#include <PlaceProbeMover.hh>

Inheritance diagram for protocols::hotspot_hashing::movers::PlaceProbeMover:

[legend]

Public Types
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

Public Member Functions
	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...

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...

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 MoverOP	clone () const
	Return a clone of the Mover object. 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

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

virtual std::string	get_name () const =0
	Each derived class must specify its name. The class name. More...

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...

Protected Member Functions
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 SearchPatternOP	create_search_pattern (core::pose::Pose const &target_pose)=0

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

virtual SearchPatternOP	create_refinement_pattern (core::pose::Pose const &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...

Protected Attributes
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_

Additional Inherited Members
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...

Member Enumeration Documentation

◆ ExecutionMode

enum protocols::hotspot_hashing::movers::PlaceProbeMover::ExecutionMode

Enumerator
RunAll
OnePerStruct

◆ StructureOutputMode

enum protocols::hotspot_hashing::movers::PlaceProbeMover::StructureOutputMode

Enumerator
None
Probe
Full

Constructor & Destructor Documentation

◆ PlaceProbeMover() [1/2]

protocols::hotspot_hashing::movers::PlaceProbeMover::PlaceProbeMover ( )

◆ PlaceProbeMover() [2/2]

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

Member Function Documentation

◆ apply()

void protocols::hotspot_hashing::movers::PlaceProbeMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::add_variant_type_to_residue(), check_and_initialize(), current_mode_, protocols::jd2::current_nstruct_index(), execute_one_search(), protocols::hotspot_hashing::StubGenerator::getStubByName(), OnePerStruct, residue_name_, core::chemical::SC_FRAGMENT, search_points_, and target_residue_.

◆ check_and_initialize()

void protocols::hotspot_hashing::movers::PlaceProbeMover::check_and_initialize ( core::pose::Pose const & target_pose )

protected

References create_partitioned_search_pattern(), initialized_pattern_, protocols::jd2::max_nstruct_index(), search_points_, and protocols::hotspot_hashing::movers::TR().

Referenced by apply().

◆ create_partitioned_search_pattern()

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

protectedvirtual

Reimplemented in protocols::hotspot_hashing::movers::PlaceSurfaceProbe.

References create_search_pattern(), search_partition_, and total_search_partition_.

Referenced by check_and_initialize().

◆ create_refinement_packing_task()

core::pack::task::PackerTaskOP protocols::hotspot_hashing::movers::PlaceProbeMover::create_refinement_packing_task	(	core::pose::Pose const &	target_pose,
		core::Size	target_residue
	)

protectedvirtual

References create_refinement_pattern(), core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), core::pack::task::TaskFactory::push_back(), core::pose::Pose::size(), and protocols::hotspot_hashing::movers::TR().

Referenced by perform_local_refinement().

◆ create_refinement_pattern()

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

protectedvirtual

Reimplemented in protocols::hotspot_hashing::movers::PlaceSurfaceProbe.

Referenced by create_refinement_packing_task().

◆ create_search_pattern()

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

protectedpure virtual

Implemented in protocols::hotspot_hashing::movers::PlaceSurfaceProbe.

Referenced by create_partitioned_search_pattern().

◆ execute_one_search()

void protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search	(	core::pose::Pose &	target_pose,
		core::Size	search_index
	)

protected

References protocols::jd2::add_string_string_pair_to_current_job(), core::conformation::Residue::get_self_ptr(), perform_local_refinement(), protocols::hotspot_hashing::StubGenerator::placeResidueAtTransform(), core::pose::Pose::residue(), protocols::hotspot_hashing::StubGenerator::residueStubCentroidFrame(), protocols::hotspot_hashing::StubGenerator::residueStubOrientFrame(), search_points_, protocols::hotspot_hashing::stub_to_points(), target_residue_, and core::id::to_string().

Referenced by apply().

◆ parse_output_mode()

PlaceProbeMover::StructureOutputMode protocols::hotspot_hashing::movers::PlaceProbeMover::parse_output_mode ( std::string name )

protected

References Full, protocols::moves::Mover::name(), None, Probe, and protocols::hotspot_hashing::movers::TR().

◆ parse_place_probe_tag()

void protocols::hotspot_hashing::movers::PlaceProbeMover::parse_place_probe_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

protected

Parses tag compoments for PlaceProbeMover.

References current_mode_, OnePerStruct, core::scoring::parse_score_function(), refinement_scorefxn_, residue_name_, RunAll, search_partition_, total_search_partition_, and protocols::hotspot_hashing::movers::TR().

Referenced by protocols::hotspot_hashing::movers::PlaceSurfaceProbe::parse_my_tag().

◆ perform_local_refinement()

void protocols::hotspot_hashing::movers::PlaceProbeMover::perform_local_refinement	(	core::pose::Pose &	target_pose,
		core::Size	target_residue
	)

protected

References create_refinement_packing_task(), and refinement_scorefxn_.

Referenced by execute_one_search().

◆ reinitialize_for_new_input()

bool protocols::hotspot_hashing::movers::PlaceProbeMover::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::moves::Mover.

Reimplemented in protocols::hotspot_hashing::movers::PlaceSurfaceProbe.

◆ shared_from_this()

PlaceProbeMoverOP protocols::hotspot_hashing::movers::PlaceProbeMover::shared_from_this ( )

inline

Referenced by protocols::hotspot_hashing::movers::PlaceSurfaceProbe::shared_from_this().

Member Data Documentation

◆ current_mode_

ExecutionMode protocols::hotspot_hashing::movers::PlaceProbeMover::current_mode_

protected

Referenced by apply(), and parse_place_probe_tag().

◆ initialized_pattern_

bool protocols::hotspot_hashing::movers::PlaceProbeMover::initialized_pattern_

protected

Referenced by check_and_initialize().

◆ refinement_scorefxn_

core::scoring::ScoreFunctionCOP protocols::hotspot_hashing::movers::PlaceProbeMover::refinement_scorefxn_

protected

Referenced by parse_place_probe_tag(), and perform_local_refinement().

◆ residue_name_

std::string protocols::hotspot_hashing::movers::PlaceProbeMover::residue_name_

protected

Referenced by apply(), and parse_place_probe_tag().

◆ residue_variants_

std::vector<std::string> protocols::hotspot_hashing::movers::PlaceProbeMover::residue_variants_

protected

◆ search_partition_

core::Size protocols::hotspot_hashing::movers::PlaceProbeMover::search_partition_

protected

Referenced by create_partitioned_search_pattern(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_partitioned_search_pattern(), and parse_place_probe_tag().

◆ search_points_

utility::vector1<core::kinematics::Stub> protocols::hotspot_hashing::movers::PlaceProbeMover::search_points_

protected

Referenced by apply(), check_and_initialize(), and execute_one_search().

◆ target_residue_

core::conformation::ResidueCOP protocols::hotspot_hashing::movers::PlaceProbeMover::target_residue_

protected

Referenced by apply(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_partitioned_search_pattern(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_search_pattern(), and execute_one_search().

◆ total_search_partition_

core::Size protocols::hotspot_hashing::movers::PlaceProbeMover::total_search_partition_

protected

Referenced by create_partitioned_search_pattern(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_partitioned_search_pattern(), and parse_place_probe_tag().

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

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

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Member Enumeration Documentation

◆ ExecutionMode

◆ StructureOutputMode

Constructor & Destructor Documentation

◆ PlaceProbeMover() [1/2]

◆ PlaceProbeMover() [2/2]

Member Function Documentation

◆ apply()

◆ check_and_initialize()

◆ create_partitioned_search_pattern()

◆ create_refinement_packing_task()

◆ create_refinement_pattern()

◆ create_search_pattern()

◆ execute_one_search()

◆ parse_output_mode()

◆ parse_place_probe_tag()

◆ perform_local_refinement()

◆ reinitialize_for_new_input()

◆ shared_from_this()

Member Data Documentation

◆ current_mode_

◆ initialized_pattern_

◆ refinement_scorefxn_

◆ residue_name_

◆ residue_variants_

◆ search_partition_

◆ search_points_

◆ target_residue_

◆ total_search_partition_