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

#include <PlaceProbeMover.hh>

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

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 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)
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)
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 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

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)
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_
< core::kinematics::Stub

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...

Member Enumeration Documentation


Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::hotspot_hashing::movers::PlaceProbeMover::apply ( Pose pose)
void protocols::hotspot_hashing::movers::PlaceProbeMover::check_and_initialize ( core::pose::Pose const &  target_pose)
SearchPatternOP protocols::hotspot_hashing::movers::PlaceProbeMover::create_partitioned_search_pattern ( core::pose::Pose const &  target_pose)
core::pack::task::PackerTaskOP protocols::hotspot_hashing::movers::PlaceProbeMover::create_refinement_packing_task ( core::pose::Pose const &  target_pose,
core::Size  target_residue 
SearchPatternOP protocols::hotspot_hashing::movers::PlaceProbeMover::create_refinement_pattern ( core::pose::Pose const &  target_pose,
core::Size  target_residue 
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 
PlaceProbeMover::StructureOutputMode protocols::hotspot_hashing::movers::PlaceProbeMover::parse_output_mode ( std::string  name)

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

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

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

Member Data Documentation

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

Referenced by apply(), and parse_place_probe_tag().

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

Referenced by check_and_initialize().

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

Referenced by parse_place_probe_tag().

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

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