#include <PlaceSurfaceProbe.hh>

Inheritance diagram for protocols::hotspot_hashing::movers::PlaceSurfaceProbe:

[legend]

Public Member Functions
	PlaceSurfaceProbe ()

	PlaceSurfaceProbe (std::string residue_name, core::Real search_density, core::Real x_angle_sampling, core::Real y_angle_sampling, core::Real refinement_distance_sampling, core::Real refinement_distance, core::Real refinement_translation_sampling, core::conformation::ResidueCOP target_residue, core::pack::task::TaskFactoryOP surface_selection=nullptr, core::Size search_partition=1, core::Size total_search_partition=1)

PlaceSurfaceProbeOP	shared_from_this ()

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

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...

bool	reinitialize_for_new_input () const override
	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...

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

Public Member Functions inherited from protocols::hotspot_hashing::movers::PlaceProbeMover
	PlaceProbeMover ()

	PlaceProbeMover (std::string const &residue_name, core::conformation::ResidueCOP target_residue, core::Size search_partition=1, core::Size total_search_partition=1)

PlaceProbeMoverOP	shared_from_this ()

void	apply (Pose &) override
	Main Method. 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 MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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...

Protected Member Functions
SearchPatternOP	create_search_pattern (core::pose::Pose const &target_pose) override

SearchPatternOP	create_partitioned_search_pattern (core::pose::Pose const &target_pose) override

SearchPatternOP	create_refinement_pattern (core::pose::Pose const &target_pose, core::Size target_residue) override

Protected Member Functions inherited from protocols::hotspot_hashing::movers::PlaceProbeMover
void	parse_place_probe_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Parses tag compoments for PlaceProbeMover. More...

StructureOutputMode	parse_output_mode (std::string name)

void	check_and_initialize (core::pose::Pose const &target_pose)

void	execute_one_search (core::pose::Pose &target_pose, core::Size search_index)

void	perform_local_refinement (core::pose::Pose &target_pose, core::Size target_residue)

virtual core::pack::task::PackerTaskOP	create_refinement_packing_task (core::pose::Pose const &target_pose, core::Size target_residue)

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...

Private Member Functions
SearchPatternOP	initialize_refinement_pattern ()

Private Attributes
core::pack::task::TaskFactoryOP	surface_selection_

core::Real	search_density_

core::Real	coarse_angle_sampling_

core::Real	coarse_sampling_

core::Real	refinement_distance_

core::Real	refinement_angle_sampling_

core::Real	refinement_sampling_

SearchPatternOP	refinement_pattern_

Additional Inherited Members
Public Types inherited from protocols::hotspot_hashing::movers::PlaceProbeMover
enum	ExecutionMode { RunAll , OnePerStruct }

enum	StructureOutputMode { None , Probe , Full }

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 Attributes inherited from protocols::hotspot_hashing::movers::PlaceProbeMover
std::string	residue_name_

std::vector< std::string >	residue_variants_

core::conformation::ResidueCOP	target_residue_

core::scoring::ScoreFunctionCOP	refinement_scorefxn_

ExecutionMode	current_mode_

core::Size	search_partition_

core::Size	total_search_partition_

bool	initialized_pattern_

utility::vector1< core::kinematics::Stub >	search_points_

Constructor & Destructor Documentation

◆ PlaceSurfaceProbe() [1/2]

protocols::hotspot_hashing::movers::PlaceSurfaceProbe::PlaceSurfaceProbe ( )

◆ PlaceSurfaceProbe() [2/2]

protocols::hotspot_hashing::movers::PlaceSurfaceProbe::PlaceSurfaceProbe	(	std::string	residue_name,
		core::Real	search_density,
		core::Real	x_angle_sampling,
		core::Real	y_angle_sampling,
		core::Real	refinement_distance_sampling,
		core::Real	refinement_distance,
		core::Real	refinement_translation_sampling,
		core::conformation::ResidueCOP	target_residue,
		core::pack::task::TaskFactoryOP	surface_selection = `nullptr`,
		core::Size	search_partition = `1`,
		core::Size	total_search_partition = `1`
	)

Member Function Documentation

◆ clone()

protocols::moves::MoverOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::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.

◆ create_partitioned_search_pattern()

SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_partitioned_search_pattern ( core::pose::Pose const & target_pose )

overrideprotectedvirtual

Reimplemented from protocols::hotspot_hashing::movers::PlaceProbeMover.

References core::pose::add_variant_type_to_residue(), coarse_angle_sampling_, protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), search_density_, protocols::hotspot_hashing::movers::PlaceProbeMover::search_partition_, surface_selection_, protocols::hotspot_hashing::movers::PlaceProbeMover::target_residue_, protocols::hotspot_hashing::movers::PlaceProbeMover::total_search_partition_, and core::chemical::VIRTUAL_BB.

