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protocols::legacy_sewing::LegacyRepeatAssemblyMover Class Reference

#include <LegacyRepeatAssemblyMover.hh>

Inheritance diagram for protocols::legacy_sewing::LegacyRepeatAssemblyMover:
Inheritance graph
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Public Types

typedef LegacyAssemblyMover parent
 
- 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
 

Public Member Functions

 LegacyRepeatAssemblyMover ()
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
std::pair< bool, AssemblyOPdfs_cycle_finder (ModelNode const *reference_node, utility::vector1< ModelNode const * > visited_nodes, AssemblyOP assembly) const
 recursive function. Start with a given reference node and randomly traverse edges in a depth-first-search of a cycle of a given size (number of nodes). More...
 
AssemblyOP generate_assembly () override
 
void output_base_stats (AssemblyOP const &assembly)
 adds single repeat unit data to score file More...
 
void add_repeats (AssemblyOP assembly) const
 adds remaining data to score file More...
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
get_segment_coords (SewSegment const &segment) const
 
void transform_segment_coords (SewSegment &segment, numeric::xyzTransform< core::Real > transformer, numeric::xyzVector< float > com, core::Size n_transformations) const
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
core::pose::Pose refine_assembly (AssemblyOP &assembly) override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::legacy_sewing::LegacyAssemblyMover
 LegacyAssemblyMover ()
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
virtual void add_starting_model (AssemblyOP assembly) const
 
virtual core::pose::Pose get_fullatom_pose (AssemblyOP assembly) const
 
virtual core::pose::Pose get_centroid_pose (AssemblyOP assembly) const
 
bool follow_random_edge_from_node (AssemblyOP assembly, ModelNode const *reference_node) const
 
bool reinitialize_for_new_input () const override
 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...
 
void append_movie_frame (AssemblyOP assembly, core::Size cycle) const
 
virtual void output_stats (AssemblyOP const &assembly, core::pose::Pose &pose, std::string indicator_whether_from_LegacyMonteCarloAssemblyMover_or_LegacyExhaustiveAssemblyMover)
 add several outputs to the score file Pose can't be const due to scoring. More...
 
virtual void parse_requirements (TagCOP tag, basic::datacache::DataMap &data)
 
virtual void parse_global_requirements (TagCOP tag, basic::datacache::DataMap &data)
 
virtual void parse_intra_segment_requirements (TagCOP tag, basic::datacache::DataMap &data)
 
- 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...
 
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...
 
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::legacy_sewing::LegacyAssemblyMover
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static
utility::tag::XMLSchemaComplexTypeGeneratorOP 
define_assembly_mover_ct_gen (utility::tag::XMLSchemaDefinition &xsd)
 
static std::string legacy_assembly_mover_ct_namer (std::string const &)
 
- 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 Attributes

core::Size num_repeating_segments_
 
core::Real threshold_score_of_complete_cycle_
 
core::Size num_repeats_
 
core::Size num_trials_
 
scoring::LegacyAssemblyScoreFunctionOP clash_scorefxn_
 

Additional Inherited Members

- 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 inherited from protocols::legacy_sewing::LegacyAssemblyMover
scoring::LegacyAssemblyScoreFunctionOP assembly_scorefxn_
 
SewGraphOP graph_
 
std::string edge_file_
 
sampling::requirements::LegacyRequirementSetOP requirement_set_
 
sampling::requirements::LegacyRequirementFactoryrequirement_factory_
 
core::scoring::ScoreFunctionOP cen_scorefxn_
 
core::scoring::ScoreFunctionOP fa_scorefxn_
 
core::Real base_native_bonus_
 
core::Size neighbor_cutoff_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::legacy_sewing::LegacyRepeatAssemblyMover::LegacyRepeatAssemblyMover ( )

References num_repeats_.

Member Function Documentation

void protocols::legacy_sewing::LegacyRepeatAssemblyMover::add_repeats ( AssemblyOP  assembly) const
protocols::moves::MoverOP protocols::legacy_sewing::LegacyRepeatAssemblyMover::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.

std::pair< bool, AssemblyOP > protocols::legacy_sewing::LegacyRepeatAssemblyMover::dfs_cycle_finder ( ModelNode const *  reference_node,
utility::vector1< ModelNode const * >  visited_nodes,
AssemblyOP  assembly 
) const
protocols::moves::MoverOP protocols::legacy_sewing::LegacyRepeatAssemblyMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

AssemblyOP protocols::legacy_sewing::LegacyRepeatAssemblyMover::generate_assembly ( )
overridevirtual
std::string protocols::legacy_sewing::LegacyRepeatAssemblyMover::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::legacy_sewing::LegacyAssemblyMover.

References mover_name().

utility::vector1< numeric::xyzVector< core::Real > > protocols::legacy_sewing::LegacyRepeatAssemblyMover::get_segment_coords ( SewSegment const &  segment) const
std::string protocols::legacy_sewing::LegacyRepeatAssemblyMover::mover_name ( )
static
void protocols::legacy_sewing::LegacyRepeatAssemblyMover::output_base_stats ( AssemblyOP const &  assembly)
void protocols::legacy_sewing::LegacyRepeatAssemblyMover::parse_my_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::legacy_sewing::LegacyAssemblyMover.

References num_repeating_segments_, protocols::legacy_sewing::LegacyAssemblyMover::parse_my_tag(), and threshold_score_of_complete_cycle_.

void protocols::legacy_sewing::LegacyRepeatAssemblyMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::pose::Pose protocols::legacy_sewing::LegacyRepeatAssemblyMover::refine_assembly ( AssemblyOP assembly)
overridevirtual
void protocols::legacy_sewing::LegacyRepeatAssemblyMover::transform_segment_coords ( SewSegment segment,
numeric::xyzTransform< core::Real transformer,
numeric::xyzVector< float >  com,
core::Size  n_transformations 
) const

Member Data Documentation

scoring::LegacyAssemblyScoreFunctionOP protocols::legacy_sewing::LegacyRepeatAssemblyMover::clash_scorefxn_
private
core::Size protocols::legacy_sewing::LegacyRepeatAssemblyMover::num_repeating_segments_
private

Referenced by dfs_cycle_finder(), and parse_my_tag().

core::Size protocols::legacy_sewing::LegacyRepeatAssemblyMover::num_repeats_
private
core::Size protocols::legacy_sewing::LegacyRepeatAssemblyMover::num_trials_
private

Referenced by generate_assembly().

core::Real protocols::legacy_sewing::LegacyRepeatAssemblyMover::threshold_score_of_complete_cycle_
private

Referenced by generate_assembly(), and parse_my_tag().


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