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Rosetta
3.8
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#include <PlaceProbeMover.hh>
Public Types | |
enum | ExecutionMode { RunAll, OnePerStruct } |
enum | StructureOutputMode { None, Probe, Full } |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef protocols::filters::Filters_map | Filters_map |
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) | |
PlaceProbeMoverOP | shared_from_this () |
virtual void | apply (Pose &) |
virtual bool | reinitialize_for_new_input () const |
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... | |
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Mover () | |
~Mover () override | |
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 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 |
void | set_type (std::string const &setting) |
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 | 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 |
Return a clone of the Mover object. More... | |
virtual void | parse_my_tag (TagCOP tag, basic::datacache::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 Strings & | info () |
non-const accessor More... | |
virtual Strings const & | info () const |
const accessor 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... | |
void | set_current_job (protocols::jobdist::BasicJobCOP job) |
jobdist::BasicJobCOP | get_current_job () const |
virtual void | show (std::ostream &output=std::cout) const |
Outputs details about the Mover, including current settings. More... | |
Protected Member Functions | |
void | parse_place_probe_tag (utility::tag::TagCOP tag, basic::datacache::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) |
virtual core::pack::task::PackerTaskOP | create_refinement_packing_task (core::pose::Pose const &target_pose, core::Size target_residue) |
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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 | |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
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 , |
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core::Size | total_search_partition = 1 |
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References create_partitioned_search_pattern(), protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), initialized_pattern_, and search_points_.
Referenced by apply().
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protectedvirtual |
Reimplemented in protocols::hotspot_hashing::movers::PlaceSurfaceProbe.
References create_search_pattern(), search_partition_, and total_search_partition_.
Referenced by check_and_initialize().
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protectedvirtual |
Reimplemented in protocols::hotspot_hashing::movers::PlaceSurfaceProbe.
Referenced by create_refinement_packing_task().
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protectedpure virtual |
Implemented in protocols::hotspot_hashing::movers::PlaceSurfaceProbe.
Referenced by create_partitioned_search_pattern().
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References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), core::conformation::Residue::get_self_ptr(), perform_local_refinement(), protocols::hotspot_hashing::StubGenerator::placeResidueAtTransform(), core::pose::Pose::residue(), protocols::hotspot_hashing::StubGenerator::residueStubCentroidFrame(), protocols::hotspot_hashing::StubGenerator::residueStubOrientFrame(), search_points_, protocols::hotspot_hashing::stub_to_points(), and target_residue_.
Referenced by apply().
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Parses tag compoments for PlaceProbeMover.
References core::pose::add_variant_type_to_residue(), current_mode_, protocols::hotspot_hashing::StubGenerator::getStubByName(), OnePerStruct, protocols::rosetta_scripts::parse_score_function(), refinement_scorefxn_, residue_name_, RunAll, core::chemical::SC_FRAGMENT, search_partition_, target_residue_, and total_search_partition_.
Referenced by protocols::hotspot_hashing::movers::PlaceSurfaceProbe::parse_my_tag().
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References create_refinement_packing_task(), and refinement_scorefxn_.
Referenced by execute_one_search().
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inlinevirtual |
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.
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Referenced by apply(), and parse_place_probe_tag().
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Referenced by check_and_initialize().
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Referenced by parse_place_probe_tag(), and perform_local_refinement().
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Referenced by parse_place_probe_tag().
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Referenced by apply(), check_and_initialize(), and execute_one_search().
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