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Rosetta 3.5
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Rosetta 3.5
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#include <PlaceSurfaceProbe.hh>
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) | |
| 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) |
| 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 | |
| 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 () |
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_ |
Definition at line 46 of file PlaceSurfaceProbe.hh.
| protocols::hotspot_hashing::movers::PlaceSurfaceProbe::PlaceSurfaceProbe | ( | ) |
Definition at line 57 of file PlaceSurfaceProbe.cc.
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, |
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| core::Size | search_partition = 1, |
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| core::Size | total_search_partition = 1 |
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| ) |
Definition at line 73 of file PlaceSurfaceProbe.cc.
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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.
Definition at line 101 of file PlaceSurfaceProbe.cc.
References PlaceSurfaceProbe().
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protectedvirtual |
Reimplemented from protocols::hotspot_hashing::movers::PlaceProbeMover.
Definition at line 151 of file PlaceSurfaceProbe.cc.
References core::pose::add_variant_type_to_residue(), coarse_angle_sampling_, protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), search_density_, protocols::hotspot_hashing::movers::PlaceProbeMover::search_partition_, surface_selection_, protocols::hotspot_hashing::movers::PlaceProbeMover::target_residue_, and protocols::hotspot_hashing::movers::PlaceProbeMover::total_search_partition_.
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protectedvirtual |
Reimplemented from protocols::hotspot_hashing::movers::PlaceProbeMover.
Definition at line 188 of file PlaceSurfaceProbe.cc.
References refinement_pattern_.
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protectedvirtual |
Implements protocols::hotspot_hashing::movers::PlaceProbeMover.
Definition at line 106 of file PlaceSurfaceProbe.cc.
References core::pose::add_variant_type_to_residue(), coarse_angle_sampling_, coarse_sampling_, protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), search_density_, surface_selection_, and protocols::hotspot_hashing::movers::PlaceProbeMover::target_residue_.
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inlinevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 64 of file PlaceSurfaceProbe.hh.
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private |
Definition at line 193 of file PlaceSurfaceProbe.cc.
References coarse_angle_sampling_, coarse_sampling_, refinement_angle_sampling_, refinement_distance_, and refinement_sampling_.
Referenced by parse_my_tag().
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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.
Definition at line 215 of file PlaceSurfaceProbe.cc.
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_.
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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.
Definition at line 75 of file PlaceSurfaceProbe.hh.
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private |
Definition at line 87 of file PlaceSurfaceProbe.hh.
Referenced by create_partitioned_search_pattern(), create_search_pattern(), initialize_refinement_pattern(), and parse_my_tag().
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private |
Definition at line 88 of file PlaceSurfaceProbe.hh.
Referenced by create_search_pattern(), initialize_refinement_pattern(), and parse_my_tag().
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private |
Definition at line 91 of file PlaceSurfaceProbe.hh.
Referenced by initialize_refinement_pattern(), and parse_my_tag().
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private |
Definition at line 90 of file PlaceSurfaceProbe.hh.
Referenced by initialize_refinement_pattern(), and parse_my_tag().
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private |
Definition at line 95 of file PlaceSurfaceProbe.hh.
Referenced by create_refinement_pattern(), and parse_my_tag().
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private |
Definition at line 92 of file PlaceSurfaceProbe.hh.
Referenced by initialize_refinement_pattern(), and parse_my_tag().
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private |
Definition at line 86 of file PlaceSurfaceProbe.hh.
Referenced by create_partitioned_search_pattern(), create_search_pattern(), and parse_my_tag().
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private |
Definition at line 84 of file PlaceSurfaceProbe.hh.
Referenced by create_partitioned_search_pattern(), create_search_pattern(), and parse_my_tag().
1.8.4