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protocols::indexed_structure_store::movers::DirectSegmentLookupMover Class Reference

#include <DirectSegmentLookupMover.hh>

Inheritance diagram for protocols::indexed_structure_store::movers::DirectSegmentLookupMover:
Inheritance graph
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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 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...
 

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...
 

Constructor & Destructor Documentation

protocols::indexed_structure_store::movers::DirectSegmentLookupMover::DirectSegmentLookupMover ( )
default

Member Function Documentation

void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::apply ( Pose )
overridevirtual
moves::MoverOP protocols::indexed_structure_store::movers::DirectSegmentLookupMover::clone ( ) const
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.

core::Size protocols::indexed_structure_store::movers::DirectSegmentLookupMover::from_chain ( )
inline

References from_chain_.

Referenced by parse_my_tag().

void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::from_chain ( core::Size  chain)
inline

References from_chain_.

core::pose::PoseOP protocols::indexed_structure_store::movers::DirectSegmentLookupMover::generate_result_pose ( core::pose::Pose source_pose,
DirectSegmentLookupResult  lookup_result 
)
private
core::pose::PoseOP protocols::indexed_structure_store::movers::DirectSegmentLookupMover::get_additional_output ( )
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_.

std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::init_structure_store ( )
private
std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::label_insertion ( )
inline

References label_insertion_.

void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::label_insertion ( std::string  name)
inline
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().

std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::mover_name ( )
static
std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::output_lookup_count ( )
inline

References output_lookup_count_.

void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::output_lookup_count ( std::string  name)
inline
std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::output_lookup_length ( )
inline

References output_lookup_length_.

void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::output_lookup_length ( std::string  name)
inline
bool protocols::indexed_structure_store::movers::DirectSegmentLookupMover::overwrite_stored_subset ( )
inline
void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::overwrite_stored_subset ( bool  overwrite)
inline
void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
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().

void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::stored_subset_name ( )
inline

References stored_subset_name_.

Referenced by apply().

void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::stored_subset_name ( std::string  name)
inline
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)
std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::structure_store_path ( )
core::Size protocols::indexed_structure_store::movers::DirectSegmentLookupMover::to_chain ( )
inline

References to_chain_.

Referenced by parse_my_tag().

void protocols::indexed_structure_store::movers::DirectSegmentLookupMover::to_chain ( core::Size  chain)
inline

References to_chain_.

Member Data Documentation

core::Size protocols::indexed_structure_store::movers::DirectSegmentLookupMover::from_chain_ = 1
private
std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::label_insertion_
private
DirectSegmentLookupConfig protocols::indexed_structure_store::movers::DirectSegmentLookupMover::lookup_config_
private

Referenced by apply(), and lookup_config().

core::Size protocols::indexed_structure_store::movers::DirectSegmentLookupMover::lookup_context_ = 2
private

Referenced by apply(), and generate_result_pose().

core::Size protocols::indexed_structure_store::movers::DirectSegmentLookupMover::lookup_result_index_ = 0
private

Referenced by apply(), and get_additional_output().

std::vector<DirectSegmentLookupResult> protocols::indexed_structure_store::movers::DirectSegmentLookupMover::lookup_results_
private

Referenced by apply(), and get_additional_output().

core::Size protocols::indexed_structure_store::movers::DirectSegmentLookupMover::max_num_results_ = 0
private
std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::output_lookup_count_
private
std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::output_lookup_length_
private
bool protocols::indexed_structure_store::movers::DirectSegmentLookupMover::overwrite_stored_subset_ = false
private
core::pose::PoseOP protocols::indexed_structure_store::movers::DirectSegmentLookupMover::source_pose_
private

Referenced by apply(), and get_additional_output().

std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::stored_subset_name_
private
search::StructureDatabaseOP protocols::indexed_structure_store::movers::DirectSegmentLookupMover::structure_database_
private
StructureStoreOP protocols::indexed_structure_store::movers::DirectSegmentLookupMover::structure_store_
private
std::string protocols::indexed_structure_store::movers::DirectSegmentLookupMover::structure_store_path_
private

Referenced by structure_store_path().

core::Size protocols::indexed_structure_store::movers::DirectSegmentLookupMover::to_chain_ = 2
private

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