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

#include <PlaceSurfaceProbe.hh>

Inheritance diagram for protocols::hotspot_hashing::movers::PlaceSurfaceProbe:
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Collaboration diagram for protocols::hotspot_hashing::movers::PlaceSurfaceProbe:
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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=NULL, core::Size search_partition=1, core::Size total_search_partition=1)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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::hotspot_hashing::movers::PlaceProbeMover
 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 &)
 
- 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)
 
Moveroperator= (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)
 
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 Stringsinfo ()
 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

virtual SearchPatternOP create_search_pattern (core::pose::Pose const &target_pose)
 
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)
 
- Protected Member Functions inherited from protocols::hotspot_hashing::movers::PlaceProbeMover
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
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::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
 
- 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...
 
- 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 ( )

Referenced by clone().

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 = NULL,
core::Size  search_partition = 1,
core::Size  total_search_partition = 1 
)

Member Function Documentation

protocols::moves::MoverOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

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.

References PlaceSurfaceProbe().

SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_partitioned_search_pattern ( core::pose::Pose const &  target_pose)
protectedvirtual
SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_refinement_pattern ( core::pose::Pose const &  target_pose,
core::Size  target_residue 
)
protectedvirtual
SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_search_pattern ( core::pose::Pose const &  target_pose)
protectedvirtual
virtual std::string protocols::hotspot_hashing::movers::PlaceSurfaceProbe::get_name ( ) const
inlinevirtual

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

Implements protocols::moves::Mover.

SearchPatternOP protocols::hotspot_hashing::movers::PlaceSurfaceProbe::initialize_refinement_pattern ( )
private
void protocols::hotspot_hashing::movers::PlaceSurfaceProbe::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References coarse_angle_sampling_, coarse_sampling_, initialize_refinement_pattern(), protocols::hotspot_hashing::movers::PlaceProbeMover::parse_place_probe_tag(), protocols::rosetta_scripts::parse_task_operations(), refinement_angle_sampling_, refinement_distance_, refinement_pattern_, refinement_sampling_, search_density_, and surface_selection_.

virtual bool protocols::hotspot_hashing::movers::PlaceSurfaceProbe::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::hotspot_hashing::movers::PlaceProbeMover.

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: