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protocols::hotspot_hashing::movers::PlaceProbeMover Class Referenceabstract

#include <PlaceProbeMover.hh>

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

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

Enumerator
RunAll 
OnePerStruct 
Enumerator
None 
Probe 
Full 

Constructor & Destructor Documentation

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

void protocols::hotspot_hashing::movers::PlaceProbeMover::apply ( Pose )
overridevirtual
void protocols::hotspot_hashing::movers::PlaceProbeMover::check_and_initialize ( core::pose::Pose const &  target_pose)
protected
SearchPatternOP protocols::hotspot_hashing::movers::PlaceProbeMover::create_partitioned_search_pattern ( core::pose::Pose const &  target_pose)
protectedvirtual
core::pack::task::PackerTaskOP protocols::hotspot_hashing::movers::PlaceProbeMover::create_refinement_packing_task ( core::pose::Pose const &  target_pose,
core::Size  target_residue 
)
protectedvirtual
SearchPatternOP protocols::hotspot_hashing::movers::PlaceProbeMover::create_refinement_pattern ( core::pose::Pose const &  target_pose,
core::Size  target_residue 
)
protectedvirtual
virtual SearchPatternOP protocols::hotspot_hashing::movers::PlaceProbeMover::create_search_pattern ( core::pose::Pose const &  target_pose)
protectedpure virtual
void protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search ( core::pose::Pose target_pose,
core::Size  search_index 
)
protected
PlaceProbeMover::StructureOutputMode protocols::hotspot_hashing::movers::PlaceProbeMover::parse_output_mode ( std::string  name)
protected

References Full, None, and Probe.

void protocols::hotspot_hashing::movers::PlaceProbeMover::parse_place_probe_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
protected
void protocols::hotspot_hashing::movers::PlaceProbeMover::perform_local_refinement ( core::pose::Pose target_pose,
core::Size  target_residue 
)
protected
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.

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

Member Data Documentation

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

Referenced by apply(), and parse_place_probe_tag().

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

Referenced by check_and_initialize().

core::scoring::ScoreFunctionCOP protocols::hotspot_hashing::movers::PlaceProbeMover::refinement_scorefxn_
protected
std::string protocols::hotspot_hashing::movers::PlaceProbeMover::residue_name_
protected

Referenced by apply(), and parse_place_probe_tag().

std::vector<std::string> protocols::hotspot_hashing::movers::PlaceProbeMover::residue_variants_
protected
core::Size protocols::hotspot_hashing::movers::PlaceProbeMover::search_partition_
protected
utility::vector1<core::kinematics::Stub> protocols::hotspot_hashing::movers::PlaceProbeMover::search_points_
protected
core::conformation::ResidueCOP protocols::hotspot_hashing::movers::PlaceProbeMover::target_residue_
protected
core::Size protocols::hotspot_hashing::movers::PlaceProbeMover::total_search_partition_
protected

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