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protocols::cluster::ClusterBase Class Reference

#include <cluster.hh>

Inheritance diagram for protocols::cluster::ClusterBase:
Inheritance graph
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Public Member Functions

 ClusterBase ()
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_cluster_radius (core::Real cluster_radius)
 
void set_population_weight (core::Real population_weight)
 
core::Real get_cluster_radius ()
 
core::Real get_median_rms ()
 
void calculate_distance_matrix ()
 
void add_structure (core::pose::Pose &pose)
 
void remove_highest_energy_member_of_each_group ()
 
void sort_each_group_by_energy ()
 
void sort_groups_by_energy ()
 
void remove_singletons ()
 
void export_only_low (bool value=false)
 
void limit_groupsize (int limit=-1)
 
void limit_groupsize (core::Real percent_limit)
 
void random_limit_groupsize (core::Real percent_limit)
 
void limit_groups (int limit=-1)
 
void limit_total_structures (int limit=-1)
 
void clean_pose_store ()
 
void print_summary ()
 
void print_raw_numbers ()
 
void print_cluster_assignment ()
 
void print_cluster_PDBs (std::string prefix)
 
void print_clusters_silentfile (std::string prefix)
 
std::vector< core::pose::PoseOPreturn_lowest_poses_in_clusters ()
 
std::vector< core::pose::PoseOPreturn_top_poses_in_clusters (core::Size count)
 
void create_constraints (std::string prefix, EnsembleConstraints &constraint_maker)
 
std::vector< Cluster > const & get_cluster_list () const
 
- Public Member Functions inherited from protocols::cluster::GatherPosesMover
 GatherPosesMover ()
 
void set_score_function (core::scoring::ScoreFunctionOP sfxn)
 
void set_filter (core::Real filter)
 
core::Real get_filter () const
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
bool check_tag (const std::string &query_tag)
 
void push_back (const core::pose::Pose &pose)
 
void clear ()
 
void set_cluster_by_protein_backbone (bool const &setting)
 
void set_cluster_by_all_atom (bool const &setting)
 
core::Size nposes () const
 Return the number of poses gathered by this mover This is the post-filtered number of poses. More...
 
std::vector< core::pose::Pose > & get_pose_list ()
 
std::vector< std::string > const & get_tag_list () const
 
virtual core::Real get_distance_measure (const core::pose::Pose &pose1, const core::pose::Pose &pose2) const
 
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 

Protected Attributes

ObjexxFCL::FArray2D< core::Realdistance_matrix
 
std::vector< Clusterclusterlist
 
bool export_only_low_
 
core::Real median_rms_
 
core::Real population_weight_
 
core::Real cluster_radius_
 
- Protected Attributes inherited from protocols::cluster::GatherPosesMover
std::vector< core::pose::Poseposelist
 

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
 
- 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...
 
- 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::cluster::ClusterBase::ClusterBase ( )

Member Function Documentation

void protocols::cluster::ClusterBase::add_structure ( core::pose::Pose pose)
void protocols::cluster::ClusterBase::calculate_distance_matrix ( )
void protocols::cluster::ClusterBase::clean_pose_store ( )
void protocols::cluster::ClusterBase::create_constraints ( std::string  prefix,
EnsembleConstraints constraint_maker 
)
void protocols::cluster::ClusterBase::export_only_low ( bool  value = false)
inline

References export_only_low_.

std::vector< Cluster > const& protocols::cluster::ClusterBase::get_cluster_list ( ) const
inline

References clusterlist.

Real protocols::cluster::ClusterBase::get_cluster_radius ( )
core::Real protocols::cluster::ClusterBase::get_median_rms ( )
inline
std::string protocols::cluster::ClusterBase::get_name ( ) const
overridevirtual
void protocols::cluster::ClusterBase::limit_groups ( int  limit = -1)
void protocols::cluster::ClusterBase::limit_groupsize ( int  limit = -1)
void protocols::cluster::ClusterBase::limit_groupsize ( core::Real  percent_limit)
void protocols::cluster::ClusterBase::limit_total_structures ( int  limit = -1)
void protocols::cluster::ClusterBase::print_cluster_assignment ( )
void protocols::cluster::ClusterBase::print_cluster_PDBs ( std::string  prefix)
void protocols::cluster::ClusterBase::print_clusters_silentfile ( std::string  prefix)
void protocols::cluster::ClusterBase::print_raw_numbers ( )
void protocols::cluster::ClusterBase::print_summary ( )
void protocols::cluster::ClusterBase::random_limit_groupsize ( core::Real  percent_limit)
void protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group ( )
void protocols::cluster::ClusterBase::remove_singletons ( )

References clusterlist.

std::vector< PoseOP > protocols::cluster::ClusterBase::return_lowest_poses_in_clusters ( )
std::vector< core::pose::PoseOP > protocols::cluster::ClusterBase::return_top_poses_in_clusters ( core::Size  count)
void protocols::cluster::ClusterBase::set_cluster_radius ( core::Real  cluster_radius)

References cluster_radius_.

void protocols::cluster::ClusterBase::set_population_weight ( core::Real  population_weight)

References population_weight_.

void protocols::cluster::ClusterBase::sort_each_group_by_energy ( )
void protocols::cluster::ClusterBase::sort_groups_by_energy ( )

Member Data Documentation

core::Real protocols::cluster::ClusterBase::cluster_radius_
protected
std::vector< Cluster > protocols::cluster::ClusterBase::clusterlist
protected
ObjexxFCL::FArray2D< core::Real > protocols::cluster::ClusterBase::distance_matrix
protected
bool protocols::cluster::ClusterBase::export_only_low_
protected
core::Real protocols::cluster::ClusterBase::median_rms_
protected
core::Real protocols::cluster::ClusterBase::population_weight_
protected

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