Rosetta Protocols  2014.35
Public Member Functions | Protected Attributes | List of all members
protocols::cluster::ClusterBase Class Reference

#include <cluster.hh>

Public Member Functions

 ClusterBase ()
virtual std::string get_name () const
 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)
virtual void apply (core::pose::Pose &pose)
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)
int processed () const
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 ~Mover ()
virtual MoverSP create ()
virtual void apply (core::io::serialization::PipeMap &pmap)
virtual void parse_state (SerializableState const &state)
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void save_state (SerializableState &state)
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 Mover (Mover const &other)
Moveroperator= (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...
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...
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 Stringsinfo ()
 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 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...
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 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::stringStrings
- 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)

References export_only_low_.

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

References clusterlist.

Real protocols::cluster::ClusterBase::get_cluster_radius ( )
core::Real protocols::cluster::ClusterBase::get_median_rms ( )
std::string protocols::cluster::ClusterBase::get_name ( ) const
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_
std::vector< Cluster > protocols::cluster::ClusterBase::clusterlist
ObjexxFCL::FArray2D< core::Real > protocols::cluster::ClusterBase::distance_matrix
bool protocols::cluster::ClusterBase::export_only_low_
core::Real protocols::cluster::ClusterBase::median_rms_
core::Real protocols::cluster::ClusterBase::population_weight_

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