◆ create_refinement_pattern()

SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_refinement_pattern	(	core::pose::Pose const &	target_pose,
		core::Size	target_residue
	)

overrideprotectedvirtual

Reimplemented from protocols::hotspot_hashing::movers::PlaceProbeMover.

References refinement_pattern_.

◆ create_search_pattern()

SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_search_pattern ( core::pose::Pose const & target_pose )

overrideprotectedvirtual

Implements protocols::hotspot_hashing::movers::PlaceProbeMover.

References core::pose::add_variant_type_to_residue(), coarse_angle_sampling_, coarse_sampling_, protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), search_density_, surface_selection_, protocols::hotspot_hashing::movers::PlaceProbeMover::target_residue_, and core::chemical::VIRTUAL_BB.

◆ get_name()

std::string protocols::hotspot_hashing::movers::PlaceSurfaceProbe::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ initialize_refinement_pattern()

SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::initialize_refinement_pattern ( )

private

References coarse_angle_sampling_, coarse_sampling_, refinement_angle_sampling_, refinement_distance_, and refinement_sampling_.

Referenced by parse_my_tag().

◆ mover_name()

std::string protocols::hotspot_hashing::movers::PlaceSurfaceProbe::mover_name ( )

static

Referenced by get_name(), protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::hotspot_hashing::movers::PlaceSurfaceProbe::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 coarse_angle_sampling_, coarse_sampling_, initialize_refinement_pattern(), protocols::hotspot_hashing::movers::PlaceProbeMover::parse_place_probe_tag(), core::pack::task::parse_task_operations(), refinement_angle_sampling_, refinement_distance_, refinement_pattern_, refinement_sampling_, search_density_, and surface_selection_.

◆ provide_xml_schema()

void protocols::hotspot_hashing::movers::PlaceSurfaceProbe::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator::provide_xml_schema().

◆ reinitialize_for_new_input()

bool protocols::hotspot_hashing::movers::PlaceSurfaceProbe::reinitialize_for_new_input ( ) const

inlineoverridevirtual

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).

Movers default to not regenerating

Reimplemented from protocols::hotspot_hashing::movers::PlaceProbeMover.

◆ shared_from_this()

PlaceSurfaceProbeOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::shared_from_this ( )

inline

References protocols::hotspot_hashing::movers::PlaceProbeMover::shared_from_this().

Member Data Documentation

◆ coarse_angle_sampling_

core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::coarse_angle_sampling_

private

Referenced by create_partitioned_search_pattern(), create_search_pattern(), initialize_refinement_pattern(), and parse_my_tag().

◆ coarse_sampling_

core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::coarse_sampling_

private

Referenced by create_search_pattern(), initialize_refinement_pattern(), and parse_my_tag().

◆ refinement_angle_sampling_

core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::refinement_angle_sampling_

private

Referenced by initialize_refinement_pattern(), and parse_my_tag().

◆ refinement_distance_

core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::refinement_distance_

private

Referenced by initialize_refinement_pattern(), and parse_my_tag().

◆ refinement_pattern_

SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::refinement_pattern_

private

Referenced by create_refinement_pattern(), and parse_my_tag().

◆ refinement_sampling_

core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::refinement_sampling_

private

Referenced by initialize_refinement_pattern(), and parse_my_tag().

◆ search_density_

core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::search_density_

private

Referenced by create_partitioned_search_pattern(), create_search_pattern(), and parse_my_tag().

◆ surface_selection_

core::pack::task::TaskFactoryOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::surface_selection_

private

Referenced by create_partitioned_search_pattern(), create_search_pattern(), and parse_my_tag().

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

src/protocols/hotspot_hashing/movers/PlaceSurfaceProbe.hh
src/protocols/hotspot_hashing/movers/PlaceSurfaceProbe.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ PlaceSurfaceProbe() [1/2]

◆ PlaceSurfaceProbe() [2/2]

Member Function Documentation

◆ clone()

◆ create_partitioned_search_pattern()

◆ create_refinement_pattern()

◆ create_search_pattern()

◆ get_name()

◆ initialize_refinement_pattern()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ reinitialize_for_new_input()

◆ shared_from_this()

Member Data Documentation

◆ coarse_angle_sampling_

◆ coarse_sampling_

◆ refinement_angle_sampling_

◆ refinement_distance_

◆ refinement_pattern_

◆ refinement_sampling_

◆ search_density_

◆ surface_selection_