy::target_residues ( core::select::residue_selector::ResidueSelectorCOP trg_res )

References target_residues_.

Referenced by apply(), and greedy_around().

◆ task()

void protocols::enzdes::PackRotamersMoverPartGreedy::task ( core::pack::task::PackerTaskOP task )

References task_.

Referenced by apply(), compute_designable_neighbors(), greedy_around(), and update_task_and_neighbors().

◆ task_factory()

void protocols::enzdes::PackRotamersMoverPartGreedy::task_factory ( core::pack::task::TaskFactoryOP p )

References task_factory_.

Referenced by parse_my_tag().

◆ update_task_and_neighbors()

void protocols::enzdes::PackRotamersMoverPartGreedy::update_task_and_neighbors	(	core::Size const &	best_neigh,
		core::pack::task::PackerTaskOP	task,
		utility::vector1< core::Size > &	current_neighbors
	)

References restrict_to_repacking_, task(), and protocols::enzdes::TR().

Referenced by greedy_around().

Member Data Documentation

◆ cstid_list_

std::string protocols::enzdes::PackRotamersMoverPartGreedy::cstid_list_

private

Referenced by apply(), and parse_my_tag().

◆ n_best_

core::Size protocols::enzdes::PackRotamersMoverPartGreedy::n_best_

private

Referenced by apply(), and parse_my_tag().

◆ restrict_to_repacking_

utility::vector1< core::Size > protocols::enzdes::PackRotamersMoverPartGreedy::restrict_to_repacking_

private

Referenced by apply(), and update_task_and_neighbors().

◆ scorefxn_minimize_

core::scoring::ScoreFunctionOP protocols::enzdes::PackRotamersMoverPartGreedy::scorefxn_minimize_

private

Referenced by greedy_around(), and parse_my_tag().

◆ scorefxn_repack_

core::scoring::ScoreFunctionOP protocols::enzdes::PackRotamersMoverPartGreedy::scorefxn_repack_

private

Referenced by apply(), and parse_my_tag().

◆ scorefxn_repack_greedy_

core::scoring::ScoreFunctionOP protocols::enzdes::PackRotamersMoverPartGreedy::scorefxn_repack_greedy_

private

Referenced by apply(), and parse_my_tag().

◆ target_residues_

core::select::residue_selector::ResidueSelectorCOP protocols::enzdes::PackRotamersMoverPartGreedy::target_residues_

private

Referenced by apply(), parse_my_tag(), and target_residues().

◆ task_

core::pack::task::PackerTaskOP protocols::enzdes::PackRotamersMoverPartGreedy::task_

private

Referenced by apply(), and task().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::enzdes::PackRotamersMoverPartGreedy::task_factory_

private

Referenced by apply(), parse_my_tag(), and task_factory().

◆ threshold_

core::Real protocols::enzdes::PackRotamersMoverPartGreedy::threshold_

private

Referenced by compute_designable_neighbors(), and parse_my_tag().

◆ use_cstids_

bool protocols::enzdes::PackRotamersMoverPartGreedy::use_cstids_

private

Referenced by apply(), and parse_my_tag().

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

src/protocols/enzdes/PackRotamersMoverPartGreedy.hh
src/protocols/enzdes/PackRotamersMoverPartGreedy.cc

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_repack_

core::scoring::ScoreFunctionOP	scorefxn_repack_greedy_

core::scoring::ScoreFunctionOP	scorefxn_minimize_

core::pack::task::PackerTaskOP	task_

core::pack::task::TaskFactoryOP	task_factory_

core::select::residue_selector::ResidueSelectorCOP	target_residues_

utility::vector1< core::Size >	restrict_to_repacking_

bool	use_cstids_

core::Real	threshold_

std::string	cstid_list_

core::Size	n_best_

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ PackerTaskOP

◆ ScoreFunctionOP

◆ TaskFactoryOP

Constructor & Destructor Documentation

◆ PackRotamersMoverPartGreedy() [1/2]

◆ PackRotamersMoverPartGreedy() [2/2]

◆ ~PackRotamersMoverPartGreedy()

Member Function Documentation

◆ apply()

◆ choose_n_best()

◆ clone()

◆ compute_designable_neighbors()

◆ fresh_instance()

◆ get_name()

◆ greedy_around()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ target_residues()

◆ task()

◆ task_factory()

◆ update_task_and_neighbors()

Member Data Documentation

◆ cstid_list_

◆ n_best_

◆ restrict_to_repacking_

◆ scorefxn_minimize_

◆ scorefxn_repack_

◆ scorefxn_repack_greedy_

◆ target_residues_

◆ task_

◆ task_factory_

◆ threshold_

◆ use_cstids_