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Rosetta
2021.16
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Rosetta
2021.16
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#include <DirectSegmentLookupMover.hh>
Public Member Functions | |
| DirectSegmentLookupMover ()=default | |
| void | structure_store_path (std::string path) |
| std::string | structure_store_path () |
| void | lookup_config (DirectSegmentLookupConfig config) |
| DirectSegmentLookupConfig | lookup_config () |
| std::string | stored_subset_name () |
| void | stored_subset_name (std::string name) |
| bool | overwrite_stored_subset () |
| void | overwrite_stored_subset (bool overwrite) |
| std::string | label_insertion () |
| void | label_insertion (std::string name) |
| std::string | output_lookup_count () |
| void | output_lookup_count (std::string name) |
| std::string | output_lookup_length () |
| void | output_lookup_length (std::string name) |
| core::Size | from_chain () |
| void | from_chain (core::Size chain) |
| core::Size | to_chain () |
| void | to_chain (core::Size chain) |
| StructureStoreOP | structure_store () |
| search::StructureDatabaseOP | structure_database () |
| moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| void | apply (Pose &pose) override |
| Main Method. More... | |
| core::pose::PoseOP | get_additional_output () override |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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 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 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... | |
| 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... | |
| 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 |
| 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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| 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... | |
Private Member Functions | |
| void | init_structure_store () |
| core::pose::PoseOP | generate_result_pose (core::pose::Pose &source_pose, DirectSegmentLookupResult lookup_result) |
Private Attributes | |
| std::string | structure_store_path_ |
| DirectSegmentLookupConfig | lookup_config_ |
| core::Size | lookup_context_ = 2 |
| std::string | stored_subset_name_ |
| bool | overwrite_stored_subset_ = false |
| std::string | label_insertion_ |
| std::string | output_lookup_count_ |
| std::string | output_lookup_length_ |
| core::Size | from_chain_ = 1 |
| core::Size | to_chain_ = 2 |
| StructureStoreOP | structure_store_ |
| search::StructureDatabaseOP | structure_database_ |
| core::pose::PoseOP | source_pose_ |
| std::vector < DirectSegmentLookupResult > | lookup_results_ |
| core::Size | lookup_result_index_ = 0 |
| core::Size | max_num_results_ = 0 |
Additional Inherited Members | |
| 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 |
| 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... | |
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default |
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overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References core::pose::motif::a(), protocols::match::upstream::b, from_chain_, core::select::residue_selector::CachedResidueSubset::from_pose_datacache(), generate_result_pose(), lookup_config_, lookup_context_, lookup_result_index_, lookup_results_, protocols::moves::MS_FAIL_DO_NOT_RETRY, protocols::indexed_structure_store::DirectSegmentLookupResult::query_results, protocols::indexed_structure_store::DirectSegmentLookup::segment_lookup(), protocols::moves::Mover::set_last_move_status(), source_pose_, stored_subset_name(), structure_database(), structure_store(), and to_chain_.
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overridevirtual |
Return a clone of the Mover object.
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.
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inline |
References from_chain_.
Referenced by parse_my_tag().
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References from_chain_.
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References protocols::indexed_structure_store::append_pose_with_overlap(), core::pack::dunbrack::c, protocols::indexed_structure_store::DELETE_DOWNSTREAM, protocols::indexed_structure_store::DELETE_UPSTREAM, from_chain_, label_insertion_, lookup_context_, output_lookup_count_, output_lookup_length_, overwrite_stored_subset_, protocols::indexed_structure_store::DirectSegmentLookupResult::query_results, protocols::indexed_structure_store::residue_entries_to_pose(), protocols::indexed_structure_store::DirectSegmentLookupResult::result_residues, core::pose::setPoseExtraScore(), core::pose::Pose::split_by_chain(), stored_subset_name_, to_chain_, protocols::indexed_structure_store::TR(), and v_to_a().
Referenced by apply(), and get_additional_output().
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overridevirtual |
Mechanism by which a mover may return multiple output poses from a single input pose.
fpd
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.
Reimplemented from protocols::moves::Mover.
References generate_result_pose(), lookup_result_index_, lookup_results_, max_num_results_, and source_pose_.
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
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private |
References structure_database_, structure_store_, and structure_store_path().
Referenced by structure_database(), and structure_store().
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References label_insertion_.
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References label_insertion_, and protocols::moves::Mover::name().
| void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::lookup_config | ( | DirectSegmentLookupConfig | config | ) |
| DirectSegmentLookupConfig protocols::indexed_structure_store::movers::DirectSegmentLookupMover::lookup_config | ( | ) |
References lookup_config_.
Referenced by parse_my_tag().
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References output_lookup_count_.
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References protocols::moves::Mover::name(), and output_lookup_count_.
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References output_lookup_length_.
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References protocols::moves::Mover::name(), and output_lookup_length_.
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References overwrite_stored_subset_.
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References overwrite_stored_subset_.
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overridevirtual |
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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References from_chain(), label_insertion_, lookup_config(), protocols::indexed_structure_store::DirectSegmentLookupConfig::max_insertion_length, max_num_results_, output_lookup_count_, output_lookup_length_, overwrite_stored_subset_, protocols::indexed_structure_store::DirectSegmentLookupConfig::rmsd_tolerance, protocols::indexed_structure_store::DirectSegmentLookupConfig::segment_cluster_tolerance, stored_subset_name_, structure_store_path(), and to_chain().
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inline |
References stored_subset_name_.
Referenced by apply().
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References protocols::moves::Mover::name(), and stored_subset_name_.
| search::StructureDatabaseOP protocols::indexed_structure_store::movers::DirectSegmentLookupMover::structure_database | ( | ) |
References init_structure_store(), and structure_database_.
Referenced by apply().
| StructureStoreOP protocols::indexed_structure_store::movers::DirectSegmentLookupMover::structure_store | ( | ) |
References init_structure_store(), and structure_store_.
Referenced by apply().
| void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::structure_store_path | ( | std::string | path | ) |
References protocols::hybridization::path, structure_database_, structure_store_, and structure_store_path_.
| std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::structure_store_path | ( | ) |
References structure_store_path_.
Referenced by init_structure_store(), and parse_my_tag().
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References to_chain_.
Referenced by parse_my_tag().
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References to_chain_.
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Referenced by apply(), from_chain(), and generate_result_pose().
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Referenced by generate_result_pose(), label_insertion(), and parse_my_tag().
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Referenced by apply(), and lookup_config().
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Referenced by apply(), and generate_result_pose().
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Referenced by apply(), and get_additional_output().
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Referenced by apply(), and get_additional_output().
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Referenced by get_additional_output(), and parse_my_tag().
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Referenced by generate_result_pose(), output_lookup_count(), and parse_my_tag().
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Referenced by generate_result_pose(), output_lookup_length(), and parse_my_tag().
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Referenced by generate_result_pose(), overwrite_stored_subset(), and parse_my_tag().
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Referenced by apply(), and get_additional_output().
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Referenced by generate_result_pose(), parse_my_tag(), and stored_subset_name().
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Referenced by init_structure_store(), structure_database(), and structure_store_path().
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Referenced by init_structure_store(), structure_store(), and structure_store_path().
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Referenced by structure_store_path().
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Referenced by apply(), generate_result_pose(), and to_chain().
1.8.7