#include <PlaceProbeMover.hh>

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

Collaboration diagram for protocols::hotspot_hashing::movers::PlaceProbeMover:

Public Types
enum	ExecutionMode { RunAll, OnePerStruct }

enum	StructureOutputMode { None, Probe, Full }

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Public Member Functions
	PlaceProbeMover ()

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

virtual void	apply (Pose &)

virtual bool	reinitialize_for_new_input () const
	this function informs 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	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	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...

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Protected Member Functions
void	parse_place_probe_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Detailed Description

Definition at line 42 of file PlaceProbeMover.hh.

Member Enumeration Documentation

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

Enumerator
RunAll
OnePerStruct

Definition at line 45 of file PlaceProbeMover.hh.

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

Enumerator
None
Probe
Full

Definition at line 50 of file PlaceProbeMover.hh.

Constructor & Destructor Documentation

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

Definition at line 65 of file PlaceProbeMover.cc.

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

Definition at line 75 of file PlaceProbeMover.cc.

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

Definition at line 89 of file PlaceProbeMover.cc.

References check_and_initialize(), protocols::jd2::JobDistributor::current_job(), current_mode_, execute_one_search(), protocols::jd2::JobDistributor::get_instance(), OnePerStruct, and search_points_.

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

protected

Definition at line 162 of file PlaceProbeMover.cc.

References create_partitioned_search_pattern(), protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), initialized_pattern_, and search_points_.

Referenced by apply().

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

protectedvirtual

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

Definition at line 194 of file PlaceProbeMover.cc.

References create_search_pattern(), search_partition_, and total_search_partition_.

Referenced by check_and_initialize().

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

protectedvirtual

Definition at line 214 of file PlaceProbeMover.cc.

References create_refinement_pattern(), core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), core::pack::task::TaskFactory::push_back(), and core::pose::Pose::total_residue().

Referenced by perform_local_refinement().

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.

Definition at line 199 of file PlaceProbeMover.cc.

Referenced by create_refinement_packing_task().

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().

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

protected

Definition at line 115 of file PlaceProbeMover.cc.

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), 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(), and target_residue_.

Referenced by apply().

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

protected

Definition at line 289 of file PlaceProbeMover.cc.

References Full, None, and Probe.

void protocols::hotspot_hashing::movers::PlaceProbeMover::parse_place_probe_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &	target_pose
	)

protected

Parses tag compoments for PlaceProbeMover.

Definition at line 236 of file PlaceProbeMover.cc.

References core::pose::add_variant_type_to_residue(), current_mode_, protocols::hotspot_hashing::StubGenerator::getStubByName(), OnePerStruct, protocols::rosetta_scripts::parse_score_function(), refinement_scorefxn_, residue_name_, RunAll, search_partition_, target_residue_, and total_search_partition_.

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

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

protected

Definition at line 204 of file PlaceProbeMover.cc.

References create_refinement_packing_task(), and refinement_scorefxn_.

Referenced by execute_one_search().

virtual bool protocols::hotspot_hashing::movers::PlaceProbeMover::reinitialize_for_new_input ( ) const

inlinevirtual

this function informs 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.

Definition at line 65 of file PlaceProbeMover.hh.