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protocols::hotspot_hashing::movers::PlaceSurfaceProbe Class Reference

#include <PlaceSurfaceProbe.hh>

Inheritance diagram for protocols::hotspot_hashing::movers::PlaceSurfaceProbe:
Inheritance graph
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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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

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

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.

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

SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::initialize_refinement_pattern ( )
private
std::string protocols::hotspot_hashing::movers::PlaceSurfaceProbe::mover_name ( )
static
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_.

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

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

Member Data Documentation

core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::coarse_angle_sampling_
private
core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::coarse_sampling_
private
core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::refinement_angle_sampling_
private
core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::refinement_distance_
private
SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::refinement_pattern_
private
core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::refinement_sampling_
private
core::Real protocols::hotspot_hashing::movers::PlaceSurfaceProbe::search_density_
private
core::pack::task::TaskFactoryOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::surface_selection_
private

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